From 66145abf792dad45431d5f93ef1d3832001c2763 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Wed, 28 Jan 2026 13:00:25 +1300 Subject: [PATCH 01/62] fixed errors in JSON schema --- .../BrAPI-Schema/BrAPI-Core/List.json | 2 +- .../BrAPI-Schema/BrAPI-Core/Study.json | 7 +- .../BrAPI-Genotyping/GenomeMap.json | 59 + .../BrAPI-Genotyping/Reference.json | 39 + .../BrAPI-Germplasm/Germplasm.json | 1554 +++++++++++------ .../BrAPI-Schema/BrAPI-Phenotyping/Image.json | 10 +- .../BrAPI-Schema/Requests/CallRequest.json | 8 +- .../BrAPI-Schema/Requests/CallSetRequest.json | 6 +- .../BrAPI-Schema/Requests/PlateRequest.json | 11 - .../BrAPI-Schema/Requests/SampleRequest.json | 11 - .../BrAPI-Schema/Requests/VarientRequest.json | 5 +- 11 files changed, 1133 insertions(+), 579 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Core/List.json b/Specification/BrAPI-Schema/BrAPI-Core/List.json index 7c58ab0f..78806be7 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/List.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/List.json @@ -104,7 +104,7 @@ "description": "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study.", "brapi-metadata": { "primaryModel": true, - "subQuery": [ + "updatableProperties": [ "data" ] } diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index e366bebf..98d9b0f5 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -1,4 +1,4 @@ -{ + { "$defs": { "Study": { "properties": { @@ -386,7 +386,10 @@ "description": "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below).", "type": "object", "brapi-metadata": { - "primaryModel": false + "primaryModel": false, + "controlledVocabularyProperties": [ + "studyType" + ] } }, "ExperimentalDesign": { diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json index 9228deee..92039e03 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json @@ -40,6 +40,20 @@ "string" ] }, + "linkageGroups": { + "title": "observationUnits", + "description": "The linkage groups present in a `GenomeMap`", + "referencedAttribute": "genomeMap", + "relationshipType": "one-to-many", + "items": { + "$ref": "GenomeMap.json#/$defs/LinkageGroup", + "description": "The `GenomeMap` to which this `LinkageGroup` belongs " + }, + "type": [ + "null", + "array" + ] + }, "linkageGroupCount": { "description": "The number of linkage groups present in a `GenomeMap`", "type": [ @@ -113,6 +127,51 @@ "brapi-metadata": { "primaryModel": true } + }, + "LinkageGroup": { + "properties": { + "additionalInfo": { + "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "relationshipType": "one-to-one", + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + "linkageGroupName": { + "description": "The Uniquely Identifiable name of a `LinkageGroup`
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable.", + "type": [ + "null", + "string" + ], + "example": "Chromosome 3" + }, + "markerCount": { + "description": "The number of markers associated with a `LinkageGroup`.", + "type": [ + "null", + "integer" + ], + "example": 150 + }, + "maxPosition": { + "description": "The maximum position of a marker within a `LinkageGroup`.", + "type": [ + "null", + "integer" + ], + "example": 2500 + }, + "genomeMap": { + "description": "The `GenomeMap` to which this `LinkageGroup` belongs ", + "$ref": "GenomeMap.json#/$defs/GenomeMap", + "relationshipType": "many-to-one", + "referencedAttribute": "linkageGroups" + } + }, + "title": "LinkageGroup", + "description": "a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json index 4ab5c409..f6f7dcc2 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json @@ -14,6 +14,11 @@ "string" ] }, + "bases": { + "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "relationshipType": "one-to-one", + "$ref": "Reference.json#/$defs/ReferenceBases" + }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", "relationshipType": "one-to-many", @@ -131,6 +136,40 @@ "brapi-metadata": { "primaryModel": true } + }, + "ReferenceBases": { + "properties": { + "nextPageToken": { + "description": "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there are not any additional results.", + "type": [ + "null", + "string" + ], + "example": "3a3d658a" + }, + "offset": { + "description": "The offset position (0-based) of the given sequence from the start of this `Reference`. This value will differ for each page in a request.", + "type": [ + "null", + "integer" + ], + "example": 20000 + }, + "sequence": { + "description": "A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`.", + "type": [ + "null", + "string" + ], + "example": "TAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATAT" + } + }, + "title": "ReferenceBases", + "description": "A string representation of the `Reference` base alleles.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index 52874487..5e860d70 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -1,565 +1,1019 @@ { - "$defs": { - "Germplasm": { - "properties": { - "accessionNumber": { - "description": "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", - "type": [ - "null", - "string" - ] - }, - "acquisitionDate": { - "description": "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", - "type": [ - "null", - "string" - ] - }, - "additionalInfo": { - "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" - }, - "biologicalStatusOfAccessionCode": { - "description": "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", - "enum": [ - "100", - "110", - "120", - "130", - "200", - "300", - "400", - "410", - "411", - "412", - "413", - "414", - "415", - "416", - "420", - "421", - "422", - "423", - "500", - "600", - "999", - null - ], - "type": [ - "null", - "string" - ] - }, - "biologicalStatusOfAccessionDescription": { - "description": "Supplemental text description for 'biologicalStatusOfAccessionCode'", - "type": [ - "null", - "string" - ] - }, - "breedingMethod": { - "$ref": "BreedingMethod.json#/$defs/BreedingMethod", - "description": "The unique identifier for the breeding method used to create this germplasm", - "referencedAttribute": "germplasm", - "relationshipType": "many-to-one" - }, - "collection": { - "description": "A specific panel/collection/population name this germplasm belongs to.", - "type": [ - "null", - "string" - ] - }, - "commonCropName": { - "description": "Common name for the crop \n\nMCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\".", - "type": "string" - }, - "countryOfOriginCode": { - "description": "3-letter ISO 3166-1 code of the country in which the sample was originally collected \n\nMCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", - "type": [ - "null", - "string" - ] - }, - "defaultDisplayName": { - "description": "Human readable name used for display purposes", - "type": [ - "null", - "string" - ] - }, - "documentationURL": { - "description": "A URL to the human readable documentation of an object", - "format": "uri", - "type": [ - "null", - "string" - ] - }, - "donors": { - "description": "List of donor institutes", - "relationshipType": "one-to-many", - "referencedAttribute": "germplasm", - "items": { - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Donor", - "description": "Donors" - }, - "title": "Donors", - "type": [ - "null", - "array" - ] - }, - "externalReferences": { - "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "relationshipType": "one-to-many", - "items": { - "$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference", - "description": "ExternalReferences" - }, - "title": "ExternalReferences", - "type": [ - "null", - "array" - ] - }, - "genus": { - "description": "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature.", - "type": [ - "null", - "string" - ] - }, - "germplasmDbId": { - "description": "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", - "type": "string" - }, - "germplasmName": { - "description": "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space.", - "type": "string" - }, - "germplasmOrigin": { - "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", - "relationshipType": "one-to-many", - "referencedAttribute": "germplasm", - "items": { - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/GermplasmOrigin", - "description": "GermplasmOrigin" - }, - "title": "GermplasmOrigin", - "type": [ - "null", - "array" - ] - }, - "germplasmPUI": { - "description": "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties.", - "type": "string" - }, - "germplasmPreprocessing": { - "description": "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary.", - "type": [ - "null", - "string" - ] - }, - "instituteCode": { - "description": "The code for the institute that maintains the material. \n\nMCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", - "type": [ - "null", - "string" - ] - }, - "instituteName": { - "description": "The name of the institute that maintains the material", - "type": [ - "null", - "string" - ] - }, - "pedigree": { - "description": "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", - "type": [ - "null", - "string" - ] - }, - "seedSource": { - "description": "An identifier for the source of the biological material\n
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: \"mother_accession X father_accession\", or, if father is unknown, as \"mother_accession X UNKNOWN\". For in situ material, the region of provenance may be used when an accession is not available.", - "type": [ - "null", - "string" - ] - }, - "seedSourceDescription": { - "description": "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source", - "type": [ - "null", - "string" - ] - }, - "species": { - "description": "Specific epithet portion of the scientific name in lowercase letters.\n\nMCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" \n\nMIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature.", - "type": [ - "null", - "string" - ] - }, - "speciesAuthority": { - "description": "The authority organization responsible for tracking and maintaining the species name \n\nMCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", - "type": [ - "null", - "string" - ] - }, - "storageTypes": { - "description": "The type of storage this germplasm is kept in at a genebank.", - "relationshipType": "one-to-many", - "referencedAttribute": "germplasm", - "items": { - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/StorageType", - "description": "StorageTypes" - }, - "title": "StorageTypes", - "type": [ - "null", - "array" - ] - }, - "subtaxa": { - "description": "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group).", - "type": [ - "null", - "string" - ] - }, - "subtaxaAuthority": { - "description": "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", - "type": [ - "null", - "string" - ] - }, - "synonyms": { - "description": "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon.", - "relationshipType": "one-to-many", - "items": { - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Synonym", - "description": "Synonyms" - }, - "title": "Synonyms", - "type": [ - "null", - "array" - ] - }, - "taxonIds": { - "description": "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species.\n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.", - "relationshipType": "one-to-many", - "referencedAttribute": "germplasm", - "items": { - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/TaxonId", - "description": "TaxonIds" - }, - "type": [ - "null", - "array" - ] - }, - "samples": { - "title": "samples", - "description": "samples", - "referencedAttribute": "germplasm", - "relationshipType": "one-to-many", - "items": { - "$ref": "../BrAPI-Genotyping/Sample.json#/$defs/Sample", - "description": "Sample" - }, - "type": [ - "null", - "array" - ] - }, - "attributeValues": { - "title": "attributeValues", - "description": "attributeValues", - "referencedAttribute": "germplasm", - "relationshipType": "one-to-many", - "items": { - "$ref": "GermplasmAttributeValue.json#/$defs/GermplasmAttributeValue", - "description": "GermplasmAttributeValue" - }, - "type": [ - "null", - "array" - ] - }, - "progenyPedigreeNodes": { - "title": "progenyPedigreeNodes", - "description": "progenyPedigreeNodes", - "relationshipType": "one-to-many", - "items": { - "$ref": "PedigreeNode.json#/$defs/PedigreeNode", - "description": "PedigreeNode" - }, - "type": [ - "null", - "array" - ] - }, - "parentPedigreeNodes": { - "title": "parentPedigreeNodes", - "description": "parentPedigreeNodes", - "relationshipType": "one-to-many", - "items": { - "$ref": "PedigreeNode.json#/$defs/PedigreeNode", - "description": "PedigreeNode" - }, - "type": [ - "null", - "array" - ] - }, - "siblingPedigreeNodes": { - "title": "SiblingPedigreeNodes", - "description": "siblingPedigreeNodes", - "relationshipType": "one-to-many", - "items": { - "$ref": "PedigreeNode.json#/$defs/PedigreeNode", - "description": "PedigreeNode" - }, - "type": [ - "null", - "array" - ] - }, - "observations": { - "title": "observations", - "description": "observations", - "referencedAttribute": "germplasm", - "relationshipType": "one-to-many", - "items": { - "$ref": "../BrAPI-Phenotyping/Observation.json#/$defs/Observation", - "description": "Observation" - }, - "type": [ - "null", - "array" - ] - }, - "observationUnits": { - "title": "observationUnits", - "description": "observationUnits", - "referencedAttribute": "germplasm", - "relationshipType": "one-to-many", - "items": { - "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/ObservationUnit", - "description": "ObservationUnit" - }, - "type": [ - "null", - "array" - ] - }, - "reference": { - "description": "Germplasm associated with a reference", - "$ref": "../BrAPI-Genotyping/Reference.json#/$defs/Reference", - "relationshipType": "many-to-one", - "referencedAttribute": "sourceGermplasm" - }, - "referenceSet": { - "description": "Germplasm associated with a reference", - "$ref": "../BrAPI-Genotyping/ReferenceSet.json#/$defs/ReferenceSet", - "relationshipType": "many-to-one", - "referencedAttribute": "sourceGermplasm" - } - }, - "required": [ - "germplasmName", - "germplasmDbId", - "germplasmPUI", - "commonCropName" - ], - "title": "Germplasm", - "description": "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy.", - "type": "object", - "brapi-metadata": { - "primaryModel": true - } + "$defs": { + "Germplasm": { + "properties": { + "accessionNumber": { + "description": "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "type": [ + "null", + "string" + ] }, - "Donor": { - "properties": { - "donorAccessionNumber": { - "description": "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", - "type": [ - "null", - "string" - ] - }, - "donorInstituteCode": { - "description": "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", - "type": [ - "null", - "string" - ] - }, - "germplasm": { - "description": "donors associated with a germplasm", - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", - "relationshipType": "many-to-one", - "referencedAttribute": "donors" - } - }, - "title": "Donor", - "description": "Identifier assigned to an accession by the material donor.", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } + "acquisitionDate": { + "description": "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "type": [ + "null", + "string" + ] + }, + "additionalInfo": { + "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" + }, + "biologicalStatusOfAccessionCode": { + "description": "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "enum": [ + "100", + "110", + "120", + "130", + "200", + "300", + "400", + "410", + "411", + "412", + "413", + "414", + "415", + "416", + "420", + "421", + "422", + "423", + "500", + "600", + "999", + null + ], + "type": [ + "null", + "string" + ] + }, + "biologicalStatusOfAccessionDescription": { + "description": "Supplemental text description for 'biologicalStatusOfAccessionCode'", + "type": [ + "null", + "string" + ] + }, + "breedingMethod": { + "$ref": "BreedingMethod.json#/$defs/BreedingMethod", + "description": "The unique identifier for the breeding method used to create this germplasm", + "referencedAttribute": "germplasm", + "relationshipType": "many-to-one" + }, + "collection": { + "description": "A specific panel/collection/population name this germplasm belongs to.", + "type": [ + "null", + "string" + ] + }, + "commonCropName": { + "description": "Common name for the crop \n\nMCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\".", + "type": "string" + }, + "countryOfOriginCode": { + "description": "3-letter ISO 3166-1 code of the country in which the sample was originally collected \n\nMCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", + "type": [ + "null", + "string" + ] + }, + "defaultDisplayName": { + "description": "Human readable name used for display purposes", + "type": [ + "null", + "string" + ] + }, + "documentationURL": { + "description": "A URL to the human readable documentation of an object", + "format": "uri", + "type": [ + "null", + "string" + ] + }, + "donors": { + "description": "List of donor institutes", + "relationshipType": "one-to-many", + "referencedAttribute": "germplasm", + "items": { + "$ref": "Germplasm.json#/$defs/Donor", + "description": "Donors" + }, + "title": "Donors", + "type": [ + "null", + "array" + ] + }, + "externalReferences": { + "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "relationshipType": "one-to-many", + "items": { + "$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference", + "description": "ExternalReferences" + }, + "title": "ExternalReferences", + "type": [ + "null", + "array" + ] + }, + "genus": { + "description": "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature.", + "type": [ + "null", + "string" + ] + }, + "germplasmDbId": { + "description": "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", + "type": "string" + }, + "germplasmName": { + "description": "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space.", + "type": "string" + }, + "germplasmOrigin": { + "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", + "relationshipType": "one-to-many", + "referencedAttribute": "germplasm", + "items": { + "$ref": "Germplasm.json#/$defs/GermplasmOrigin", + "description": "GermplasmOrigin" + }, + "title": "GermplasmOrigin", + "type": [ + "null", + "array" + ] + }, + "germplasmPUI": { + "description": "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties.", + "type": "string" + }, + "germplasmPreprocessing": { + "description": "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary.", + "type": [ + "null", + "string" + ] + }, + "instituteCode": { + "description": "The code for the institute that maintains the material. \n\nMCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "type": [ + "null", + "string" + ] + }, + "instituteName": { + "description": "The name of the institute that maintains the material", + "type": [ + "null", + "string" + ] + }, + "mcpd": { + "$ref": "Germplasm.json#/$defs/GermplasmMCPD", + "description": "The mulit-crop passport descriptors (MCPD) for this germplasm", + "referencedAttribute": "germplasm", + "relationshipType": "one-to-one" + }, + "pedigree": { + "description": "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", + "type": [ + "null", + "string" + ] + }, + "seedSource": { + "description": "An identifier for the source of the biological material\n
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: \"mother_accession X father_accession\", or, if father is unknown, as \"mother_accession X UNKNOWN\". For in situ material, the region of provenance may be used when an accession is not available.", + "type": [ + "null", + "string" + ] + }, + "seedSourceDescription": { + "description": "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source", + "type": [ + "null", + "string" + ] + }, + "species": { + "description": "Specific epithet portion of the scientific name in lowercase letters.\n\nMCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" \n\nMIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature.", + "type": [ + "null", + "string" + ] + }, + "speciesAuthority": { + "description": "The authority organization responsible for tracking and maintaining the species name \n\nMCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", + "type": [ + "null", + "string" + ] + }, + "storageTypes": { + "description": "The type of storage this germplasm is kept in at a genebank.", + "relationshipType": "one-to-many", + "referencedAttribute": "germplasm", + "items": { + "$ref": "Germplasm.json#/$defs/StorageType", + "description": "StorageTypes" + }, + "title": "StorageTypes", + "type": [ + "null", + "array" + ] + }, + "subtaxa": { + "description": "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group).", + "type": [ + "null", + "string" + ] + }, + "subtaxaAuthority": { + "description": "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", + "type": [ + "null", + "string" + ] }, - "GermplasmOrigin": { - "properties": { + "synonyms": { + "description": "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon.", + "relationshipType": "one-to-many", + "items": { + "$ref": "Germplasm.json#/$defs/Synonym", + "description": "Synonyms" + }, + "title": "Synonyms", + "type": [ + "null", + "array" + ] + }, + "taxonIds": { + "description": "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species.\n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.", + "relationshipType": "one-to-many", + "referencedAttribute": "germplasm", + "items": { + "$ref": "Germplasm.json#/$defs/TaxonId", + "description": "TaxonIds" + }, + "type": [ + "null", + "array" + ] + }, + "samples": { + "title": "samples", + "description": "samples", + "referencedAttribute": "germplasm", + "relationshipType": "one-to-many", + "items": { + "$ref": "../BrAPI-Genotyping/Sample.json#/$defs/Sample", + "description": "Sample" + }, + "type": [ + "null", + "array" + ] + }, + "attributeValues": { + "title": "attributeValues", + "description": "attributeValues", + "referencedAttribute": "germplasm", + "relationshipType": "one-to-many", + "items": { + "$ref": "GermplasmAttributeValue.json#/$defs/GermplasmAttributeValue", + "description": "GermplasmAttributeValue" + }, + "type": [ + "null", + "array" + ] + }, + "progenyPedigreeNodes": { + "title": "progenyPedigreeNodes", + "description": "progenyPedigreeNodes", + "relationshipType": "one-to-many", + "items": { + "$ref": "PedigreeNode.json#/$defs/PedigreeNode", + "description": "PedigreeNode" + }, + "type": [ + "null", + "array" + ] + }, + "parentPedigreeNodes": { + "title": "parentPedigreeNodes", + "description": "parentPedigreeNodes", + "relationshipType": "one-to-many", + "items": { + "$ref": "PedigreeNode.json#/$defs/PedigreeNode", + "description": "PedigreeNode" + }, + "type": [ + "null", + "array" + ] + }, + "siblingPedigreeNodes": { + "title": "SiblingPedigreeNodes", + "description": "siblingPedigreeNodes", + "relationshipType": "one-to-many", + "items": { + "$ref": "PedigreeNode.json#/$defs/PedigreeNode", + "description": "PedigreeNode" + }, + "type": [ + "null", + "array" + ] + }, + "observations": { + "title": "observations", + "description": "observations", + "referencedAttribute": "germplasm", + "relationshipType": "one-to-many", + "items": { + "$ref": "../BrAPI-Phenotyping/Observation.json#/$defs/Observation", + "description": "Observation" + }, + "type": [ + "null", + "array" + ] + }, + "observationUnits": { + "title": "observationUnits", + "description": "observationUnits", + "referencedAttribute": "germplasm", + "relationshipType": "one-to-many", + "items": { + "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/ObservationUnit", + "description": "ObservationUnit" + }, + "type": [ + "null", + "array" + ] + }, + "reference": { + "description": "Germplasm associated with a reference", + "$ref": "../BrAPI-Genotyping/Reference.json#/$defs/Reference", + "relationshipType": "many-to-one", + "referencedAttribute": "sourceGermplasm" + }, + "referenceSet": { + "description": "Germplasm associated with a reference", + "$ref": "../BrAPI-Genotyping/ReferenceSet.json#/$defs/ReferenceSet", + "relationshipType": "many-to-one", + "referencedAttribute": "sourceGermplasm" + } + }, + "required": [ + "germplasmName", + "germplasmDbId", + "germplasmPUI", + "commonCropName" + ], + "title": "Germplasm", + "description": "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy.", + "type": "object", + "brapi-metadata": { + "primaryModel": true + } + }, + "GermplasmMCPD": { + "properties": { + "accessionNames": { + "description": "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered names or other designations given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase.", + "items": { + "type": "string" + }, + "type": [ + "null", + "array" + ], + "examples": [ + "Symphony", + "Emma" + ] + }, + "accessionNumber": { + "description": "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "type": [ + "null", + "string" + ], + "example": "A0000003" + }, + "acquisitionDate": { + "description": "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "type": [ + "null", + "string" + ], + "format": "date" + }, + "acquisitionSourceCode": { + "description": "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)", + "enum": [ + "10", + "11", + "12", + "13", + "14", + "15", + "20", + "21", + "22", + "23", + "24", + "25", + "26", + "27", + "28", + "30", + "40", + "50", + "60", + "61", + "62", + "99" + ], + "type": [ + "null", + "string" + ], + "example": "26" + }, + "alternateIDs": { + "description": "MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. ", + "items": { + "type": "string" + }, + "type": [ + "null", + "array" + ], + "examples": [ + "PER001:3", + "PER001:http://pui.per/accession/A0000003", + "USA001:A0000003" + ] + }, + "ancestralData": { + "description": "MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", + "type": [ + "null", + "string" + ], + "example": "A0000001/A0000002" + }, + "biologicalStatusOfAccessionCode": { + "description": "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "enum": [ + "100", + "110", + "120", + "130", + "200", + "300", + "400", + "410", + "411", + "412", + "413", + "414", + "415", + "416", + "420", + "421", + "422", + "423", + "500", + "600", + "999" + ], + "type": [ + "null", + "string" + ], + "example": "421" + }, + "breedingInstitutes": { + "description": "A list of institutes that were involved with breeding a material/germplasm\n
MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard.\n
MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available.", + "type": [ + "null", + "array" + ], + "items": { + "$ref": "Germplasm.json#/$defs/Institute" + } + }, + "collectingInfo": { + "description": "Information about the collection of a germplasm", + "title": "CollectingInfo", + "properties": { + "collectingDate": { + "description": "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "type": [ + "null", + "string" + ], + "format": "date" + }, + "collectingInstitutes": { + "description": "Institutes which collected the sample", + "type": [ + "null", + "array" + ], + "items": { + "$ref": "Germplasm.json#/$defs/Institute" + } + }, + "collectingMissionIdentifier": { + "description": "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\").", + "type": [ + "null", + "string" + ], + "example": "CIATFOR_052" + }, + "collectingNumber": { + "description": "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections.", + "type": [ + "null", + "string" + ], + "example": "ab109909" + }, + "collectingSite": { + "description": "Information about the location where the sample was collected", + "properties": { "coordinateUncertainty": { - "description": "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.", - "type": [ - "null", - "string" - ] - }, - "coordinates": { - "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", - "relationshipType": "one-to-many", - "referencedAttribute": "germplasmOrigin", - "items": { - "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON", - "description": "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed." - }, - "title": "GeoJSON", - "type": [ - "null", - "array" - ] - }, - "germplasm": { - "description": "associated germplasm", - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", - "relationshipType": "many-to-one", - "referencedAttribute": "germplasmOrigin" + "description": "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown.", + "type": [ + "null", + "string" + ], + "example": "20" + }, + "elevation": { + "description": "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed.", + "type": [ + "null", + "string" + ], + "example": "35" + }, + "georeferencingMethod": { + "description": "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known.", + "type": [ + "null", + "string" + ], + "example": "WGS84" + }, + "latitudeDecimal": { + "description": "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975).", + "type": [ + "null", + "string" + ], + "example": "+42.445295" + }, + "latitudeDegrees": { + "description": "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10", + "type": [ + "null", + "string" + ], + "example": "42 26 43.1 N" + }, + "locationDescription": { + "description": "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville).", + "type": [ + "null", + "string" + ], + "example": "South east hill near institute buildings" + }, + "longitudeDecimal": { + "description": "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123).", + "type": [ + "null", + "string" + ], + "example": "-076.471934" + }, + "longitudeDegrees": { + "description": "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076", + "type": [ + "null", + "string" + ], + "example": "76 28 19.0 W" + }, + "spatialReferenceSystem": { + "description": "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum.", + "type": [ + "null", + "string" + ], + "example": "WGS84" } - }, - "title": "GermplasmOrigin", - "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", - "type": "object", - "brapi-metadata": { - "primaryModel": false + }, + "type": [ + "null", + "object" + ] } + }, + "type": "object" }, - "StorageType": { - "properties": { - "code": { - "description": "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", - "enum": [ - "10", - "11", - "12", - "13", - "20", - "30", - "40", - "50", - "99", - null - ], - "type": [ - "null", - "string" - ], - "title": "StorageTypeCode" - }, - "description": { - "description": "A supplemental text description of the storage type", - "type": [ - "null", - "string" - ] - }, - "germplasm": { - "description": "associated germplasm", - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", - "relationshipType": "many-to-one", - "referencedAttribute": "storageTypes" - } - }, - "title": "StorageType", - "description": "The type of storage this germplasm is kept in at a genebank.", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } + "commonCropName": { + "description": "MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\". ", + "type": [ + "null", + "string" + ], + "example": "malting barley" }, - "Synonym": { - "description": "Alternative way to refer to a Germplasm, Cultivar of Variety", - "properties": { - "synonym": { - "description": "Alternative name or ID used to reference this germplasm", - "type": [ - "null", - "string" - ] - }, - "type": { - "description": "A descriptive classification for this synonym", - "type": [ - "null", - "string" - ] - }, - "germplasm": { - "description": "associated germplasm", - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", - "relationshipType": "many-to-one", - "referencedAttribute": "synonyms" - } + "countryOfOrigin": { + "description": "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers\" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", + "type": [ + "null", + "string" + ], + "example": "Peru" + }, + "donorInfo": { + "type": "object", + "description": "Information about an accession donor", + "properties": { + "donorAccessionPui": { + "description": "PUI (DOI mostly) of the accession in the donor system.", + "type": [ + "null", + "string" + ], + "example": "http://pui.per/accession/A0010025" }, - "title": "Synonym", - "description": "Alternative names or IDs used to reference this germplasm", - "type": "object", - "brapi-metadata": { - "primaryModel": false + "donorAccessionNumber": { + "description": "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", + "type": [ + "null", + "string" + ], + "example": "A0090204" + }, + "donorInstitute": { + "description": "The identifying information for the entity acting as an accession donor\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.\n
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.", + "$ref": "Germplasm.json#/$defs/Institute" } + } }, - "TaxonId": { - "description": "The Taxon of the Germplasm", - "properties": { - "taxonId": { - "description": "The identifier (name, ID, URI) of a particular taxonomy within the source provider", - "type": "string" - }, - "sourceName": { - "description": "The human readable name of the taxonomy provider", - "type": "string" - }, - "germplasm": { - "description": "associated germplasm", - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", - "relationshipType": "many-to-one", - "referencedAttribute": "taxonIds" - } - }, - "required": [ - "sourceName", - "taxonId" + "genus": { + "description": "MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.", + "type": [ + "null", + "string" + ], + "example": "Aspergillus" + }, + "germplasm": { + "description": "donors associated with a germplasm", + "$ref": "Germplasm.json#/$defs/Germplasm", + "relationshipType": "one-to-one", + "referencedAttribute": "mcpd" + }, + "instituteCode": { + "description": "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "type": [ + "null", + "string" + ], + "example": "PER001" + }, + "mlsStatus": { + "description": "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")", + "enum": [ + "", + "0", + "1", + "99" + ], + "type": [ + "null", + "string" + ], + "example": "0" + }, + "remarks": { + "description": "MCPD (v2.1) (REMARKS) 28. The remarks field is used to add notes or to elaborate on descriptors with value 99 or 999 (= Other). Prefix remarks with the field name they refer to and a colon (:) without space (e.g. COLLSRC:riverside). Distinct remarks referring to different fields are separated by semi-colons without space.", + "type": [ + "null", + "string" + ], + "example": "This is an example remark to demonstrate that any notable information can be put here" + }, + "safetyDuplicateInstitutes": { + "items": { + "$ref": "Germplasm.json#/$defs/Institute" + }, + "type": [ + "null", + "array" + ] + }, + "species": { + "description": "MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" ", + "type": [ + "null", + "string" + ], + "example": "fructus" + }, + "speciesAuthority": { + "description": "MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", + "type": [ + "null", + "string" + ], + "example": "Smith, 1822" + }, + "storageTypeCodes": { + "description": "MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) 10) Seed collection 11) Short term 12) Medium term 13) Long term 20) Field collection 30) In vitro collection 40) Cryo-preserved collection 50) DNA collection 99) Other (elaborate in REMARKS field)", + "items": { + "enum": [ + "10", + "11", + "12", + "13", + "20", + "30", + "40", + "50", + "99" ], - "title": "TaxonId", - "description": "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } + "type": "string" + }, + "type": [ + "null", + "array" + ], + "examples": [ + "11", + "13" + ] + }, + "subtaxon": { + "description": "MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").", + "type": [ + "null", + "string" + ], + "example": "Aspergillus fructus A" + }, + "subtaxonAuthority": { + "description": "MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", + "type": [ + "null", + "string" + ], + "example": "Smith, 1822" } + }, + "required": [ + "germplasm", + "commonCropName" + ], + "title": "GermplasmMCPD", + "description": "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } }, - "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json", - "$schema": "http://json-schema.org/draft/2020-12/schema" + "Institute": { + "properties": { + "instituteAddress": { + "description": "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "type": [ + "null", + "string" + ], + "example": "123 Main Street, Lima, Peru, 5555" + }, + "instituteCode": { + "description": "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space.", + "type": [ + "null", + "string" + ], + "example": "PER001" + }, + "instituteName": { + "description": "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "type": [ + "null", + "string" + ], + "example": "The BrAPI Institute" + } + }, + "title": "Institute", + "description": "The details of an Institute or other simular entity.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } + }, + "Donor": { + "properties": { + "donorAccessionNumber": { + "description": "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", + "type": [ + "null", + "string" + ] + }, + "donorInstituteCode": { + "description": "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", + "type": [ + "null", + "string" + ] + }, + "germplasm": { + "description": "donors associated with a germplasm", + "$ref": "Germplasm.json#/$defs/Germplasm", + "relationshipType": "many-to-one", + "referencedAttribute": "donors" + } + }, + "title": "Donor", + "description": "Identifier assigned to an accession by the material donor.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } + }, + "GermplasmOrigin": { + "properties": { + "coordinateUncertainty": { + "description": "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.", + "type": [ + "null", + "string" + ] + }, + "coordinates": { + "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "relationshipType": "one-to-many", + "referencedAttribute": "germplasmOrigin", + "items": { + "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON", + "description": "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed." + }, + "title": "GeoJSON", + "type": [ + "null", + "array" + ] + }, + "germplasm": { + "description": "associated germplasm", + "$ref": "Germplasm.json#/$defs/Germplasm", + "relationshipType": "many-to-one", + "referencedAttribute": "germplasmOrigin" + } + }, + "title": "GermplasmOrigin", + "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } + }, + "StorageType": { + "properties": { + "code": { + "description": "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", + "enum": [ + "10", + "11", + "12", + "13", + "20", + "30", + "40", + "50", + "99", + null + ], + "type": [ + "null", + "string" + ], + "title": "StorageTypeCode" + }, + "description": { + "description": "A supplemental text description of the storage type", + "type": [ + "null", + "string" + ] + }, + "germplasm": { + "description": "associated germplasm", + "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", + "relationshipType": "many-to-one", + "referencedAttribute": "storageTypes" + } + }, + "title": "StorageType", + "description": "The type of storage this germplasm is kept in at a genebank.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } + }, + "Synonym": { + "description": "Alternative way to refer to a Germplasm, Cultivar of Variety", + "properties": { + "synonym": { + "description": "Alternative name or ID used to reference this germplasm", + "type": [ + "null", + "string" + ] + }, + "type": { + "description": "A descriptive classification for this synonym", + "type": [ + "null", + "string" + ] + }, + "germplasm": { + "description": "associated germplasm", + "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", + "relationshipType": "many-to-one", + "referencedAttribute": "synonyms" + } + }, + "title": "Synonym", + "description": "Alternative names or IDs used to reference this germplasm", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } + }, + "TaxonId": { + "description": "The Taxon of the Germplasm", + "properties": { + "taxonId": { + "description": "The identifier (name, ID, URI) of a particular taxonomy within the source provider", + "type": "string" + }, + "sourceName": { + "description": "The human readable name of the taxonomy provider", + "type": "string" + }, + "germplasm": { + "description": "associated germplasm", + "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", + "relationshipType": "many-to-one", + "referencedAttribute": "taxonIds" + } + }, + "required": [ + "sourceName", + "taxonId" + ], + "title": "TaxonId", + "description": "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } + } + }, + "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json", + "$schema": "http://json-schema.org/draft/2020-12/schema" } \ No newline at end of file diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json index 9eb5683e..75b29587 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json @@ -43,6 +43,11 @@ "array" ] }, + "imageContent": { + "description": "The content of the image", + "type": "string", + "format": "binary" + }, "imageDbId": { "description": "The unique identifier of an image", "type": "string" @@ -134,7 +139,10 @@ "description": "The metadata for an image file that is connected to some phenotypic observation data.", "type": "object", "brapi-metadata": { - "primaryModel": true + "primaryModel": true, + "writableProperties": [ + "imageContent" + ] } } }, diff --git a/Specification/BrAPI-Schema/Requests/CallRequest.json b/Specification/BrAPI-Schema/Requests/CallRequest.json index daf37c9a..7cd32a73 100644 --- a/Specification/BrAPI-Schema/Requests/CallRequest.json +++ b/Specification/BrAPI-Schema/Requests/CallRequest.json @@ -58,7 +58,13 @@ } }, "brapi-metadata": { - "request": true + "request": true, + "subQueryProperties" : [ + "expandHomozygotes", + "unknownString", + "sepPhased", + "sepUnphased" + ] } } }, diff --git a/Specification/BrAPI-Schema/Requests/CallSetRequest.json b/Specification/BrAPI-Schema/Requests/CallSetRequest.json index 6344162d..82709225 100644 --- a/Specification/BrAPI-Schema/Requests/CallSetRequest.json +++ b/Specification/BrAPI-Schema/Requests/CallSetRequest.json @@ -79,7 +79,11 @@ } ], "brapi-metadata": { - "request": true + "request": true, + "subQueryProperties" : [ + "callSetDbIds", + "callSetNames" + ] } } }, diff --git a/Specification/BrAPI-Schema/Requests/PlateRequest.json b/Specification/BrAPI-Schema/Requests/PlateRequest.json index 7ec737f1..ff02bea8 100644 --- a/Specification/BrAPI-Schema/Requests/PlateRequest.json +++ b/Specification/BrAPI-Schema/Requests/PlateRequest.json @@ -96,17 +96,6 @@ "45e1e2d7", "6cc6dd28" ] - }, - "germplasmDbIds": { - "description": "The ID which uniquely identifies a germplasm", - "items": { - "type": "string" - }, - "type": "array", - "example": [ - "d745e1e2", - "6dd28d74" - ] } } } diff --git a/Specification/BrAPI-Schema/Requests/SampleRequest.json b/Specification/BrAPI-Schema/Requests/SampleRequest.json index f390995e..a71f3847 100644 --- a/Specification/BrAPI-Schema/Requests/SampleRequest.json +++ b/Specification/BrAPI-Schema/Requests/SampleRequest.json @@ -85,17 +85,6 @@ "45e1e2d7", "6cc6dd28" ] - }, - "germplasmDbIds": { - "description": "The ID which uniquely identifies a `Germplasm`", - "items": { - "type": "string" - }, - "type": "array", - "example": [ - "d745e1e2", - "6dd28d74" - ] } } } diff --git a/Specification/BrAPI-Schema/Requests/VarientRequest.json b/Specification/BrAPI-Schema/Requests/VarientRequest.json index 68d62037..a337bbb1 100644 --- a/Specification/BrAPI-Schema/Requests/VarientRequest.json +++ b/Specification/BrAPI-Schema/Requests/VarientRequest.json @@ -93,7 +93,10 @@ } ], "brapi-metadata": { - "request": true + "request": true, + "subQueryProperties" : [ + "variantDbIds" + ] } } }, From c2a39c1a1cec2e287fbec36d7a895051ff2abec9 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Thu, 29 Jan 2026 12:50:54 +1300 Subject: [PATCH 02/62] updated schema tools version --- generator/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/generator/build.gradle b/generator/build.gradle index b0e4e8d9..af8679ca 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.37.0' + brapiSchemaToolsVersion = '0.46.0' } repositories { From 34e593ae52a080a5d0611df85f94dbb06267ffc6 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Thu, 29 Jan 2026 20:31:01 +1300 Subject: [PATCH 03/62] updated schema tools version --- generator/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/generator/build.gradle b/generator/build.gradle index af8679ca..9510f65e 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.46.0' + brapiSchemaToolsVersion = '0.49.0' } repositories { From 9696a785a6698a49193313bc5213c25c5cc1154a Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 3 Feb 2026 21:40:03 +1300 Subject: [PATCH 04/62] added controlledVocabulary for attributeCategory and study --- Specification/BrAPI-Schema/BrAPI-Common/Attribute.json | 5 ++++- Specification/BrAPI-Schema/BrAPI-Core/Study.json | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json b/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json index 59a6c5a7..2ddfa209 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json @@ -39,7 +39,10 @@ } ], "brapi-metadata": { - "interface": true + "interface": true, + "controlledVocabularyProperties": [ + "attributeCategory" + ] } } }, diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index 98d9b0f5..e67368b5 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -386,7 +386,7 @@ "description": "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below).", "type": "object", "brapi-metadata": { - "primaryModel": false, + "primaryModel": true, "controlledVocabularyProperties": [ "studyType" ] From 7ce168fb341cb970c0e455c879185377a6b2e84c Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 13 Mar 2026 17:32:06 +1300 Subject: [PATCH 05/62] Update JSON schemas to reflect changes in request parameters and add new properties --- .../BrAPI-Schema/BrAPI-Core/Study.json | 10 +- .../Requests/AlleleMatrixRequest.json | 2 +- .../Requests/GenomeMapRequest.json | 2 +- .../BrAPI-Schema/Requests/ListRequest.json | 169 ++++++++++-------- .../BrAPI-Schema/Requests/MethodRequest.json | 2 +- .../Requests/ObservationRequest.json | 49 +++++ .../Requests/ObservationUnitRequest.json | 49 +++++ .../Requests/ReferenceBasesRequest.json | 31 ++++ .../BrAPI-Schema/Requests/StudyRequest.json | 25 +++ .../BrAPI-Schema/Requests/TrialRequest.json | 23 +++ 10 files changed, 275 insertions(+), 87 deletions(-) create mode 100644 Specification/BrAPI-Schema/Requests/ReferenceBasesRequest.json diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index e67368b5..534053eb 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -317,7 +317,10 @@ "description": "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies.", "type": "object", "brapi-metadata": { - "primaryModel": true + "primaryModel": true, + "controlledVocabularyProperties": [ + "studyType" + ] } }, "EnvironmentParameter": { @@ -386,10 +389,7 @@ "description": "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below).", "type": "object", "brapi-metadata": { - "primaryModel": true, - "controlledVocabularyProperties": [ - "studyType" - ] + "primaryModel": false } }, "ExperimentalDesign": { diff --git a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json index 4f536c2b..f941b9b3 100644 --- a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json +++ b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json @@ -4,11 +4,11 @@ "type": "object", "properties": { "pagination": { - "title": "AlleleMatrixPagination", "description": "Pagination for the matrix", "type": "array", "items": { "type": "object", + "title": "AlleleMatrixPagination", "properties": { "dimension": { "description": "the dimension of the matrix being paginated", diff --git a/Specification/BrAPI-Schema/Requests/GenomeMapRequest.json b/Specification/BrAPI-Schema/Requests/GenomeMapRequest.json index c321669a..6891732c 100644 --- a/Specification/BrAPI-Schema/Requests/GenomeMapRequest.json +++ b/Specification/BrAPI-Schema/Requests/GenomeMapRequest.json @@ -24,7 +24,7 @@ }, "type": "array" }, - "mapPUI": { + "mapPUIs": { "description": "The DOI or other permanent identifier for a `GenomeMap`", "items": { "type": "string" diff --git a/Specification/BrAPI-Schema/Requests/ListRequest.json b/Specification/BrAPI-Schema/Requests/ListRequest.json index 0256400f..e99fa9e5 100644 --- a/Specification/BrAPI-Schema/Requests/ListRequest.json +++ b/Specification/BrAPI-Schema/Requests/ListRequest.json @@ -1,88 +1,99 @@ { "$defs": { "ListRequest": { - "type": "object", - "properties": { - "dateCreatedRangeStart": { - "description": "Define the beginning for an interval of time and only include Lists that are created within this interval.", - "format": "date-time", - "type": "string" + "allOf": [ + { + "$ref": "Parameters/CommonCropNamesParameters.json#/$defs/CommonCropNamesParameters" }, - "dateCreatedRangeEnd": { - "description": "Define the end for an interval of time and only include Lists that are created within this interval.", - "format": "date-time", - "type": "string" + { + "$ref": "Parameters/ProgramParameters.json#/$defs/ProgramParameters" }, - "dateModifiedRangeStart": { - "description": "Define the beginning for an interval of time and only include Lists that are modified within this interval.", - "format": "date-time", - "type": "string" - }, - "dateModifiedRangeEnd": { - "description": "Define the end for an interval of time and only include Lists that are modified within this interval.", - "format": "date-time", - "type": "string" - }, - "listDbIds": { - "description": "An array of primary database identifiers to identify a set of Lists", - "type": "array", - "items": { - "type": "string" - }, - "example": [ - "55f20cf6", - "3193ca3d" - ] - }, - "listNames": { - "description": "An array of human readable names to identify a set of Lists", - "type": "array", - "items": { - "type": "string" - }, - "example": [ - "Planing List 1", - "Bobs List" - ] - }, - "listOwnerNames": { - "description": "An array of names for the people or entities who are responsible for a set of Lists", - "type": "array", - "items": { - "type": "string" - }, - "example": [ - "Bob Robertson", - "Rob Robertson" - ] - }, - "listOwnerPersonDbIds": { - "description": "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", - "type": "array", - "items": { - "type": "string" - }, - "example": [ - "bob@bob.com", - "rob@bob.com" - ] - }, - "listSources": { - "description": "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", - "type": "array", - "items": { - "type": "string" - }, - "example": [ - "USER", - "SYSTEM", - "EXTERNAL" - ] - }, - "listType": { - "$ref": "../BrAPI-Core/ListType.json#/$defs/ListType" + { + "type": "object", + "properties": + { + "dateCreatedRangeStart": { + "description": "Define the beginning for an interval of time and only include Lists that are created within this interval.", + "format": "date-time", + "type": "string" + }, + "dateCreatedRangeEnd": { + "description": "Define the end for an interval of time and only include Lists that are created within this interval.", + "format": "date-time", + "type": "string" + }, + "dateModifiedRangeStart": { + "description": "Define the beginning for an interval of time and only include Lists that are modified within this interval.", + "format": "date-time", + "type": "string" + }, + "dateModifiedRangeEnd": { + "description": "Define the end for an interval of time and only include Lists that are modified within this interval.", + "format": "date-time", + "type": "string" + }, + "listDbIds": { + "description": "An array of primary database identifiers to identify a set of Lists", + "type": "array", + "items": { + "type": "string" + }, + "example": [ + "55f20cf6", + "3193ca3d" + ] + }, + "listNames": { + "description": "An array of human readable names to identify a set of Lists", + "type": "array", + "items": { + "type": "string" + }, + "example": [ + "Planing List 1", + "Bobs List" + ] + }, + "listOwnerNames": { + "description": "An array of names for the people or entities who are responsible for a set of Lists", + "type": "array", + "items": { + "type": "string" + }, + "example": [ + "Bob Robertson", + "Rob Robertson" + ] + }, + "listOwnerPersonDbIds": { + "description": "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", + "type": "array", + "items": { + "type": "string" + }, + "example": [ + "bob@bob.com", + "rob@bob.com" + ] + }, + "listSources": { + "description": "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", + "type": "array", + "items": { + "type": "string" + }, + "example": [ + "USER", + "SYSTEM", + "EXTERNAL" + ] + }, + "listType": { + "$ref": "../BrAPI-Core/ListType.json#/$defs/ListType" + } + } } - }, + ], "brapi-metadata": { "request": true } diff --git a/Specification/BrAPI-Schema/Requests/MethodRequest.json b/Specification/BrAPI-Schema/Requests/MethodRequest.json index 015b6674..95a8bb7f 100644 --- a/Specification/BrAPI-Schema/Requests/MethodRequest.json +++ b/Specification/BrAPI-Schema/Requests/MethodRequest.json @@ -14,7 +14,7 @@ { "type": "object", "properties": { - "scaleDbIds": { + "methodDbIds": { "description": "The unique identifier for a method.", "items": { "type": "string" diff --git a/Specification/BrAPI-Schema/Requests/ObservationRequest.json b/Specification/BrAPI-Schema/Requests/ObservationRequest.json index 4a78811a..76bd4f28 100644 --- a/Specification/BrAPI-Schema/Requests/ObservationRequest.json +++ b/Specification/BrAPI-Schema/Requests/ObservationRequest.json @@ -82,6 +82,55 @@ } ] }, + "observationUnitLevelNames": { + "description": "The Observation Unit Level. Returns only the observation unit of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelOrders": { + "description": "The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelCodes": { + "description": "The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelRelationshipNames": { + "description": "The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. \n
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. \n
Use this parameter to identify groups of observation units that share a relationship level. \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelRelationshipOrders": { + "description": "The Observation Unit Level Order Number. \n
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelRelationshipCodes": { + "description": "The Observation Unit Level Code. \n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelRelationshipDbIds": { + "description": "The observationUnitDbId associated with a particular level and code.\n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, "observationTimeStampRangeEnd": { "description": "Timestamp range end", "format": "date-time", diff --git a/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json b/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json index 9a7407dc..7b11365b 100644 --- a/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json +++ b/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json @@ -82,6 +82,55 @@ } ] }, + "observationUnitLevelNames": { + "description": "The Observation Unit Level. Returns only the observation unit of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelOrders": { + "description": "The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelCodes": { + "description": "The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelRelationshipNames": { + "description": "The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. \n
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. \n
Use this parameter to identify groups of observation units that share a relationship level. \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelRelationshipOrders": { + "description": "The Observation Unit Level Order Number. \n
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelRelationshipCodes": { + "description": "The Observation Unit Level Code. \n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, + "observationUnitLevelRelationshipDbIds": { + "description": "The observationUnitDbId associated with a particular level and code.\n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items": { + "type": "string" + }, + "type": "array" + }, "includeObservations": { "description": "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", "type": "boolean", diff --git a/Specification/BrAPI-Schema/Requests/ReferenceBasesRequest.json b/Specification/BrAPI-Schema/Requests/ReferenceBasesRequest.json new file mode 100644 index 00000000..f9280aba --- /dev/null +++ b/Specification/BrAPI-Schema/Requests/ReferenceBasesRequest.json @@ -0,0 +1,31 @@ +{ + "$defs": { + "ReferenceBasesRequest": { + "type": "object", + "properties": { + "start": { + "description": "The start position (0-based) of this query. Defaults to 0.\nGenomic positions are non-negative integers less than reference length.\nRequests spanning the join of circular genomes are represented as\ntwo requests one on each side of the join (position 0).", + "type": "integer" + }, + "end": { + "description": "The end position (0-based, exclusive) of this query. Defaults to the length of this `Reference`.", + "type": "integer" + }, + "pageToken": { + "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response.", + "type": "string" + } + }, + "brapi-metadata": { + "request": true, + "subQueryProperties" : [ + "start", + "end", + "pageToken" + ] + } + } + }, + "$id": "https://brapi.org/Specification/BrAPI-Schema/Requests/ReferenceBasesRequest.json", + "$schema": "http://json-schema.org/draft/2020-12/schema" +} \ No newline at end of file diff --git a/Specification/BrAPI-Schema/Requests/StudyRequest.json b/Specification/BrAPI-Schema/Requests/StudyRequest.json index d1e21695..0cdbec78 100644 --- a/Specification/BrAPI-Schema/Requests/StudyRequest.json +++ b/Specification/BrAPI-Schema/Requests/StudyRequest.json @@ -74,6 +74,31 @@ "doi:10.155454/12349537312", "https://pui.per/d8dd35e1" ] + }, + "sortBy": { + "description": "Name of the field to sort by.", + "enum": [ + "studyDbId", + "trialDbId", + "programDbId", + "locationDbId", + "seasonDbId", + "studyType", + "studyName", + "studyLocation", + "programName" + ], + "type": "string" + }, + "sortOrder": { + "description": "Sort order direction. Ascending/Descending.", + "enum": [ + "asc", + "ASC", + "desc", + "DESC" + ], + "type": "string" } } } diff --git a/Specification/BrAPI-Schema/Requests/TrialRequest.json b/Specification/BrAPI-Schema/Requests/TrialRequest.json index ad1307b0..a5b56511 100644 --- a/Specification/BrAPI-Schema/Requests/TrialRequest.json +++ b/Specification/BrAPI-Schema/Requests/TrialRequest.json @@ -59,6 +59,29 @@ "https://doi.org/01093190", "https://doi.org/11192409" ] + }, + "sortBy": { + "description": "Name of the field to sort by.", + "enum": [ + "trialDbId", + "trialName", + "programDbId", + "programName", + "locationDbId", + "startDate", + "endDate" + ], + "type": "string" + }, + "sortOrder": { + "description": "Sort order direction. Ascending/Descending.", + "enum": [ + "asc", + "ASC", + "desc", + "DESC" + ], + "type": "string" } } } From b9faeb8ef876bff66c8e215cd9be3b0e45f76e1c Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 13 Mar 2026 17:41:37 +1300 Subject: [PATCH 06/62] Update JSON schemas to correct naming conventions and descriptions for search requests --- .../AlleleMatrix/Search_AlleleMatrix_POST.yaml | 2 +- .../CallSets/Schemas/CallSetsSearchRequest.yaml | 2 +- .../BrAPI-Genotyping/CallSets/Search_CallSets_POST.yaml | 4 ++-- Specification/BrAPI-Genotyping/Calls/Search_Calls_POST.yaml | 2 +- .../BrAPI-Genotyping/VariantSets/Search_VariantSets_POST.yaml | 2 +- .../VariantSets/VariantSets_Extract_POST.yaml | 2 +- .../Variants/Schemas/VariantsSearchRequest.yaml | 2 +- .../BrAPI-Genotyping/Variants/Search_Variants_POST.yaml | 4 ++-- 8 files changed, 10 insertions(+), 10 deletions(-) diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_POST.yaml b/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_POST.yaml index 2a3149f0..41130240 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_POST.yaml +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_POST.yaml @@ -18,7 +18,7 @@ paths: application/json: schema: $ref: '#/components/schemas/AlleleMatrixSearchRequest' - description: Study Search request + description: AlleleMatrix Search request responses: '200': $ref: '#/components/responses/AlleleMatrixResponse' diff --git a/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSetsSearchRequest.yaml b/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSetsSearchRequest.yaml index fe8e00e1..a8d57c88 100644 --- a/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSetsSearchRequest.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSetsSearchRequest.yaml @@ -5,7 +5,7 @@ openapi: 3.0.0 paths: {} components: schemas: - callSetsSearchRequest: + CallSetsSearchRequest: allOf: - $ref: '#/components/schemas/SearchRequestParametersPaging' - $ref: '#/components/schemas/SearchRequestParametersGermplasm' diff --git a/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_POST.yaml b/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_POST.yaml index 9056c927..ef049b5b 100644 --- a/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_POST.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_POST.yaml @@ -18,8 +18,8 @@ paths: content: application/json: schema: - $ref: '#/components/schemas/callSetsSearchRequest' - description: Study Search request + $ref: '#/components/schemas/CallSetsSearchRequest' + description: CallSet Search request responses: '200': $ref: '#/components/responses/CallSetsListResponse' diff --git a/Specification/BrAPI-Genotyping/Calls/Search_Calls_POST.yaml b/Specification/BrAPI-Genotyping/Calls/Search_Calls_POST.yaml index f2ecd44f..d95492c7 100644 --- a/Specification/BrAPI-Genotyping/Calls/Search_Calls_POST.yaml +++ b/Specification/BrAPI-Genotyping/Calls/Search_Calls_POST.yaml @@ -23,7 +23,7 @@ paths: application/json: schema: $ref: '#/components/schemas/CallsSearchRequest' - description: Study Search request + description: Calls Search request responses: '200': $ref: '#/components/responses/CallsListResponse' diff --git a/Specification/BrAPI-Genotyping/VariantSets/Search_VariantSets_POST.yaml b/Specification/BrAPI-Genotyping/VariantSets/Search_VariantSets_POST.yaml index a907cef6..5fb49b25 100644 --- a/Specification/BrAPI-Genotyping/VariantSets/Search_VariantSets_POST.yaml +++ b/Specification/BrAPI-Genotyping/VariantSets/Search_VariantSets_POST.yaml @@ -19,7 +19,7 @@ paths: application/json: schema: $ref: '#/components/schemas/VariantSetsSearchRequest' - description: Study Search request + description: VariantSet Search request responses: '200': $ref: '#/components/responses/VariantSetsListResponse' diff --git a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_Extract_POST.yaml b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_Extract_POST.yaml index 734f7dcb..9f2e094b 100644 --- a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_Extract_POST.yaml +++ b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_Extract_POST.yaml @@ -14,7 +14,7 @@ paths: application/json: schema: $ref: '#/components/schemas/VariantSetsExtractRequest' - description: Study Search request + description: VariantSet Search request responses: '200': content: diff --git a/Specification/BrAPI-Genotyping/Variants/Schemas/VariantsSearchRequest.yaml b/Specification/BrAPI-Genotyping/Variants/Schemas/VariantsSearchRequest.yaml index 33753866..4861a680 100644 --- a/Specification/BrAPI-Genotyping/Variants/Schemas/VariantsSearchRequest.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Schemas/VariantsSearchRequest.yaml @@ -5,7 +5,7 @@ openapi: 3.0.0 paths: {} components: schemas: - variantsSearchRequest: + VariantsSearchRequest: allOf: - $ref: '#/components/schemas/SearchRequestParametersTokenPaging' - $ref: '#/components/schemas/SearchRequestParametersCommonCropNames' diff --git a/Specification/BrAPI-Genotyping/Variants/Search_Variants_POST.yaml b/Specification/BrAPI-Genotyping/Variants/Search_Variants_POST.yaml index 254bf560..1a02b6c7 100644 --- a/Specification/BrAPI-Genotyping/Variants/Search_Variants_POST.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Search_Variants_POST.yaml @@ -22,8 +22,8 @@ paths: content: application/json: schema: - $ref: '#/components/schemas/variantsSearchRequest' - description: Study Search request + $ref: '#/components/schemas/VariantsSearchRequest' + description: Variant Search request responses: '200': $ref: '#/components/responses/VariantsListResponse' From c54076e55fd46b1fbcd29c11ab7ba8bf3adab58c Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 31 Mar 2026 17:59:54 +1300 Subject: [PATCH 07/62] Update JSON schemas to correct naming conventions and descriptions for search requests --- Specification/BrAPI-Schema/BrAPI-Common/Attribute.json | 5 +++-- .../BrAPI-Schema/BrAPI-Common/ExternalReference.json | 5 +++-- Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json | 5 +++-- Specification/BrAPI-Schema/BrAPI-Core/Location.json | 2 +- Specification/BrAPI-Schema/BrAPI-Core/Study.json | 2 +- Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json | 2 ++ .../BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json | 5 +++-- Specification/BrAPI-Schema/Requests/ProgramRequest.json | 1 + .../BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json | 5 +++-- 9 files changed, 20 insertions(+), 12 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json b/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json index 2ddfa209..83933600 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json @@ -43,9 +43,10 @@ "controlledVocabularyProperties": [ "attributeCategory" ] - } + }, + "description": "An Attribute is a Variable that is associated with certain entities which may have a\nAttribute Value for instances of that entity and\nis not an ObservationVariable that was record during the execution of a Study.\n\nAttributes are available for the following entities:\n* Cultivar see Cultivar Attribute\n* Locale see LocaleAttribute\n* Germplasm see GermplasmAttribute\n* Observation Unit see ObservationUnitAttribute\n* Inventory Lot see InventoryLotAttribute\n\n### Phenome Implementation\n\nIn phenome attributes are variables associated with a specific entity.\n\n### PRISM Implementation\n\nIn PRISM attributes are columns associated with a specific entity." } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/Attribute.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json b/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json index 3332d5ec..c612a6cf 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json @@ -17,9 +17,10 @@ ] } }, - "type": "object" + "type": "object", + "description": "External References are used to link entities to equivalent entities. The External Reference has two fields:\n\n* **referenceId** - The external reference ID. Could be a simple string or a URI.\n* **referenceSource**\t- An identifier for the source system or database of this reference.\n\nThere are two main uses of External References.\n\n* An array of External References are provided in the result of many queries, which allows equivalent entities\n to be found in other systems using these identifiers.\n* External References can be provided as arguments in many queries, which allows querying by\n\nThe value of the **referenceSource** field provides the context of the **referenceId** field. \n\nThe table below shows the currently available `referenceSources` for different entities, a description of the `referenceId`, and an example:\n\n| Reference Source | Entities | Description | Example |\n|---------------------|---------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------|--------------------------------------|\n| CROP_2_LETTER_CODE | Crop | The 2 letter code for the crop defined in the Crop Ontology | WH |\n| CROP_3_LETTER_CODE | Crop | The 3 letter code for the crop defined in the Crop Ontology | TRI |\n| CROP_ONTOLOGY_ID | Crop | The ID of the crop in the Crop Ontology | a9d1511d-a50b-3838-a3fe-58219510e6f4 |\n| PRISM_CROP_CODE | Crop | The crop code for the crop defined in PRISM | WH |\n| PRISM_CROP_ID | Crop | The business code for a crop in PRISM. It is in the format ^PCRP(?=FCR VEG)[0-9]{4}[1-9]? | PCRPFCR1004 | \n| PRISM_MATERIAL_ID | Germplasm/Cultivar | The ID used for Material, which can be used to uniquely identify Cultivars or to identify Germplasm belong to a PRISM material. | PMWH20743430 |\n| PRISM_MATERIAL_NAME | Germplasm/Cultivar | The Name used for Material, which might be the Cultivar name or the name of PRISM material associated with a Germplasm | G16Q2x0749.WTHCMSt |\n| PRISM_NFB_ID | Study/Locale | The ID of the Nursery Field Book in PRISM. Provided when the Study or Locale originates from a PRISM Nursery Field Book | PDCEFCR565640 | \n| PRISM_NFB_NAME | Study/Locale | The name of the Nursery Field Book in PRISM. Provided when the Study or Locale originates from a PRISM Nursery Field Book | | \n| PRISM_YTFB_ID | Study/Locale | The ID of the Yield Trial Field Book in PRISM. Provided when the Study or Locale originates from a Yield Trial Field Book | PDCEFCR565569 |\n| PRISM_YTFB_NAME | Study/Locale | The name of the Yield Trial Field Book in PRISM. Provided when the Study or Locale originates from a Yield Trial Field Book | |\n| TRAM_CODE | Observation Variable | The code of the equivalent variable in TRAM | TTOC:0005045 | \n\n### Implementation\n\nExternal References are implemented consistently across data providers (PRISM and Phenome),\nbut a Data Provider may not provide all possible External References for a specific Entity." } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/Components/Common/ExternalReference.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json index f948029c..4e4445f9 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json @@ -59,9 +59,10 @@ ], "type": "object" } - ] + ], + "description": "GeoJSONGeometry can either be a GeoJSONPoint \nor a GeoJSONPolygon.\n\nIt is used by geometry in GeoJSON\n\n### Implementation\n\nSee the fields in which GeoJSON is used." } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/Components/Common/AdditionalInfo.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Location.json b/Specification/BrAPI-Schema/BrAPI-Core/Location.json index 81ddcdc2..e05e3d8d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Location.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Location.json @@ -119,7 +119,7 @@ }, "childLocations": { "title": "ChildLocations", - "description": "", + "description": "The child locations that belong to this Location. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", "referencedAttribute": "parentLocation", "relationshipType": "one-to-many", "items": { diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index 534053eb..ed3a836d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -455,7 +455,7 @@ "LastUpdate": { "properties": { "lastUpdateDbId": { - "description": "The date and time when this study was last modified", + "description": "The ID which uniquely identifies a LastUpdate within the given database server", "type": "string" }, "timestamp": { diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index 5e860d70..a792ec25 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -180,6 +180,7 @@ ] }, "mcpd": { + "deprecated": true, "$ref": "Germplasm.json#/$defs/GermplasmMCPD", "description": "The mulit-crop passport descriptors (MCPD) for this germplasm", "referencedAttribute": "germplasm", @@ -396,6 +397,7 @@ } }, "GermplasmMCPD": { + "deprecated": true, "properties": { "accessionNames": { "description": "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered names or other designations given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase.", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json index ccd00194..fcca7440 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json @@ -62,9 +62,10 @@ ], "brapi-metadata": { "primaryModel": true - } + }, + "description": "An **Observation Variable** is a parameter of the observation unit that is assessed in the context of a study. An ObservationVariable is defined at **crop**-level.\n\nSeveral Observation Variables can be related to the same phenotypic characteristic\n(e.g. height) but will be considered as different observation variables\nif they are measured at a different scale.\nFor example, the Observation Variable 'height in centimeters' differs from the \nObservation Variable 'height in inches'.\n\nAn Observation Variable is typically used to capture phenotypic measurements such as \nheight, yield, weight, etc. However, it can also capture genotypic or other characteristics. \n\n### Phenome Implementation\n\nObservation Variables are Variables with the Variable type 'Variate'\nthat have been assigned to the Germplasm entity.\n\n### PRISM Implementation\n\n> TODO Breeding Services please check\n\nIn Field Crops and Vegetable Observation Variables are held different workbooks depending\non the type of Study and are columns in the corresponding field book table." } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/Requests/ProgramRequest.json b/Specification/BrAPI-Schema/Requests/ProgramRequest.json index dc08fd71..8b4392ae 100644 --- a/Specification/BrAPI-Schema/Requests/ProgramRequest.json +++ b/Specification/BrAPI-Schema/Requests/ProgramRequest.json @@ -59,6 +59,7 @@ "description": "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", "items": { "type": "string", + "description": "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", "enum": [ "STANDARD", "PROJECT" diff --git a/Specification/BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json b/Specification/BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json index ef0be9a6..36ffea2a 100644 --- a/Specification/BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json +++ b/Specification/BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json @@ -40,9 +40,10 @@ ], "brapi-metadata": { "request": true - } + }, + "description": "The GeoJSONSearchArea provides a way to search by position.\nIt is used in coordinates in LocationRequest\nand imageLocation in ImageRequest\n\n### Implementation\n\nGeoJSONSearchArea is not currently implemented in BrAPI+." } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} From f504a4ad5d95eb0d248e7a2c869600cf3d8ab661 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 31 Mar 2026 19:30:53 +1300 Subject: [PATCH 08/62] revert description changes --- Specification/BrAPI-Schema/BrAPI-Common/Attribute.json | 3 +-- .../BrAPI-Schema/BrAPI-Common/ExternalReference.json | 3 +-- Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json | 3 +-- .../BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json | 5 ++--- Specification/BrAPI-Schema/Requests/ProgramRequest.json | 2 +- .../BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json | 3 +-- 6 files changed, 7 insertions(+), 12 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json b/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json index 83933600..cf1fe76a 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Attribute.json @@ -43,8 +43,7 @@ "controlledVocabularyProperties": [ "attributeCategory" ] - }, - "description": "An Attribute is a Variable that is associated with certain entities which may have a\nAttribute Value for instances of that entity and\nis not an ObservationVariable that was record during the execution of a Study.\n\nAttributes are available for the following entities:\n* Cultivar see Cultivar Attribute\n* Locale see LocaleAttribute\n* Germplasm see GermplasmAttribute\n* Observation Unit see ObservationUnitAttribute\n* Inventory Lot see InventoryLotAttribute\n\n### Phenome Implementation\n\nIn phenome attributes are variables associated with a specific entity.\n\n### PRISM Implementation\n\nIn PRISM attributes are columns associated with a specific entity." + } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/Attribute.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json b/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json index c612a6cf..37ac18c8 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json @@ -17,8 +17,7 @@ ] } }, - "type": "object", - "description": "External References are used to link entities to equivalent entities. The External Reference has two fields:\n\n* **referenceId** - The external reference ID. Could be a simple string or a URI.\n* **referenceSource**\t- An identifier for the source system or database of this reference.\n\nThere are two main uses of External References.\n\n* An array of External References are provided in the result of many queries, which allows equivalent entities\n to be found in other systems using these identifiers.\n* External References can be provided as arguments in many queries, which allows querying by\n\nThe value of the **referenceSource** field provides the context of the **referenceId** field. \n\nThe table below shows the currently available `referenceSources` for different entities, a description of the `referenceId`, and an example:\n\n| Reference Source | Entities | Description | Example |\n|---------------------|---------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------|--------------------------------------|\n| CROP_2_LETTER_CODE | Crop | The 2 letter code for the crop defined in the Crop Ontology | WH |\n| CROP_3_LETTER_CODE | Crop | The 3 letter code for the crop defined in the Crop Ontology | TRI |\n| CROP_ONTOLOGY_ID | Crop | The ID of the crop in the Crop Ontology | a9d1511d-a50b-3838-a3fe-58219510e6f4 |\n| PRISM_CROP_CODE | Crop | The crop code for the crop defined in PRISM | WH |\n| PRISM_CROP_ID | Crop | The business code for a crop in PRISM. It is in the format ^PCRP(?=FCR VEG)[0-9]{4}[1-9]? | PCRPFCR1004 | \n| PRISM_MATERIAL_ID | Germplasm/Cultivar | The ID used for Material, which can be used to uniquely identify Cultivars or to identify Germplasm belong to a PRISM material. | PMWH20743430 |\n| PRISM_MATERIAL_NAME | Germplasm/Cultivar | The Name used for Material, which might be the Cultivar name or the name of PRISM material associated with a Germplasm | G16Q2x0749.WTHCMSt |\n| PRISM_NFB_ID | Study/Locale | The ID of the Nursery Field Book in PRISM. Provided when the Study or Locale originates from a PRISM Nursery Field Book | PDCEFCR565640 | \n| PRISM_NFB_NAME | Study/Locale | The name of the Nursery Field Book in PRISM. Provided when the Study or Locale originates from a PRISM Nursery Field Book | | \n| PRISM_YTFB_ID | Study/Locale | The ID of the Yield Trial Field Book in PRISM. Provided when the Study or Locale originates from a Yield Trial Field Book | PDCEFCR565569 |\n| PRISM_YTFB_NAME | Study/Locale | The name of the Yield Trial Field Book in PRISM. Provided when the Study or Locale originates from a Yield Trial Field Book | |\n| TRAM_CODE | Observation Variable | The code of the equivalent variable in TRAM | TTOC:0005045 | \n\n### Implementation\n\nExternal References are implemented consistently across data providers (PRISM and Phenome),\nbut a Data Provider may not provide all possible External References for a specific Entity." + "type": "object" } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/Components/Common/ExternalReference.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json index 4e4445f9..0993e0eb 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json @@ -59,8 +59,7 @@ ], "type": "object" } - ], - "description": "GeoJSONGeometry can either be a GeoJSONPoint \nor a GeoJSONPolygon.\n\nIt is used by geometry in GeoJSON\n\n### Implementation\n\nSee the fields in which GeoJSON is used." + ] } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/Components/Common/AdditionalInfo.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json index fcca7440..ccd00194 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json @@ -62,10 +62,9 @@ ], "brapi-metadata": { "primaryModel": true - }, - "description": "An **Observation Variable** is a parameter of the observation unit that is assessed in the context of a study. An ObservationVariable is defined at **crop**-level.\n\nSeveral Observation Variables can be related to the same phenotypic characteristic\n(e.g. height) but will be considered as different observation variables\nif they are measured at a different scale.\nFor example, the Observation Variable 'height in centimeters' differs from the \nObservation Variable 'height in inches'.\n\nAn Observation Variable is typically used to capture phenotypic measurements such as \nheight, yield, weight, etc. However, it can also capture genotypic or other characteristics. \n\n### Phenome Implementation\n\nObservation Variables are Variables with the Variable type 'Variate'\nthat have been assigned to the Germplasm entity.\n\n### PRISM Implementation\n\n> TODO Breeding Services please check\n\nIn Field Crops and Vegetable Observation Variables are held different workbooks depending\non the type of Study and are columns in the corresponding field book table." + } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationVariable.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} +} \ No newline at end of file diff --git a/Specification/BrAPI-Schema/Requests/ProgramRequest.json b/Specification/BrAPI-Schema/Requests/ProgramRequest.json index 8b4392ae..3f6e16a9 100644 --- a/Specification/BrAPI-Schema/Requests/ProgramRequest.json +++ b/Specification/BrAPI-Schema/Requests/ProgramRequest.json @@ -59,7 +59,7 @@ "description": "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", "items": { "type": "string", - "description": "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "description": "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding.", "enum": [ "STANDARD", "PROJECT" diff --git a/Specification/BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json b/Specification/BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json index 36ffea2a..060a689a 100644 --- a/Specification/BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json +++ b/Specification/BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json @@ -40,8 +40,7 @@ ], "brapi-metadata": { "request": true - }, - "description": "The GeoJSONSearchArea provides a way to search by position.\nIt is used in coordinates in LocationRequest\nand imageLocation in ImageRequest\n\n### Implementation\n\nGeoJSONSearchArea is not currently implemented in BrAPI+." + } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/Requests/Schemas/GeoJSONSearchArea.json", From 2da8003d7ccab297741bb25d93e7359e7adbeb99 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Mon, 20 Apr 2026 18:31:21 +1200 Subject: [PATCH 09/62] removed fromSeedLotTransactions and toSeedLotTransactions, revert to transactions. This avoids changing the model in this version. --- .../BrAPI-Schema/BrAPI-Germplasm/SeedLot.json | 21 +++---------------- .../BrAPI-Germplasm/SeedLotTransaction.json | 2 -- 2 files changed, 3 insertions(+), 20 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json index c3159b0a..8a040568 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json @@ -105,24 +105,9 @@ "string" ] }, - "fromSeedLotTransactions": { - "title": "fromSeedLotTransactions", - "description": "fromSeedLotTransactions", - "referencedAttribute": "fromSeedLot", - "relationshipType": "one-to-many", - "items": { - "$ref": "SeedLotTransaction.json#/$defs/SeedLotTransaction", - "description": "SeedLotTransaction" - }, - "type": [ - "null", - "array" - ] - }, - "toSeedLotTransactions": { - "title": "toSeedLotTransactions", - "description": "toSeedLotTransactions", - "referencedAttribute": "toSeedLot", + "transactions": { + "title": "transactions", + "description": "The complete history of transactions for this seed lot. This includes seed increases, seed usage (planting), and trading with other breeding programs.", "relationshipType": "one-to-many", "items": { "$ref": "SeedLotTransaction.json#/$defs/SeedLotTransaction", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json index 260115cb..a1b03084 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json @@ -30,13 +30,11 @@ "fromSeedLot": { "$ref": "SeedLot.json#/$defs/SeedLot", "description": "The identifier for the Seed Lot being transferred out of", - "referencedAttribute": "fromSeedLotTransactions", "relationshipType": "many-to-one" }, "toSeedLot": { "$ref": "SeedLot.json#/$defs/SeedLot", "description": "The identifier for the Seed Lot being transferred into", - "referencedAttribute": "toSeedLotTransactions", "relationshipType": "many-to-one" }, "transactionDbId": { From 12ef2ed4a434ff4c9682b5e101c07f56bf80e9ba Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 28 Apr 2026 15:49:14 +1200 Subject: [PATCH 10/62] Add missing responses pt1 --- .../BrAPI-Core/Programs/Programs_ProgramDbId_GET_PUT.yaml | 4 ++++ .../BrAPI-Core/Seasons/Seasons_SeasonDbId_GET_PUT.yaml | 4 ++++ .../CallSets/CallSets_CallSetId_Calls_GET.yaml | 2 ++ .../ReferenceSets/ReferenceSets_RefernceSetId_GET.yaml | 8 ++++++++ .../VariantSets/VariantSets_VariantSetId_Calls_GET.yaml | 2 ++ .../Variants/Variants_VariantId_Calls_GET.yaml | 2 ++ .../CrossingProjects_CrossingProjectDbId_GET_PUT.yaml | 4 ++++ .../AttributeValues_AttributeValueDbId_GET_PUT.yaml | 4 ++++ .../Attributes_AttributeDbId_GET_PUT.yaml | 4 ++++ .../Ontologies/Ontologies_OntologyDbId_GET_PUT.yaml | 4 ++++ 10 files changed, 38 insertions(+) diff --git a/Specification/BrAPI-Core/Programs/Programs_ProgramDbId_GET_PUT.yaml b/Specification/BrAPI-Core/Programs/Programs_ProgramDbId_GET_PUT.yaml index ae263ff7..92fbe9b3 100644 --- a/Specification/BrAPI-Core/Programs/Programs_ProgramDbId_GET_PUT.yaml +++ b/Specification/BrAPI-Core/Programs/Programs_ProgramDbId_GET_PUT.yaml @@ -24,6 +24,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Programs put: @@ -51,6 +53,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Programs components: diff --git a/Specification/BrAPI-Core/Seasons/Seasons_SeasonDbId_GET_PUT.yaml b/Specification/BrAPI-Core/Seasons/Seasons_SeasonDbId_GET_PUT.yaml index 423c0426..bcab8acb 100644 --- a/Specification/BrAPI-Core/Seasons/Seasons_SeasonDbId_GET_PUT.yaml +++ b/Specification/BrAPI-Core/Seasons/Seasons_SeasonDbId_GET_PUT.yaml @@ -25,6 +25,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Seasons put: @@ -53,6 +55,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Seasons components: diff --git a/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_Calls_GET.yaml b/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_Calls_GET.yaml index f41802cd..85ac4629 100644 --- a/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_Calls_GET.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/CallSets_CallSetId_Calls_GET.yaml @@ -52,5 +52,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Call Sets \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_RefernceSetId_GET.yaml b/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_RefernceSetId_GET.yaml index 123bcf02..e526cc19 100644 --- a/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_RefernceSetId_GET.yaml +++ b/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_RefernceSetId_GET.yaml @@ -33,5 +33,13 @@ paths: $ref: '#/components/schemas/metadata' result: $ref: '#/components/schemas/ReferenceSet' + '400': + $ref: '#/components/responses/400BadRequest' + '401': + $ref: '#/components/responses/401Unauthorized' + '403': + $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Reference Sets \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_Calls_GET.yaml b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_Calls_GET.yaml index e2488224..cd726aba 100644 --- a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_Calls_GET.yaml +++ b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_Calls_GET.yaml @@ -52,5 +52,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Variant Sets \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_Calls_GET.yaml b/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_Calls_GET.yaml index 35046806..fd2ef1f9 100644 --- a/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_Calls_GET.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Variants_VariantId_Calls_GET.yaml @@ -52,5 +52,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Variants \ No newline at end of file diff --git a/Specification/BrAPI-Germplasm/CrossingProjects/CrossingProjects_CrossingProjectDbId_GET_PUT.yaml b/Specification/BrAPI-Germplasm/CrossingProjects/CrossingProjects_CrossingProjectDbId_GET_PUT.yaml index 46bfdbf6..905a4e43 100644 --- a/Specification/BrAPI-Germplasm/CrossingProjects/CrossingProjects_CrossingProjectDbId_GET_PUT.yaml +++ b/Specification/BrAPI-Germplasm/CrossingProjects/CrossingProjects_CrossingProjectDbId_GET_PUT.yaml @@ -24,6 +24,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Crossing Projects put: @@ -51,6 +53,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Crossing Projects components: diff --git a/Specification/BrAPI-Germplasm/Germplasm_Attribute_Values/AttributeValues_AttributeValueDbId_GET_PUT.yaml b/Specification/BrAPI-Germplasm/Germplasm_Attribute_Values/AttributeValues_AttributeValueDbId_GET_PUT.yaml index ccce971a..5cbcfd0f 100644 --- a/Specification/BrAPI-Germplasm/Germplasm_Attribute_Values/AttributeValues_AttributeValueDbId_GET_PUT.yaml +++ b/Specification/BrAPI-Germplasm/Germplasm_Attribute_Values/AttributeValues_AttributeValueDbId_GET_PUT.yaml @@ -24,6 +24,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Germplasm Attribute Values put: @@ -51,6 +53,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Germplasm Attribute Values components: diff --git a/Specification/BrAPI-Germplasm/Germplasm_Attributes/Attributes_AttributeDbId_GET_PUT.yaml b/Specification/BrAPI-Germplasm/Germplasm_Attributes/Attributes_AttributeDbId_GET_PUT.yaml index 8f8def3b..47d24cbd 100644 --- a/Specification/BrAPI-Germplasm/Germplasm_Attributes/Attributes_AttributeDbId_GET_PUT.yaml +++ b/Specification/BrAPI-Germplasm/Germplasm_Attributes/Attributes_AttributeDbId_GET_PUT.yaml @@ -24,6 +24,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Germplasm Attributes put: @@ -51,6 +53,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Germplasm Attributes components: diff --git a/Specification/BrAPI-Phenotyping/Ontologies/Ontologies_OntologyDbId_GET_PUT.yaml b/Specification/BrAPI-Phenotyping/Ontologies/Ontologies_OntologyDbId_GET_PUT.yaml index 2993b682..0105f1c3 100644 --- a/Specification/BrAPI-Phenotyping/Ontologies/Ontologies_OntologyDbId_GET_PUT.yaml +++ b/Specification/BrAPI-Phenotyping/Ontologies/Ontologies_OntologyDbId_GET_PUT.yaml @@ -29,6 +29,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Ontologies put: @@ -61,6 +63,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Ontologies components: From 7abaaa7caa3aa84a84e3a6b69b9a1f5e307dfffe Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 28 Apr 2026 15:49:31 +1200 Subject: [PATCH 11/62] add nullable on ref --- .../BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json index 7315cd7c..5504eaa2 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json @@ -28,7 +28,10 @@ ] }, "variant": { - "$ref": "Variant.json#/$defs/Variant", + "anyOf": [ + {"$ref": "Variant.json#/$defs/Variant"}, + {"type": "null"} + ], "description": "The ID which uniquely identifies a `Variant` within the given database server\n
A `Variant` can also represent a Marker ", "referencedAttribute": "markerPositions", "relationshipType": "many-to-one" From 6cef65728e5abcf3179df388d2ef3cdf65ccd7bf Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 28 Apr 2026 15:49:49 +1200 Subject: [PATCH 12/62] missing require properties --- .../BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json | 11 +++-------- .../BrAPI-Schema/BrAPI-Germplasm/BreedingMethod.json | 5 +---- 2 files changed, 4 insertions(+), 12 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json index 92039e03..89c0607b 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json @@ -63,17 +63,11 @@ }, "mapDbId": { "description": "The unique identifier for a `GenomeMap`", - "type": [ - "null", - "string" - ] + "type": "string" }, "mapName": { "description": "The human readable identifier for a `GenomeMap`", - "type": [ - "null", - "string" - ] + "type": "string" }, "mapPUI": { "description": "The DOI or other permanent identifier for a `GenomeMap`", @@ -118,6 +112,7 @@ }, "required": [ "mapDbId", + "mapName", "commonCropName", "type" ], diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/BreedingMethod.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/BreedingMethod.json index 9776f7d3..67985397 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/BreedingMethod.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/BreedingMethod.json @@ -57,10 +57,7 @@ } }, "required": [ - "abbreviation", - "breedingMethodDbId", - "breedingMethodName", - "description" + "breedingMethodDbId" ], "title": "Breeding Method", "description": "The techniques and protocol used to produce a Cross or Germplasm", From 6eb1dc1c4d27425a664e5f32a331980e4df5289f Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 28 Apr 2026 16:21:40 +1200 Subject: [PATCH 13/62] update brapiSchemaToolsVersion to 0.63.0 --- generator/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/generator/build.gradle b/generator/build.gradle index 9510f65e..5d5a10a0 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.49.0' + brapiSchemaToolsVersion = '0.63.0' } repositories { From 10c98f8fb2757397e30fbff1377004c951710395 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 28 Apr 2026 19:45:08 +1200 Subject: [PATCH 14/62] update brapiSchemaToolsVersion to 0.64.0 --- generator/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/generator/build.gradle b/generator/build.gradle index 5d5a10a0..c778469d 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.63.0' + brapiSchemaToolsVersion = '0.64.0' } repositories { From e6d06aabb6d5513ae6878dd33922ca7f2c4b45d9 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 28 Apr 2026 19:49:34 +1200 Subject: [PATCH 15/62] add '-r' option to the schema generation command --- generator/build.gradle | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/generator/build.gradle b/generator/build.gradle index c778469d..a72170c4 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -101,7 +101,8 @@ tasks.register("generateOWL", JavaExec) { '-f', filename, '-m', 'generator/ont-model-metadata.yaml', '-x', - '-t'] + '-t', + '-r'] } tasks.register("generateAll") { From d977b9abf02e7fc2e61edd0bb033ee5e04202095 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 28 Apr 2026 21:19:58 +1200 Subject: [PATCH 16/62] add '-r' option to the schema generation command --- generator/build.gradle | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/generator/build.gradle b/generator/build.gradle index a72170c4..9344dd52 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -47,7 +47,8 @@ tasks.register("generateGraphQL", JavaExec) { '-l', 'GRAPHQL', '-f', filename, '-x', - '-t'] + '-t', + '-r'] } tasks.register("generateOpenAPI", JavaExec) { @@ -66,7 +67,8 @@ tasks.register("generateOpenAPI", JavaExec) { '-m', metadatafilename, '-c', 'Specification/OpenAPI-Components', '-x', - '-t'] + '-t', + '-r'] } tasks.register("generateOpenAPIJSON", JavaExec) { @@ -85,7 +87,8 @@ tasks.register("generateOpenAPIJSON", JavaExec) { '-m', metadatafilename, '-c', 'Specification/OpenAPI-Components', '-x', - '-t'] + '-t', + '-r'] } From ad63def2bae5fc189b266666d0f3f3cc828cefe7 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 28 Apr 2026 21:27:35 +1200 Subject: [PATCH 17/62] add '-c' option for component specification and include '-r' in markdown generation --- generator/build.gradle | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/generator/build.gradle b/generator/build.gradle index 9344dd52..d79f69cc 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -103,6 +103,7 @@ tasks.register("generateOWL", JavaExec) { '-l', 'OWL', '-f', filename, '-m', 'generator/ont-model-metadata.yaml', + '-c', 'Specification/Components', '-x', '-t', '-r'] @@ -129,7 +130,8 @@ tasks.register("compareOpenAPI", JavaExec) { '-f', filename, '-w', 'MARKDOWN', '-x', - '-t'] + '-t', + '-r'] } tasks.register("compareAll") { From 9096c4d19dba23e54a84da6644180b5b62a562c6 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 28 Apr 2026 21:31:16 +1200 Subject: [PATCH 18/62] add '-c' option for component specification in schema generation commands --- generator/build.gradle | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/generator/build.gradle b/generator/build.gradle index d79f69cc..16382b9a 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -102,8 +102,7 @@ tasks.register("generateOWL", JavaExec) { args = ['generate', 'Specification/BrAPI-Schema', '-l', 'OWL', '-f', filename, - '-m', 'generator/ont-model-metadata.yaml', - '-c', 'Specification/Components', + '-m', 'generator/ont-model-metadata.yaml' '-x', '-t', '-r'] @@ -129,6 +128,7 @@ tasks.register("compareOpenAPI", JavaExec) { '-l', 'OPEN_API', '-f', filename, '-w', 'MARKDOWN', + '-c', 'Specification/Components', '-x', '-t', '-r'] From 74b77649a56296385f0bef710a75c509b1f0d504 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 28 Apr 2026 21:36:46 +1200 Subject: [PATCH 19/62] update schema generation command to include a trailing comma for improved syntax --- generator/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/generator/build.gradle b/generator/build.gradle index 16382b9a..479990ab 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -102,7 +102,7 @@ tasks.register("generateOWL", JavaExec) { args = ['generate', 'Specification/BrAPI-Schema', '-l', 'OWL', '-f', filename, - '-m', 'generator/ont-model-metadata.yaml' + '-m', 'generator/ont-model-metadata.yaml', '-x', '-t', '-r'] From 98e085629f1133edbd54fe8e2f38f80bb6a5f819 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Wed, 29 Apr 2026 12:22:09 +1200 Subject: [PATCH 20/62] add automatic commit action for generated files in schema generation --- .github/workflows/generate-schema.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/generate-schema.yml b/.github/workflows/generate-schema.yml index dac9ad03..fd71b5e6 100644 --- a/.github/workflows/generate-schema.yml +++ b/.github/workflows/generate-schema.yml @@ -75,5 +75,11 @@ jobs: - name: Compare OpenAPI working-directory: ./generator run: ./gradlew compareAll - - if: needs.check.outputs.skip_commit == 'false' + - name: Commit generated files + if: needs.check.outputs.skip_commit == 'false' uses: stefanzweifel/git-auto-commit-action@v5 + with: + commit_message: "Apply automatic changes" + file_pattern: "Specification/Generated/*" + commit_user_name: "github-actions[bot]" + commit_user_email: "github-actions[bot]@users.noreply.github.com" From a43d4afb35ca6bb059a1c3066b3432b1ff29bc8c Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Wed, 29 Apr 2026 12:24:15 +1200 Subject: [PATCH 21/62] set environment variable to enforce Node.js 24 for JavaScript actions --- .github/workflows/generate-schema.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/generate-schema.yml b/.github/workflows/generate-schema.yml index fd71b5e6..63ef9411 100644 --- a/.github/workflows/generate-schema.yml +++ b/.github/workflows/generate-schema.yml @@ -3,6 +3,10 @@ name: Build specifications, schemas and comparisions on: push: workflow_dispatch: + +env: + FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true + jobs: check: runs-on: ubuntu-latest From b5c1460a9ba3ab4a1c192d50e078d4f3b09fa4c7 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Wed, 29 Apr 2026 12:30:44 +1200 Subject: [PATCH 22/62] update generate-schema.yml to handle commit messages based on trigger type --- .github/workflows/generate-schema.yml | 23 +++++++++++++++++------ 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/.github/workflows/generate-schema.yml b/.github/workflows/generate-schema.yml index 63ef9411..644bed38 100644 --- a/.github/workflows/generate-schema.yml +++ b/.github/workflows/generate-schema.yml @@ -13,6 +13,7 @@ jobs: outputs: skip_job: ${{ steps.skip.outputs.skip_job }} skip_commit: ${{ steps.check-tag.outputs.skip_commit }} + commit_message: ${{ steps.check-tag.outputs.commit_message }} steps: - name: Checkout code uses: actions/checkout@v4 @@ -29,13 +30,23 @@ jobs: - name: Check Branch with Regex id: check-tag run: | - regex="^refs/heads/brapi-V[0-9]+\.[0-9]+$" - if [[ "${{ github.ref }}" =~ $regex ]]; then + # Always commit if manually triggered + if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then echo "skip_commit=false" >> "$GITHUB_OUTPUT" - echo "Release branch - WILL commit of generated files" + echo "commit_message=Generate specifications (manually triggered)" >> "$GITHUB_OUTPUT" + echo "Manual trigger - WILL commit generated files" else - echo "skip_commit=true" >> "$GITHUB_OUTPUT" - echo "Normal branch - Will NOT commit of generated files" + # Otherwise, only commit on release branches + regex="^refs/heads/brapi-V[0-9]+\.[0-9]+$" + if [[ "${{ github.ref }}" =~ $regex ]]; then + echo "skip_commit=false" >> "$GITHUB_OUTPUT" + echo "commit_message=Apply automatic changes" >> "$GITHUB_OUTPUT" + echo "Release branch - WILL commit of generated files" + else + echo "skip_commit=true" >> "$GITHUB_OUTPUT" + echo "commit_message=" >> "$GITHUB_OUTPUT" + echo "Normal branch - Will NOT commit of generated files" + fi fi generate: runs-on: ubuntu-latest @@ -83,7 +94,7 @@ jobs: if: needs.check.outputs.skip_commit == 'false' uses: stefanzweifel/git-auto-commit-action@v5 with: - commit_message: "Apply automatic changes" + commit_message: "${{ needs.check.outputs.commit_message }}" file_pattern: "Specification/Generated/*" commit_user_name: "github-actions[bot]" commit_user_email: "github-actions[bot]@users.noreply.github.com" From 59aa4d894430e8dd1db9625c05880e459ab7f7eb Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Wed, 29 Apr 2026 00:35:59 +0000 Subject: [PATCH 23/62] Generate specifications (manually triggered) --- Specification/Generated/BrAPI-Core.yaml | 5917 ++++- Specification/Generated/BrAPI-Genotyping.yaml | 8647 +++++-- Specification/Generated/BrAPI-Germplasm.yaml | 8269 +++++-- .../Generated/BrAPI-Phenotyping.yaml | 6423 ++++- .../Generated/brapi_generated.graphqls | 1066 +- Specification/Generated/brapi_generated.json | 18289 +++++++++++---- Specification/Generated/brapi_generated.ttl | 1354 +- Specification/Generated/brapi_openapi.json | 1759 +- .../Generated/brapi_openapi_comparison.md | 19393 ++-------------- 9 files changed, 42252 insertions(+), 28865 deletions(-) diff --git a/Specification/Generated/BrAPI-Core.yaml b/Specification/Generated/BrAPI-Core.yaml index 6cf39963..b5230fe1 100644 --- a/Specification/Generated/BrAPI-Core.yaml +++ b/Specification/Generated/BrAPI-Core.yaml @@ -77,31 +77,25 @@ paths: summary: Get a filtered list of List description: Get a list of List parameters: - - name: dateCreatedRangeStart - in: query - description: Define the beginning for an interval of time and only include - Lists that are created within this interval. - required: false - schema: - type: string - - name: dateCreatedRangeEnd - in: query - description: Define the end for an interval of time and only include Lists - that are created within this interval. - required: false - schema: - type: string - - name: dateModifiedRangeStart + - name: commonCropName in: query - description: Define the beginning for an interval of time and only include - Lists that are modified within this interval. + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." required: false schema: type: string - - name: dateModifiedRangeEnd + - name: programDbId in: query - description: Define the end for an interval of time and only include Lists - that are modified within this interval. + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." required: false schema: type: string @@ -118,20 +112,6 @@ paths: required: false schema: type: string - - name: listOwnerName - in: query - description: An array of names for the people or entities who are responsible - for a set of Lists - required: false - schema: - type: string - - name: listOwnerPersonDbId - in: query - description: An array of primary database identifiers to identify people or - entities who are responsible for a set of Lists - required: false - schema: - type: string - name: listSource in: query description: "An array of terms identifying lists from different sources (ie\ @@ -144,7 +124,6 @@ paths: required: false schema: $ref: "#/components/schemas/ListType" - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -170,7 +149,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ListNewRequest" + type: array + items: + $ref: "#/components/schemas/ListNewRequest" responses: "200": $ref: "#/components/responses/ListListResponse" @@ -221,63 +202,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - - name: abbreviation - in: query - description: A list of shortened human readable names for a set of Locations - required: false - schema: - type: string - - name: altitudeMin - in: query - description: The minimum altitude to search for - required: false - schema: - type: number - - name: altitudeMax - in: query - description: The maximum altitude to search for - required: false - schema: - type: number - - name: countryCode - in: query - description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ - \ spec" - required: false - schema: - type: string - - name: countryName - in: query - description: The full name of the country to search for - required: false - schema: - type: string - - name: coordinate - in: query - required: false - schema: - $ref: "#/components/schemas/GeoJSONSearchArea" - - name: instituteAddress - in: query - description: The street address of the institute to search for - required: false - schema: - type: string - - name: instituteName - in: query - description: The name of the institute to search for - required: false - schema: - type: string - name: locationType in: query description: "The type of location this represents (ex. Breeding Location,\ @@ -303,7 +227,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -329,7 +252,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/LocationNewRequest" + type: array + items: + $ref: "#/components/schemas/LocationNewRequest" responses: "200": $ref: "#/components/responses/LocationListResponse" @@ -368,21 +293,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - - name: emailAddress - in: query - description: email address for this person - required: false - schema: - type: string - name: firstName in: query description: Persons first name @@ -395,30 +305,12 @@ paths: required: false schema: type: string - - name: mailingAddress - in: query - description: physical address of this person - required: false - schema: - type: string - - name: middleName - in: query - description: Persons middle name - required: false - schema: - type: string - name: personDbId in: query description: Unique ID for this person required: false schema: type: string - - name: phoneNumber - in: query - description: phone number of this person - required: false - schema: - type: string - name: userID in: query description: A systems user ID associated with this person. Different from @@ -426,7 +318,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -452,7 +343,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/PersonNewRequest" + type: array + items: + $ref: "#/components/schemas/PersonNewRequest" responses: "200": $ref: "#/components/responses/PersonListResponse" @@ -506,24 +399,6 @@ paths: required: false schema: type: string - - name: leadPersonDbId - in: query - description: The person DbIds of the program leader to search for - required: false - schema: - type: string - - name: leadPersonName - in: query - description: The names of the program leader to search for - required: false - schema: - type: string - - name: objectife - in: query - description: A program objective to search for - required: false - schema: - type: string - name: programType in: query description: "The type of program entity this object represents\n
'STANDARD'\ @@ -532,10 +407,13 @@ paths: required: false schema: type: string + description: |- + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding. enum: - STANDARD - PROJECT - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -561,7 +439,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ProgramNewRequest" + type: array + items: + $ref: "#/components/schemas/ProgramNewRequest" responses: "200": $ref: "#/components/responses/ProgramListResponse" @@ -628,7 +508,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/Season" + type: array + items: + $ref: "#/components/schemas/Season" responses: "200": $ref: "#/components/responses/SeasonListResponse" @@ -663,25 +545,12 @@ paths: required: false schema: type: string - - name: germplasmName - in: query - description: List of human readable names to identify germplasm to search - for - required: false - schema: - type: string - name: locationDbId in: query description: The location ids to search for required: false schema: type: string - - name: locationName - in: query - description: A human readable names to search for - required: false - schema: - type: string - name: programDbId in: query description: "A BrAPI Program represents the high level organization or group\ @@ -692,15 +561,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for @@ -719,32 +579,13 @@ paths: required: false schema: type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - name: observationVariableDbId in: query description: The DbIds of Variables to search for required: false schema: type: string - - name: observationVariableName - in: query - description: The names of Variables to search for - required: false - schema: - type: string - - name: observationVariablePUI - in: query - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - required: false - schema: - type: string - - name: actife + - name: active in: query description: A flag to indicate if a Study is currently active and ongoing required: false @@ -775,7 +616,35 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" + - name: sortBy + in: query + description: Name of the field to sort by. + required: false + schema: + type: string + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + - name: sortOrder + in: query + description: Sort order direction. Ascending/Descending. + required: false + schema: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -801,7 +670,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/StudyNewRequest" + type: array + items: + $ref: "#/components/schemas/StudyNewRequest" responses: "200": $ref: "#/components/responses/StudyListResponse" @@ -836,31 +707,6 @@ paths: required: false schema: type: string - - name: locationName - in: query - description: A human readable names to search for - required: false - schema: - type: string - - name: observationVariableDbId - in: query - description: The DbIds of Variables to search for - required: false - schema: - type: string - - name: observationVariableName - in: query - description: The names of Variables to search for - required: false - schema: - type: string - - name: observationVariablePUI - in: query - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - required: false - schema: - type: string - name: programDbId in: query description: "A BrAPI Program represents the high level organization or group\ @@ -871,27 +717,12 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for required: false schema: type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - name: trialDbId in: query description: The ID which uniquely identifies a trial to search for @@ -904,7 +735,7 @@ paths: required: false schema: type: string - - name: actife + - name: active in: query description: A flag to indicate if a Trial is currently active and ongoing required: false @@ -929,6 +760,7 @@ paths: required: false schema: type: string + format: date - name: searchDateRangeEnd in: query description: "The end of the overlapping search date range. `searchDateRangeStart`\ @@ -942,6 +774,7 @@ paths: required: false schema: type: string + format: date - name: trialPUI in: query description: A permanent identifier for a trial. Could be DOI or other URI @@ -949,7 +782,33 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" + - name: sortBy + in: query + description: Name of the field to sort by. + required: false + schema: + type: string + description: Name of the field to sort by. + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + - name: sortOrder + in: query + description: Sort order direction. Ascending/Descending. + required: false + schema: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -975,7 +834,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/TrialNewRequest" + type: array + items: + $ref: "#/components/schemas/TrialNewRequest" responses: "200": $ref: "#/components/responses/TrialListResponse" @@ -985,12 +846,39 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + /studytypes: + get: + tags: + - Studies + summary: Get the studyTypes of Study + description: List all available Study studyTypes + parameters: + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/StudyStudyTypeListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" /lists/{listDbId}: get: tags: - Lists summary: Get the details of a specific List description: Get details for a List + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: listDbId + in: path + description: The unique identifier for a List + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/ListSingleResponse" @@ -1000,6 +888,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Lists @@ -1007,6 +897,12 @@ paths: description: Update the details for an existing List parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: listDbId + in: path + description: The unique identifier for a List + required: true + schema: + type: string requestBody: content: application/json: @@ -1021,21 +917,63 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - /locations/{locationDbId}: - get: + "404": + $ref: "#/components/responses/404NotFound" + /lists/{listDbId}/data: + post: tags: - - Locations - summary: Get the details of a specific Location - description: Get details for a Location - responses: - "200": - $ref: "#/components/responses/LocationSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": + - Lists + summary: Create new string + description: Add new string to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: listDbId + in: path + description: The unique identifier for a List + required: true + schema: + type: string + requestBody: + content: + application/json: + schema: + type: string + responses: + "200": + $ref: "#/components/responses/ListSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /locations/{locationDbId}: + get: + tags: + - Locations + summary: Get the details of a specific Location + description: Get details for a Location + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: locationDbId + in: path + description: The unique identifier for a Location + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/LocationSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Locations @@ -1043,6 +981,12 @@ paths: description: Update the details for an existing Location parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: locationDbId + in: path + description: The unique identifier for a Location + required: true + schema: + type: string requestBody: content: application/json: @@ -1057,12 +1001,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /people/{personDbId}: get: tags: - People summary: Get the details of a specific Person description: Get details for a Person + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: personDbId + in: path + description: Unique ID for a person + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/PersonSingleResponse" @@ -1072,6 +1026,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - People @@ -1079,6 +1035,12 @@ paths: description: Update the details for an existing Person parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: personDbId + in: path + description: Unique ID for a person + required: true + schema: + type: string requestBody: content: application/json: @@ -1093,12 +1055,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /programs/{programDbId}: get: tags: - Programs summary: Get the details of a specific Program description: Get details for a Program + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: programDbId + in: path + description: The ID which uniquely identifies the program + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/ProgramSingleResponse" @@ -1108,6 +1080,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Programs @@ -1115,6 +1089,12 @@ paths: description: Update the details for an existing Program parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: programDbId + in: path + description: The ID which uniquely identifies the program + required: true + schema: + type: string requestBody: content: application/json: @@ -1129,12 +1109,23 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /seasons/{seasonDbId}: get: tags: - Seasons summary: Get the details of a specific Season description: Get details for a Season + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: seasonDbId + in: path + description: "The ID which uniquely identifies a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'" + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/SeasonSingleResponse" @@ -1144,6 +1135,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Seasons @@ -1151,6 +1144,13 @@ paths: description: Update the details for an existing Season parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: seasonDbId + in: path + description: "The ID which uniquely identifies a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'" + required: true + schema: + type: string requestBody: content: application/json: @@ -1165,12 +1165,25 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /studies/{studyDbId}: get: tags: - Studies summary: Get the details of a specific Study description: Get details for a Study + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: studyDbId + in: path + description: |- + The ID which uniquely identifies a study within the given database server + + MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/StudySingleResponse" @@ -1180,6 +1193,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Studies @@ -1187,6 +1202,15 @@ paths: description: Update the details for an existing Study parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: studyDbId + in: path + description: |- + The ID which uniquely identifies a study within the given database server + + MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + required: true + schema: + type: string requestBody: content: application/json: @@ -1201,12 +1225,25 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /trials/{trialDbId}: get: tags: - Trials summary: Get the details of a specific Trial description: Get details for a Trial + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: trialDbId + in: path + description: |- + The ID which uniquely identifies a trial + + MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/TrialSingleResponse" @@ -1216,6 +1253,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Trials @@ -1223,6 +1262,15 @@ paths: description: Update the details for an existing Trial parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: trialDbId + in: path + description: |- + The ID which uniquely identifies a trial + + MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + required: true + schema: + type: string requestBody: content: application/json: @@ -1237,6 +1285,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/lists: post: tags: @@ -1249,6 +1299,13 @@ paths: \ `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.\ \
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ListSearchRequest" responses: "200": $ref: "#/components/responses/ListListResponse" @@ -1272,6 +1329,13 @@ paths: \ `GET /search/location/{searchResultsDbId}` to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/LocationSearchRequest" responses: "200": $ref: "#/components/responses/LocationListResponse" @@ -1295,6 +1359,13 @@ paths: \ `GET /search/person/{searchResultsDbId}` to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PersonSearchRequest" responses: "200": $ref: "#/components/responses/PersonListResponse" @@ -1318,6 +1389,13 @@ paths: \ `GET /search/program/{searchResultsDbId}` to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ProgramSearchRequest" responses: "200": $ref: "#/components/responses/ProgramListResponse" @@ -1341,6 +1419,13 @@ paths: \ `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.\ \
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/StudySearchRequest" responses: "200": $ref: "#/components/responses/StudyListResponse" @@ -1364,6 +1449,13 @@ paths: \ `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.\ \
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/TrialSearchRequest" responses: "200": $ref: "#/components/responses/TrialListResponse" @@ -1394,6 +1486,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/ListListResponse" @@ -1422,6 +1524,16 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/LocationListResponse" @@ -1450,6 +1562,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/PersonListResponse" @@ -1478,6 +1600,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/ProgramListResponse" @@ -1506,6 +1638,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/StudyListResponse" @@ -1534,6 +1676,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/TrialListResponse" @@ -1641,123 +1793,633 @@ components: items: $ref: "#/components/schemas/Service" AdditionalInfo: - type: object - properties: - additionalProperties: - type: string + type: string + additionalProperties: + description: A free space containing any additional information related to + a particular object. description: "A free space containing any additional information related to\ \ a particular object. A data source may provide any JSON object, unrestricted\ \ by the BrAPI specification." + nullable: true + AlleleMatrixPagination: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension of + the matrix + format: int32 + example: 500 + AlleleMatrixRequest: + type: object + properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + dataMatrixAbbreviations: + type: array + description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ + \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ + \ in the response." + items: + type: string + dataMatrixNames: + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + germplasmDbIds: + type: array + description: A list of IDs which uniquely identify `Germplasm` within the + given database server + items: + type: string + germplasmNames: + type: array + description: A list of human readable `Germplasm` names + items: + type: string + germplasmPUIs: + type: array + description: A list of permanent unique identifiers associated with `Germplasm` + items: + type: string + pagination: + type: array + description: Pagination for the matrix + items: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension + of the matrix + format: int32 + example: 500 + positionRanges: + type: array + description: "The postion range to search\n
\nUses the format \":-\"\ + \ where is the chromosome name, is \nthe starting position\ + \ of the range, and is the ending position of the range" + items: + type: string + preview: + type: boolean + description: "Default Value = false\n
\nIf 'preview' is set to true,\ + \ then the server should only return the lists of 'callSetDbIds', \n'variantDbIds',\ + \ and 'variantSetDbIds'. The server should not return any matrix data.\ + \ This\nis intended to be a preview and give the client a sense of how\ + \ large the matrix returned will be\n
\nIf 'preview' is set to false\ + \ or not set (default), then the server should return all the matrix\n\ + data as requested." + example: true + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + items: + type: string + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + example: "." + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string Attribute: required: - attributeName - - method - - scale - - trait + - methodDbId + - methodName + - scaleDbId + - scaleName + - traitName type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" attributeCategory: type: string + description: General category for the attribute. very similar to Trait class. + example: Morphological attributeDbId: type: string + description: The ID which uniquely identifies this attribute within the + given database server attributeDescription: type: string + description: A human readable description of this attribute + example: Height of the plant measured in meters by a tape attributeName: type: string + description: A human readable name for this attribute + example: Plant Height 1 attributePUI: type: string + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + example: http://my-traits.com/trait/CO_123:0008012 commonCropName: type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true contextOfUse: type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true items: type: string defaultValue: type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" growthStage: type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true institution: type: string + description: Name of institution submitting the variable + nullable: true language: type: string - method: - $ref: "#/components/schemas/Method" + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string ontologyReference: $ref: "#/components/schemas/OntologyReference" - scale: - $ref: "#/components/schemas/Scale" + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string scientist: type: string + description: Name of scientist submitting the variable. + nullable: true status: type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true submissionTimestamp: type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true synonyms: type: array + description: Other variable names + nullable: true items: type: string - trait: - $ref: "#/components/schemas/Trait" - Contact: - required: - - contactDbId - type: object - properties: - contactDbId: + traitDbId: type: string - email: - type: string - instituteName: - type: string - name: - type: string - orcid: + traitName: type: string - type: + traitPUI: type: string - description: A persons contact information - ContentTypes: - type: string - enum: - - application/json - - text/csv - - text/tsv - - application/flapjack - Context: - title: context - type: array - description: "The JSON-LD Context is used to provide JSON-LD definitions to\ - \ each field in a JSON object. By providing an array of context file urls,\ - \ a BrAPI response object becomes JSON-LD compatible. \n\nFor more information,\ - \ see https://w3c.github.io/json-ld-syntax/#the-context" - example: + CallRequest: + type: object + properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + example: "." + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variant` within the + given database server + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string + CallSetRequest: + type: object + properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + callSetNames: + type: array + description: A list of human readable names associated with `CallSets` + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + items: + type: string + sampleNames: + type: array + description: A list of human readable names associated with `Samples` + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string + CommonCropNamesParameters: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + Contact: + required: + - contactDbId + type: object + properties: + contactDbId: + type: string + description: |- + The ID which uniquely identifies this contact + + MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. + email: + type: string + description: |- + The contacts email address + + MIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person. + nullable: true + instituteName: + type: string + description: |- + The name of the institution which this contact is part of + + MIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to + nullable: true + name: + type: string + description: |- + The full name of this contact person + + MIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications) + nullable: true + orcid: + type: string + description: |- + The Open Researcher and Contributor ID for this contact person (orcid.org) + + MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. + nullable: true + type: + type: string + description: |- + The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.) + + MIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation + nullable: true + description: A persons contact information + ContentTypes: + type: string + enum: + - application/json + - text/csv + - text/tsv + - application/flapjack + Context: + title: context + type: array + description: "The JSON-LD Context is used to provide JSON-LD definitions to\ + \ each field in a JSON object. By providing an array of context file urls,\ + \ a BrAPI response object becomes JSON-LD compatible. \n\nFor more information,\ + \ see https://w3c.github.io/json-ld-syntax/#the-context" + example: - https://brapi.org/jsonld/context/metadata.jsonld items: type: string format: uri + CrossRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + CrossStatus: + type: string + enum: + - TODO + - DONE + - SKIPPED + CrossingProjectRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + includePotentialParents: + type: boolean + description: "If the parameter 'includePotentialParents' is false, the array\ + \ 'potentialParents' should be empty, null, or excluded from the response\ + \ object." + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string DataLink: type: object properties: dataFormat: type: string + description: |- + The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy) + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + nullable: true description: type: string + description: |- + The general description of this data link + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + nullable: true fileFormat: type: string + description: |- + The MIME type of the file (ie text/csv, application/excel, application/zip). + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + nullable: true name: type: string + description: |- + The name of the external data link + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + nullable: true provenance: type: string + description: "The description of the origin or ownership of this linked\ + \ data. Could be a formal reference to software, method, or workflow." + nullable: true scientificType: type: string + description: "The general type of data. For example- Genotyping, Phenotyping\ + \ raw data, Phenotyping reduced data, Environmental, etc" + nullable: true url: type: string + description: |- + URL describing the location of this data file to view or download + + MIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission. + format: uri + nullable: true version: type: string + description: "The version number for this data \n\nMIAPPE V1.1 (DM-39) Data\ + \ file version - The version of the dataset (the actual data)." + nullable: true description: "A link to extra data files associated with this study. Extra data\ \ could include notes, images, and reference data." DatasetAuthorships: @@ -1765,12 +2427,25 @@ components: properties: datasetPUI: type: string + description: The DOI or other permanent unique identifier for this published + dataset + nullable: true license: type: string + description: MIAPPE V1.1 (DM-7) License - License for the reuse of the data + associated with this investigation. The Creative Commons licenses cover + most use cases and are recommended. + nullable: true publicReleaseDate: type: string + description: MIAPPE V1.1 (DM-6) Public release date - Date of first public + release of the dataset presently being described. + nullable: true submissionDate: type: string + description: MIAPPE V1.1 (DM-5) Submission date - Date of submission of + the dataset presently being described to a host repository. + nullable: true trialDbId: type: string trialName: @@ -1787,12 +2462,21 @@ components: properties: description: type: string + description: Human-readable value of the environment parameter (defined + above) constant within the experiment environmentParametersDbId: type: string + description: Human-readable value of the environment parameter (defined + above) constant within the experiment parameterName: type: string + description: "Name of the environment parameter constant within the experiment\n\ + \nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment\ + \ parameter constant within the experiment. " parameterPUI: type: string + description: URI pointing to an ontology class for the parameter + nullable: true studyDbId: type: string studyName: @@ -1801,25 +2485,82 @@ components: type: string unit: type: string + description: Unit of the value for this parameter + nullable: true unitPUI: type: string + description: URI pointing to an ontology class for the unit + nullable: true value: type: string + description: |- + Numerical or categorical value + + MIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment. + nullable: true valuePUI: type: string + description: URI pointing to an ontology class for the parameter value + nullable: true description: "Environmental parameters that were kept constant throughout the\ \ study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57)\ \ Environment - Environmental parameters that were kept constant throughout\ \ the study and did not change between observation units or assays. Environment\ \ characteristics that vary over time, i.e. environmental variables, should\ \ be recorded as Observed Variables (see below)." + EventRequest: + type: object + properties: + dateRangeEnd: + type: string + description: Filter based on an Event start date. + format: date-time + dateRangeStart: + type: string + description: Filter based on an Event start date. + format: date-time + eventDbIds: + type: array + description: Filter based on an Event DbId. + items: + type: string + eventTypes: + type: array + description: Filter based on an Event Type + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string ExperimentalDesign: type: object properties: PUI: type: string + description: "MIAPPE V1.1 (DM-23) Type of experimental design - Type of\ + \ experimental design of the study, in the form of an accession number\ + \ from the Crop Ontology." + nullable: true description: type: string + description: "MIAPPE V1.1 (DM-22) Description of the experimental design\ + \ - Short description of the experimental design, possibly including statistical\ + \ design. In specific cases, e.g. legacy datasets or data computed from\ + \ several studies, the experimental design can be \"unknown\"/\"NA\",\ + \ \"aggregated/reduced data\", or simply 'none'." + nullable: true studyDbId: type: string studyName: @@ -1833,8 +2574,85 @@ components: properties: referenceId: type: string + description: The external reference ID. Could be a simple string or a URI. + nullable: true referenceSource: type: string + description: An identifier for the source system or database of this reference + nullable: true + GenomeMapRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + mapDbIds: + type: array + description: The ID which uniquely identifies a `GenomeMap` + items: + type: string + mapPUIs: + type: array + description: The DOI or other permanent identifier for a `GenomeMap` + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scientificName: + type: array + description: "Full scientific binomial format name. This includes Genus,\ + \ Species, and Sub-species" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + types: + type: array + description: "The type of map, usually \"Genetic\" or \"Physical\"" + items: + type: string GeoJSON: type: object properties: @@ -1842,6 +2660,8 @@ components: $ref: "#/components/schemas/GeoJSONGeometry" type: type: string + description: The literal string "Feature" + example: Feature description: |- One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. @@ -1858,10 +2678,12 @@ components: properties: coordinates: type: array + description: A single position items: type: number type: type: string + description: The literal string "Point" description: |- Copied from RFC 7946 Section 3.1.1 @@ -1874,6 +2696,7 @@ components: properties: coordinates: type: array + description: An array of linear rings items: type: array items: @@ -1882,11 +2705,54 @@ components: type: number type: type: string + description: The literal string "Polygon" description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ \ precisely in that order and using decimal numbers. Altitude or elevation\ \ MAY be included as an optional third element." + GeoJSONPoint: + required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + description: A single position + items: + type: number + type: + type: string + description: The literal string "Point" + description: |- + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + GeoJSONPolygon: + required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + description: An array of linear rings + items: + type: array + items: + type: array + items: + type: number + type: + type: string + description: The literal string "Polygon" + description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ + \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ + \ The first two elements are longitude and latitude, or\neasting and northing,\ + \ precisely in that order and using decimal numbers. Altitude or elevation\ + \ MAY be included as an optional third element." GeoJSONSearchArea: type: object properties: @@ -1904,28 +2770,566 @@ components: $ref: "#/components/schemas/ObservationUnitPosition" type: type: string - GrowthFacility: - type: object - properties: - PUI: - type: string - description: - type: string - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - description: Short description of the facility in which the study was carried - out. - LastUpdate: - required: - - lastUpdateDbId + description: The literal string "Feature" + example: Feature + GermplasmAttributeRequest: type: object properties: - lastUpdateDbId: - type: string + attributeCategories: + type: array + description: General category for the attribute. very similar to Trait class. + items: + type: string + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + items: + type: string + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + items: + type: string + attributePUIs: + type: array + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + GermplasmAttributeValueRequest: + type: object + properties: + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + items: + type: string + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + items: + type: string + attributeValueDbIds: + type: array + description: List of Germplasm Attribute Value IDs to search for + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: List of scales to filter search results + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: List of trait unique ID to filter search results + items: + type: string + GermplasmParameters: + type: object + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + GermplasmRequest: + type: object + properties: + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + items: + type: string + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + items: + type: string + parentDbIds: + type: array + description: Search for Germplasm with these parents + items: + type: string + progenyDbIds: + type: array + description: Search for Germplasm with these children + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + GrowthFacility: + type: object + properties: + PUI: + type: string + description: "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth\ + \ facility in which the study was carried out, in the form of an accession\ + \ number from the Crop Ontology." + nullable: true + description: + type: string + description: MIAPPE V1.1 (DM-26) Description of growth facility - Short + description of the facility in which the study was carried out. + nullable: true + description: Short description of the facility in which the study was carried + out. + ImageRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + descriptiveOntologyTerms: + type: array + description: "A list of terms to formally describe the image to search for.\ + \ Each item could be a simple Tag, an Ontology reference Id, or a full\ + \ ontology URL." + items: + type: string + imageDbIds: + type: array + description: A list of image Ids to search for + items: + type: string + imageFileNames: + type: array + description: Image file names to search for. + items: + type: string + imageFileSizeMax: + type: integer + description: A maximum image file size to search for. + format: int32 + example: 20000000 + imageFileSizeMin: + type: integer + description: A minimum image file size to search for. + format: int32 + example: 1000 + imageHeightMax: + type: integer + description: A maximum image height to search for. + format: int32 + example: 1080 + imageHeightMin: + type: integer + description: A minimum image height to search for. + format: int32 + example: 720 + imageLocation: + $ref: "#/components/schemas/GeoJSONSearchArea" + imageNames: + type: array + description: Human readable names to search for. + items: + type: string + imageTimeStampRangeEnd: + type: string + description: The latest timestamp to search for. + format: date-time + imageTimeStampRangeStart: + type: string + description: The earliest timestamp to search for. + format: date-time + imageWidthMax: + type: integer + description: A maximum image width to search for. + format: int32 + example: 1920 + imageWidthMin: + type: integer + description: A minimum image width to search for. + format: int32 + example: 1280 + mimeTypes: + type: array + description: A set of image file types to search for. + items: + type: string + observationDbIds: + type: array + description: A list of observation Ids this image is associated with to + search for + items: + type: string + observationUnitDbIds: + type: array + description: A set of observation unit identifiers to search for. + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + LastUpdate: + required: + - lastUpdateDbId + type: object + properties: + lastUpdateDbId: + type: string + description: The ID which uniquely identifies a LastUpdate within the given + database server studyDbId: type: string studyName: @@ -1934,33 +3338,80 @@ components: type: string timestamp: type: string + description: The timestamp of the update. + format: date-time + nullable: true version: type: string + description: The version of the update. + nullable: true description: The date and time when this study was last modified List: + allOf: + - $ref: "#/components/schemas/ListNewRequest" + - required: + - listDbId + type: object + properties: + listDbId: + type: string + description: The unique identifier for a List + description: "A List represents a collection of other BrAPI data objects.\ + \ Typically these are custom lists generated by a user to keep track of\ + \ interesting data. For example, a user might build a List of Germplasm\ + \ that they have manually marked for further study." + ListNewRequest: required: - - listDbId - listName - listType type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" + data: + type: array + description: The array of DbIds of the BrAPI objects contained in a List + nullable: true + items: + type: string dateCreated: type: string + description: Timestamp when the entity was first created + format: date-time + nullable: true dateModified: type: string + description: Timestamp when the entity was last updated + format: date-time + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" listDescription: type: string + description: Description of a List + nullable: true listName: type: string + description: Human readable name of a List listOwnerName: type: string + description: Human readable name of a List Owner. (usually a user or person) + nullable: true listSize: type: integer + description: The number of elements in a List format: int32 + nullable: true listSource: type: string + description: The description of where a List originated from + nullable: true listType: $ref: "#/components/schemas/ListType" personDbId: @@ -1969,54 +3420,172 @@ components: \ these are custom lists generated by a user to keep track of interesting\ \ data. For example, a user might build a List of Germplasm that they have\ \ manually marked for further study." - ListNewRequest: - required: - - listDbId - - listDbId - - listName - - listType + ListRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - dateCreated: - type: string - dateModified: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dateCreatedRangeEnd: type: string - listDbId: + description: Define the end for an interval of time and only include Lists + that are created within this interval. + format: date-time + dateCreatedRangeStart: type: string - listDescription: + description: Define the beginning for an interval of time and only include + Lists that are created within this interval. + format: date-time + dateModifiedRangeEnd: type: string - listName: + description: Define the end for an interval of time and only include Lists + that are modified within this interval. + format: date-time + dateModifiedRangeStart: type: string - listOwnerName: + description: Define the beginning for an interval of time and only include + Lists that are modified within this interval. + format: date-time + listDbIds: + type: array + description: An array of primary database identifiers to identify a set + of Lists + items: + type: string + listNames: + type: array + description: An array of human readable names to identify a set of Lists + items: + type: string + listOwnerNames: + type: array + description: An array of names for the people or entities who are responsible + for a set of Lists + items: + type: string + listOwnerPersonDbIds: + type: array + description: An array of primary database identifiers to identify people + or entities who are responsible for a set of Lists + items: + type: string + listSources: + type: array + description: "An array of terms identifying lists from different sources\ + \ (ie 'USER', 'SYSTEM', etc)" + items: + type: string + listType: + $ref: "#/components/schemas/ListType" + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + ListSearchRequest: + type: object + properties: + dateCreatedRangeStart: type: string - listSize: - type: integer - format: int32 - listSource: + description: Define the beginning for an interval of time and only include + Lists that are created within this interval. + format: date-time + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + dateModifiedRangeEnd: type: string + description: Define the end for an interval of time and only include Lists + that are modified within this interval. + format: date-time + listSources: + type: array + description: "An array of terms identifying lists from different sources\ + \ (ie 'USER', 'SYSTEM', etc)" + items: + type: string listType: $ref: "#/components/schemas/ListType" - personDbId: - type: string - description: "A List represents a collection of other BrAPI data objects. Typically\ - \ these are custom lists generated by a user to keep track of interesting\ - \ data. For example, a user might build a List of Germplasm that they have\ - \ manually marked for further study." - ListSearchRequest: - type: object - properties: dateCreatedRangeEnd: type: string - dateCreatedRangeStart: - type: string - dateModifiedRangeEnd: - type: string + description: Define the end for an interval of time and only include Lists + that are created within this interval. + format: date-time + listDbIds: + type: array + description: An array of primary database identifiers to identify a set + of Lists + items: + type: string + listNames: + type: array + description: An array of human readable names to identify a set of Lists + items: + type: string + listOwnerPersonDbIds: + type: array + description: An array of primary database identifiers to identify people + or entities who are responsible for a set of Lists + items: + type: string dateModifiedRangeStart: type: string - listType: - $ref: "#/components/schemas/ListType" + description: Define the beginning for an interval of time and only include + Lists that are modified within this interval. + format: date-time + listOwnerNames: + type: array + description: An array of names for the people or entities who are responsible + for a set of Lists + items: + type: string description: "A List represents a collection of other BrAPI data objects. Typically\ \ these are custom lists generated by a user to keep track of interesting\ \ data. For example, a user might build a List of Germplasm that they have\ @@ -2036,124 +3605,634 @@ components: - observationVariables - samples Location: + allOf: + - $ref: "#/components/schemas/LocationNewRequest" + - required: + - locationDbId + type: object + properties: + locationDbId: + type: string + description: The unique identifier for a Location + description: "A geographic Location on earth. This is usually used to describe\ + \ the general area where an experiment took place. For example, a natural\ + \ site, an experimental field, a greenhouse, a phenotyping facility, etc." + LocationNewRequest: required: - - locationDbId - locationName type: object properties: abbreviation: type: string + description: A shortened version of the human readable name for a Location + nullable: true additionalInfo: $ref: "#/components/schemas/AdditionalInfo" childLocationDbIds: type: array + description: "The child locations that belong to this Location. \nFor example,\ + \ an Institution might have multiple Field Stations inside it and each\ + \ Field Station might have multiple Fields." + nullable: true items: type: string coordinateDescription: type: string + description: "Describes the precision and landmarks of the coordinate values\ + \ used for a Location. (ex. the site, the nearest town, a 10 kilometers\ + \ radius circle, +/- 20 meters, etc)" + nullable: true coordinateUncertainty: type: string + description: Uncertainty associated with the coordinates in meters. Leave + the value empty if the uncertainty is unknown. + nullable: true coordinates: $ref: "#/components/schemas/GeoJSON" countryCode: type: string + description: |- + [ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec +
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.' + nullable: true countryName: type: string + description: |- + The full name of the country where a Location is located +
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code. + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true environmentType: type: string + description: "Describes the general type of environment of a Location. (ex.\ + \ forest, field, nursery, etc)" + nullable: true exposure: type: string + description: Describes the level of protection/exposure for things like + sun light and wind at a particular Location + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" instituteAddress: type: string + description: |- + The street address of the institute at a particular Location +
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. + nullable: true instituteName: type: string + description: |- + The full name of the institute at a particular Location +
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. + nullable: true locationDbId: type: string locationName: type: string locationType: type: string + description: "A short description of a type of Location (ex. Field Station,\ + \ Breeding Location, Storage Location, etc)" + nullable: true siteStatus: type: string + description: "Description of the accessibility of the location (ex. Public,\ + \ Private)" + nullable: true slope: type: string + description: Describes the approximate slope (height/distance) of a Location. + nullable: true topography: type: string + description: "Describes the topography of the land at a Location. (ex. Plateau,\ + \ Cirque, Hill, Valley, etc)" + nullable: true description: "A geographic Location on earth. This is usually used to describe\ \ the general area where an experiment took place. For example, a natural\ \ site, an experimental field, a greenhouse, a phenotyping facility, etc." - LocationNewRequest: - required: - - locationDbId - - locationDbId - - locationName + LocationParameters: type: object properties: - abbreviation: + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + LocationRequest: + type: object + properties: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Locations + items: + type: string + altitudeMax: + type: number + description: The maximum altitude to search for + example: 200 + altitudeMin: + type: number + description: The minimum altitude to search for + example: 20 + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + coordinates: + $ref: "#/components/schemas/GeoJSONSearchArea" + countryCodes: + type: array + description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ + \ spec" + items: + type: string + countryNames: + type: array + description: The full name of the country to search for + items: + type: string + instituteAddresses: + type: array + description: The street address of the institute to search for + items: + type: string + instituteNames: + type: array + description: The name of the institute to search for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + locationTypes: + type: array + description: "The type of location this represents (ex. Breeding Location,\ + \ Storage Location, etc)" + items: + type: string + parentLocationDbIds: + type: array + description: "The unique identifier for a Location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + items: + type: string + parentLocationNames: + type: array + description: "A human readable name for a location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + LocationSearchRequest: + type: object + properties: + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + countryNames: + type: array + description: The full name of the country to search for + items: + type: string + coordinates: + $ref: "#/components/schemas/GeoJSONSearchArea" + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + altitudeMax: + type: number + description: The maximum altitude to search for + example: 200 + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + instituteNames: + type: array + description: The name of the institute to search for + items: + type: string + countryCodes: + type: array + description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ + \ spec" + items: + type: string + parentLocationNames: + type: array + description: "A human readable name for a location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + items: + type: string + locationTypes: + type: array + description: "The type of location this represents (ex. Breeding Location,\ + \ Storage Location, etc)" + items: + type: string + parentLocationDbIds: + type: array + description: "The unique identifier for a Location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + items: + type: string + instituteAddresses: + type: array + description: The street address of the institute to search for + items: + type: string + altitudeMin: + type: number + description: The minimum altitude to search for + example: 20 + abbreviations: + type: array + description: A list of shortened human readable names for a set of Locations + items: + type: string + description: "A geographic Location on earth. This is usually used to describe\ + \ the general area where an experiment took place. For example, a natural\ + \ site, an experimental field, a greenhouse, a phenotyping facility, etc." + MarkerPositionRequest: + type: object + properties: + linkageGroupNames: + type: array + description: A list of Uniquely Identifiable linkage group names + items: + type: string + mapDbIds: + type: array + description: A list of IDs which uniquely identify `GenomeMaps` within the + given database server + items: + type: string + maxPosition: + type: integer + description: The maximum position of markers in a given map + format: int32 + example: 4000 + minPosition: + type: integer + description: The minimum position of markers in a given map + format: int32 + example: 250 + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server + items: + type: string + MethodRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + methodDbIds: + type: array + description: The unique identifier for a method. + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + ObservationRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationDbIds: + type: array + description: The unique id of an Observation + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationTimeStampRangeEnd: type: string - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - childLocationDbIds: + description: Timestamp range end + format: date-time + observationTimeStampRangeStart: + type: string + description: Timestamp range start + format: date-time + observationUnitDbIds: + type: array + description: The unique id of an Observation Unit + items: + type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for items: type: string - coordinateDescription: - type: string - coordinateUncertainty: - type: string - coordinates: - $ref: "#/components/schemas/GeoJSON" - countryCode: - type: string - countryName: - type: string - documentationURL: - type: string - environmentType: - type: string - exposure: - type: string - instituteAddress: - type: string - instituteName: - type: string - locationDbId: - type: string - locationName: - type: string - locationType: - type: string - siteStatus: - type: string - slope: - type: string - topography: - type: string - description: "A geographic Location on earth. This is usually used to describe\ - \ the general area where an experiment took place. For example, a natural\ - \ site, an experimental field, a greenhouse, a phenotyping facility, etc." - LocationSearchRequest: - type: object - properties: - altitudeMax: - type: number - altitudeMin: - type: number - coordinates: - $ref: "#/components/schemas/GeoJSONSearchArea" - description: "A geographic Location on earth. This is usually used to describe\ - \ the general area where an experiment took place. For example, a natural\ - \ site, an experimental field, a greenhouse, a phenotyping facility, etc." ObservationUnitHierarchyLevel: type: object properties: levelName: type: string + description: "A name for this level \n\n**Standard Level Names: study, field,\ + \ entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\ + \nFor more information on Observation Levels, please review the Observation Levels documentation. " + nullable: true levelOrder: type: integer + description: "`levelOrder` defines where that level exists in the hierarchy\ + \ of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy\ + \ (ie field -> 1) and higher numbers are at the bottom of the hierarchy\ + \ (ie plant -> 9). \n\nFor more information on Observation Levels, please\ + \ review the Observation Levels documentation. " format: int32 + nullable: true description: "The exact level and level code of an observation unit. \n\nFor\ \ more information on Observation Levels, please review the Observation\ @@ -2166,103 +4245,1020 @@ components: \ associated observed variable (see observed variables). \nAlternatively,\ \ it is possible to use samples for more detailed tracing of sub-plant units,\ \ attaching the observations to them instead.\" " + ObservationUnitRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + includeObservations: + type: boolean + description: "Use this parameter to include a list of observations embedded\ + \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ + \ your own risk. It may return large, unpaginated lists of observation\ + \ data. Only set this value to True if you are sure you need to." + example: false + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationUnitDbIds: + type: array + description: The unique id of an observation unit + items: + type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitNames: + type: array + description: The human readable identifier for an Observation Unit + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ObservationVariableParameters: + type: object + properties: + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + ObservationVariableRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + OntologyParameters: + type: object + properties: + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + OntologyRequest: + type: object + properties: + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + ontologyNames: + type: array + description: The human readable identifier for an ontology definition. + items: + type: string OntologyTerm: type: object properties: term: type: string + description: Ontology term - the label of the ontology term the termId is + pointing to. + nullable: true termURI: type: string + description: Ontology term identifier - the CURIE for an ontology term. + It differs from the standard GA4GH schema's :ref:`id ` in that it is a + CURIE pointing to an information resource outside of the scope of the + schema or its resource implementation. + nullable: true description: A pointer to an ontology used by a genomic reference - Person: - required: - - personDbId + PedigreeNodeRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - description: - type: string - emailAddress: - type: string - firstName: - type: string - lastName: - type: string - mailingAddress: - type: string - middleName: - type: string - phoneNumber: - type: string - userID: - type: string - description: "A generic object used to maintain the metadata needed to describe\ - \ a human. The Person might be a software user, a field technician, or a primary\ - \ contact for a Program." + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + items: + type: string + includeFullTree: + type: boolean + description: "If this parameter is true, recursively include ALL of the\ + \ nodes available in this pedigree tree" + example: true + includeParents: + type: boolean + description: "If this parameter is true, include the array of parents in\ + \ the response" + example: true + includeProgeny: + type: boolean + description: "If this parameter is true, include the array of progeny in\ + \ the response" + example: true + includeSiblings: + type: boolean + description: "If this parameter is true, include the array of siblings in\ + \ the response" + example: true + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + items: + type: string + pedigreeDepth: + type: integer + description: "Recursively include this number of levels up the tree in the\ + \ response (parents, grand-parents, great-grand-parents, etc)" + format: int32 + example: 3 + progenyDepth: + type: integer + description: "Recursively include this number of levels down the tree in\ + \ the response (children, grand-children, great-grand-children, etc)" + format: int32 + example: 3 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + Person: + allOf: + - $ref: "#/components/schemas/PersonNewRequest" + - required: + - personDbId + type: object + properties: + personDbId: + type: string + description: Unique ID for a person + description: "A generic object used to maintain the metadata needed to describe\ + \ a human. The Person might be a software user, a field technician, or a\ + \ primary contact for a Program." PersonNewRequest: - required: - - personDbId - - personDbId type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" description: type: string + description: description of this person + nullable: true emailAddress: type: string + description: email address for this person + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" firstName: type: string + description: Persons first name + nullable: true lastName: type: string + description: Persons last name + nullable: true mailingAddress: type: string + description: physical address of this person + nullable: true middleName: type: string - personDbId: - type: string + description: Persons middle name + nullable: true phoneNumber: type: string + description: phone number of this person + nullable: true userID: type: string + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + nullable: true description: "A generic object used to maintain the metadata needed to describe\ \ a human. The Person might be a software user, a field technician, or a primary\ \ contact for a Program." + PersonRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + emailAddresses: + type: array + description: email address for this person + items: + type: string + firstNames: + type: array + description: Persons first name + items: + type: string + lastNames: + type: array + description: Persons last name + items: + type: string + mailingAddresses: + type: array + description: physical address of this person + items: + type: string + middleNames: + type: array + description: Persons middle name + items: + type: string + personDbIds: + type: array + description: Unique ID for this person + items: + type: string + phoneNumbers: + type: array + description: phone number of this person + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + userIDs: + type: array + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + items: + type: string PersonSearchRequest: type: object - properties: {} + properties: + middleNames: + type: array + description: Persons middle name + items: + type: string + emailAddresses: + type: array + description: email address for this person + items: + type: string + userIDs: + type: array + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + items: + type: string + personDbIds: + type: array + description: Unique ID for this person + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + firstNames: + type: array + description: Persons first name + items: + type: string + lastNames: + type: array + description: Persons last name + items: + type: string + mailingAddresses: + type: array + description: physical address of this person + items: + type: string + phoneNumbers: + type: array + description: phone number of this person + items: + type: string description: "A generic object used to maintain the metadata needed to describe\ \ a human. The Person might be a software user, a field technician, or a primary\ \ contact for a Program." + PlannedCrossRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + plannedCrossDbIds: + type: array + description: Search for Planned Cross with this unique id + items: + type: string + plannedCrossNames: + type: array + description: Search for Planned Cross with this human readable name + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + statuses: + type: array + description: "The status of this planned cross. Is it waiting to be performed\ + \ ('TODO'), has it been completed successfully ('DONE'), or has it not\ + \ been done on purpose ('SKIPPED')." + items: + type: string + enum: + - TODO + - DONE + - SKIPPED + PlateRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit + items: + type: string + plateBarcodes: + type: array + description: A unique identifier physically attached to the plate + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a plate of samples + items: + type: string + plateNames: + type: array + description: The human readable name of a plate of samples + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a sample + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related Samples + items: + type: string + sampleNames: + type: array + description: The human readable name of the sample + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string Program: + allOf: + - $ref: "#/components/schemas/ProgramNewRequest" + - required: + - programDbId + type: object + properties: + programDbId: + type: string + description: The ID which uniquely identifies the program + description: A BrAPI Program represents the high level organization or group + who is responsible for conducting trials and studies. Things like Breeding + Programs and Funded Projects are considered BrAPI Programs. A Program can + contain multiple Trials. A Trial can contain multiple Studies. + ProgramNewRequest: required: - - programDbId - programName type: object properties: abbreviation: type: string + description: A shortened version of the human readable name for a Program + nullable: true additionalInfo: $ref: "#/components/schemas/AdditionalInfo" commonCropName: type: string + description: Common name for the crop which this program is for + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" fundingInformation: type: string + description: Information describing the grant or funding source for this + program + nullable: true objective: type: string + description: The primary objective of the program + nullable: true personDbId: type: string programName: type: string + description: Human readable name of the program programType: type: string description: "The type of program entity this object represents\n
'STANDARD'\ \ represents a standard, permanent breeding program\n
'PROJECT' represents\ \ a short term project, usually with a set time limit based on funding\ \ " + nullable: true enum: - STANDARD - PROJECT @@ -2270,67 +5266,546 @@ components: who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. - ProgramNewRequest: - required: - - programDbId - - programDbId - - programName + ProgramParameters: type: object properties: - abbreviation: - type: string - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - documentationURL: - type: string - fundingInformation: - type: string - objective: - type: string - personDbId: - type: string - programDbId: - type: string - programName: - type: string - programType: - type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + ProgramRequest: + type: object + properties: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Programs + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + leadPersonDbIds: + type: array + description: The person DbIds of the program leader to search for + items: + type: string + leadPersonNames: + type: array + description: The names of the program leader to search for + items: + type: string + objectives: + type: array + description: A program objective to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + programTypes: + type: array description: "The type of program entity this object represents\n
'STANDARD'\ \ represents a standard, permanent breeding program\n
'PROJECT' represents\ - \ a short term project, usually with a set time limit based on funding\ - \ " - enum: - - STANDARD - - PROJECT - description: A BrAPI Program represents the high level organization or group - who is responsible for conducting trials and studies. Things like Breeding - Programs and Funded Projects are considered BrAPI Programs. A Program can - contain multiple Trials. A Trial can contain multiple Studies. + \ a short term project, usually with a set time limit based on funding " + items: + type: string + description: |- + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding. + enum: + - STANDARD + - PROJECT ProgramSearchRequest: type: object - properties: {} + properties: + leadPersonNames: + type: array + description: The names of the program leader to search for + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + objectives: + type: array + description: A program objective to search for + items: + type: string + leadPersonDbIds: + type: array + description: The person DbIds of the program leader to search for + items: + type: string + programTypes: + type: array + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding " + items: + type: string + description: |- + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding. + enum: + - STANDARD + - PROJECT + abbreviations: + type: array + description: A list of shortened human readable names for a set of Programs + items: + type: string description: A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. + ProgramType: + type: string + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding " + enum: + - STANDARD + - PROJECT Publication: type: object properties: - publicationPUI: - type: string - publicationReference: - type: string - trialDbId: - type: string - trialName: - type: string - trialPUI: - type: string - description: MIAPPE V1.1 (DM-9) Associated publication - An identifier for a - literature publication where the investigation is described. Use of DOIs is - recommended. + publicationPUI: + type: string + description: The permanent unique identifier of the publication. + nullable: true + publicationReference: + type: string + description: The publication reference. + nullable: true + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: MIAPPE V1.1 (DM-9) Associated publication - An identifier for a + literature publication where the investigation is described. Use of DOIs is + recommended. + ReferenceBasesRequest: + type: object + properties: + end: + type: integer + description: "The end position (0-based, exclusive) of this query. Defaults\ + \ to the length of this `Reference`." + format: int32 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + start: + type: integer + description: |- + The start position (0-based) of this query. Defaults to 0. + Genomic positions are non-negative integers less than reference length. + Requests spanning the join of circular genomes are represented as + two requests one on each side of the join (position 0). + format: int32 + ReferenceRequest: + type: object + properties: + accessions: + type: array + description: "If specified, return the references for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + isDerived: + type: boolean + description: "A sequence X is said to be derived from source sequence Y,\ + \ if X and Y are of the same length and the per-base sequence divergence\ + \ at A/C/G/T bases is sufficiently small. Two sequences derived from the\ + \ same official sequence share the same coordinates and annotations, and\ + \ can be replaced with the official sequence for certain use cases." + format: boolean + maxLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 90000 + md5checksums: + type: array + description: "If specified, return the references for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + minLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 4000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: A list of IDs which uniquely identify `References` within the + given database server + items: + type: string + referenceSetDbIds: + type: array + description: A list of IDs which uniquely identify `ReferenceSets` within + the given database server + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ReferenceSetRequest: + type: object + properties: + accessions: + type: array + description: "If set, return the reference sets for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + assemblyPUIs: + type: array + description: "If set, return the reference sets for which the `assemblyId`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + md5checksums: + type: array + description: "If set, return the reference sets for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceSetDbIds: + type: array + description: The `ReferenceSets` to search. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + SampleRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an `ObservationUnit` + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a `Plate` of `Samples` + items: + type: string + plateNames: + type: array + description: The human readable name of a `Plate` of `Samples` + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a `Sample` + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related `Samples` + items: + type: string + sampleNames: + type: array + description: The human readable name of the `Sample` + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ScaleRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a scale. + items: + type: string Season: required: - seasonDbId @@ -2338,157 +5813,568 @@ components: properties: seasonDbId: type: string + description: "The ID which uniquely identifies a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'" seasonName: type: string + description: "Name of the season. ex. 'Spring', 'Q2', 'Season A', etc." + nullable: true year: type: integer + description: The 4 digit year of the season. format: int32 + nullable: true description: "A Season defines a period in time. A Season is made of two parts;\ \ (1) the primary year and (2) a term which defines a segment of the year.\ \ This term could be a traditional season, like \"Spring\" or \"Summer\",\ \ or this term could be a month, like \"May\" or \"June\", or this could be\ \ an arbitrary season name which is meaningful to the breeding Program like\ \ \"PlantingTime_3\" or \"Season E\"." + SeasonRequest: + type: object + properties: + seasonDbIds: + type: array + description: "The unique identifier for a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'." + items: + type: string + seasonNames: + type: array + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + items: + type: string + seasons: + type: array + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + items: + type: string + years: + type: array + description: The 4 digit year of a season. Example "2017" + items: + type: string + SeedLotRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seedLotDbIds: + type: array + description: Unique id for a seed lot on this server + items: + type: string + SortBy: + type: string + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + SortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC Study: + allOf: + - $ref: "#/components/schemas/StudyNewRequest" + - required: + - studyDbId + type: object + properties: + studyDbId: + type: string + description: |- + The ID which uniquely identifies a study within the given database server + + MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + description: A Study represents an experiment that has taken place at a single + location. The Study contains metadata about the parameters and design of + the experiment. It can also be used to group results and data sets generated + from the experiment. A Trial can represent a collection of one or more Studies. + StudyNewRequest: required: - - studyDbId - studyName type: object properties: active: type: boolean + description: A flag to indicate if a Study is currently active and ongoing + nullable: true additionalInfo: $ref: "#/components/schemas/AdditionalInfo" commonCropName: type: string - contactDbIds: - type: array - items: - type: string + description: Common name for the crop associated with this study + nullable: true culturalPractices: type: string + description: MIAPPE V1.1 (DM-28) Cultural practices - General description + of the cultural practices of the study. + nullable: true + dataLinks: + type: array + description: "List of links to extra data files associated with this study.\ + \ Extra data could include notes, images, and reference data." + nullable: true + items: + $ref: "#/components/schemas/DataLink" documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true endDate: type: string + description: |- + The date the study ends + + MIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended + format: date-time + nullable: true + environmentParameters: + type: array + description: |- + Environmental parameters that were kept constant throughout the study and did not change between observation units. + + MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). + nullable: true + items: + $ref: "#/components/schemas/EnvironmentParameter" experimentalDesign: $ref: "#/components/schemas/ExperimentalDesign" + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" growthFacility: $ref: "#/components/schemas/GrowthFacility" - lastUpdateDbId: - type: string + lastUpdate: + $ref: "#/components/schemas/LastUpdate" license: type: string + description: The usage license associated with the study data + nullable: true locationDbId: type: string locationName: type: string - observationLevelDbIds: + observationLevels: + type: array + description: "Observation levels indicate the granularity level at which\ + \ the measurements are taken. `levelName` \ndefines the level, `levelOrder`\ + \ defines where that level exists in the hierarchy of levels. \n`levelOrder`s\ + \ lower numbers are at the top of the hierarchy (ie field > 0) and higher\ + \ numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard\ + \ Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot,\ + \ plant, pot, sample** \n\nFor more information on Observation Levels,\ + \ please review the Observation Levels documentation. " + nullable: true + items: + $ref: "#/components/schemas/ObservationUnitHierarchyLevel" + observationUnitsDescription: + type: string + description: MIAPPE V1.1 (DM-25) Observation unit description - General + description of the observation units in the study. + nullable: true + seasons: + type: array + description: List of seasons over which this study was performed. + nullable: true + items: + type: string + startDate: + type: string + description: |- + The date this study started + + MIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started + format: date-time + nullable: true + studyCode: + type: string + description: A short human readable code for a study + nullable: true + studyDescription: + type: string + description: |- + The description of this study + + MIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study + nullable: true + studyName: + type: string + description: |- + The human readable name for a study + + MIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study + studyPUI: + type: string + description: "A permanent unique identifier associated with this study data.\ + \ For example, a URI or DOI" + nullable: true + studyType: + type: string + description: "The type of study being performed. ex. \"Yield Trial\", etc" + nullable: true + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: A Study represents an experiment that has taken place at a single + location. The Study contains metadata about the parameters and design of the + experiment. It can also be used to group results and data sets generated from + the experiment. A Trial can represent a collection of one or more Studies. + StudyParameters: + type: object + properties: + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + StudyRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Study is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: The ID which uniquely identifies a season + items: + type: string + sortBy: + type: string + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + studyCodes: + type: array + description: A short human readable code for a study + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + studyPUIs: + type: array + description: "Permanent unique identifier associated with study data. For\ + \ example, a URI or DOI" + items: + type: string + studyTypes: + type: array + description: "The type of study being performed. ex. \"Yield Trial\", etc" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + StudySearchRequest: + type: object + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: The ID which uniquely identifies a season + items: + type: string + active: + type: boolean + description: A flag to indicate if a Study is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + studyCodes: type: array + description: A short human readable code for a study items: type: string - observationUnitsDescription: - type: string - observationVariableDbIds: + studyPUIs: type: array + description: "Permanent unique identifier associated with study data. For\ + \ example, a URI or DOI" items: type: string - startDate: - type: string - studyCode: - type: string - studyDescription: - type: string - studyName: - type: string - studyPUI: - type: string - studyType: - type: string - trialDbId: - type: string - trialName: - type: string - trialPUI: - type: string - description: A Study represents an experiment that has taken place at a single - location. The Study contains metadata about the parameters and design of the - experiment. It can also be used to group results and data sets generated from - the experiment. A Trial can represent a collection of one or more Studies. - StudyNewRequest: - required: - - studyDbId - - studyDbId - - studyName - type: object - properties: - active: - type: boolean - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - contactDbIds: + observationVariablePUIs: type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" items: type: string - culturalPractices: - type: string - documentationURL: - type: string - endDate: - type: string - experimentalDesign: - $ref: "#/components/schemas/ExperimentalDesign" - growthFacility: - $ref: "#/components/schemas/GrowthFacility" - lastUpdateDbId: - type: string - license: - type: string - locationDbId: - type: string - locationName: - type: string - observationLevelDbIds: + trialDbIds: type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results items: type: string - observationUnitsDescription: - type: string observationVariableDbIds: type: array + description: The DbIds of Variables to search for items: type: string - startDate: - type: string - studyCode: - type: string - studyDbId: - type: string - studyDescription: + sortOrder: type: string - studyName: - type: string - studyPUI: - type: string - studyType: - type: string - trialDbId: - type: string - trialName: - type: string - trialPUI: + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + sortBy: type: string - description: A Study represents an experiment that has taken place at a single - location. The Study contains metadata about the parameters and design of the - experiment. It can also be used to group results and data sets generated from - the experiment. A Trial can represent a collection of one or more Studies. - StudySearchRequest: - type: object - properties: - active: - type: boolean + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + studyTypes: + type: array + description: "The type of study being performed. ex. \"Yield Trial\", etc" + items: + type: string description: A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from @@ -2512,147 +6398,874 @@ components: - Numerical - Ordinal - Text + TraitRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a trait. + items: + type: string Trial: + allOf: + - $ref: "#/components/schemas/TrialNewRequest" + - required: + - trialDbId + type: object + properties: + trialDbId: + type: string + description: |- + The ID which uniquely identifies a trial + + MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + description: "A Trial represents a collection of Study objects, and the metadata\ + \ associated with that collection. A Trial could represent a multi-location\ + \ experiment, and could contain information related to publications and\ + \ data licensing." + TrialNewRequest: required: - - trialDbId - trialName type: object properties: active: type: boolean + description: A flag to indicate if a Trial is currently active and ongoing + nullable: true additionalInfo: $ref: "#/components/schemas/AdditionalInfo" commonCropName: type: string + description: Common name for the crop associated with this trial + nullable: true contacts: type: array + description: List of contact entities associated with this trial + nullable: true items: $ref: "#/components/schemas/Contact" + datasetAuthorships: + type: array + description: License and citation information for the data in this trial + nullable: true + items: + $ref: "#/components/schemas/DatasetAuthorships" documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true endDate: type: string + description: The date this trial ends + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" programDbId: type: string programName: type: string + publications: + type: array + description: MIAPPE V1.1 (DM-9) Associated publication - An identifier for + a literature publication where the investigation is described. Use of + DOIs is recommended. + nullable: true + items: + $ref: "#/components/schemas/Publication" startDate: type: string + description: The date this trial started + nullable: true studyDbIds: type: array + description: "" + nullable: true items: type: string trialDescription: type: string + description: |- + The human readable description of a trial + + MIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail. + nullable: true trialName: type: string + description: |- + The human readable name of a trial + + MIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation. trialPUI: type: string + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + nullable: true description: "A Trial represents a collection of Study objects, and the metadata\ \ associated with that collection. A Trial could represent a multi-location\ \ experiment, and could contain information related to publications and data\ \ licensing." - TrialNewRequest: - required: - - trialDbId - - trialDbId - - trialName + TrialParameters: + type: object + properties: + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + TrialRequest: type: object properties: active: type: boolean - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: + description: A flag to indicate if a Trial is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + contactDbIds: + type: array + description: List of contact entities associated with this trial + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + searchDateRangeEnd: type: string - contacts: + description: "The end of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + searchDateRangeStart: + type: string + description: "The start of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + sortBy: + type: string + description: Name of the field to sort by. + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + trialPUIs: + type: array + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + items: + type: string + TrialSearchRequest: + type: object + properties: + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + searchDateRangeEnd: + type: string + description: "The end of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + active: + type: boolean + description: A flag to indicate if a Trial is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + trialPUIs: + type: array + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + observationVariableDbIds: type: array + description: The DbIds of Variables to search for items: - $ref: "#/components/schemas/Contact" - documentationURL: - type: string - endDate: - type: string - programDbId: - type: string - programName: + type: string + sortOrder: type: string - startDate: + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + sortBy: type: string - studyDbIds: + description: Name of the field to sort by. + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + contactDbIds: type: array + description: List of contact entities associated with this trial items: type: string - trialDbId: - type: string - trialDescription: - type: string - trialName: - type: string - trialPUI: - type: string - description: "A Trial represents a collection of Study objects, and the metadata\ - \ associated with that collection. A Trial could represent a multi-location\ - \ experiment, and could contain information related to publications and data\ - \ licensing." - TrialSearchRequest: - type: object - properties: - active: - type: boolean - searchDateRangeEnd: - type: string searchDateRangeStart: type: string + description: "The start of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date description: "A Trial represents a collection of Study objects, and the metadata\ \ associated with that collection. A Trial could represent a multi-location\ \ experiment, and could contain information related to publications and data\ \ licensing." Variable: required: - - method - - scale - - trait + - methodDbId + - methodName + - scaleDbId + - scaleName + - traitName type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" commonCropName: type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true contextOfUse: type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true items: type: string defaultValue: type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" growthStage: type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true institution: type: string + description: Name of institution submitting the variable + nullable: true language: type: string - method: - $ref: "#/components/schemas/Method" + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string ontologyReference: $ref: "#/components/schemas/OntologyReference" - scale: - $ref: "#/components/schemas/Scale" + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string scientist: type: string + description: Name of scientist submitting the variable. + nullable: true status: type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true submissionTimestamp: type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true synonyms: type: array + description: Other variable names + nullable: true items: type: string - trait: - $ref: "#/components/schemas/Trait" + traitDbId: + type: string + traitName: + type: string + traitPUI: + type: string description: "A unique combination of Trait, Method, and Scale to define a clear\ \ context for an Observation." + VariableBaseClassParameters: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + VariantRequest: + type: object + properties: + callSetDbIds: + type: array + description: "**Deprecated in v2.1** Parameter unnecessary. Github issue\ + \ number #474 \n
Only return variant calls which belong to call sets\ + \ with these IDs. If unspecified, return all variants and no variant call\ + \ objects." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + end: + type: integer + description: "The end of the window (0-based, exclusive) for which overlapping\ + \ variants should be returned." + format: int32 + example: 1500 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbId: + type: string + description: |- + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + example: 120a2d5c + referenceDbIds: + type: array + description: The unique identifier representing a genotype `Reference` + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype `ReferenceSet` + items: + type: string + start: + type: integer + description: "The beginning of the window (0-based, inclusive) for which\ + \ overlapping variants should be returned. Genomic positions are non-negative\ + \ integers less than reference length. Requests spanning the join of circular\ + \ genomes are represented as two requests one on each side of the join\ + \ (position 0)." + format: int32 + example: 100 + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` + items: + type: string + VariantSetRequest: + type: object + properties: + callSetDbIds: + type: array + description: The unique identifier representing a CallSet + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: The unique identifier representing a genotype Reference + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype ReferenceSet + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantDbIds: + type: array + description: The unique identifier representing a Variant + items: + type: string + variantSetDbIds: + type: array + description: The unique identifier representing a VariantSet + items: + type: string basePagination: required: - currentPage @@ -2844,6 +7457,30 @@ components: searchResultsDbId: type: string example: 551ae08c + StudyStudyTypeListResponse: + description: OK + content: + application/json: + schema: + title: StudyStudyTypeListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: string StudySingleResponse: description: OK content: @@ -3223,6 +7860,18 @@ components: schema: type: integer example: 1000 + authorizationHeader: + name: Authorization + in: header + description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ + \ {token_string} " + required: false + style: simple + explode: false + schema: + pattern: ^Bearer .*$ + type: string + example: Bearer XXXX page: name: page in: query @@ -3251,18 +7900,6 @@ components: schema: type: string example: 33c27874 - authorizationHeader: - name: Authorization - in: header - description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ - \ {token_string} " - required: false - style: simple - explode: false - schema: - pattern: ^Bearer .*$ - type: string - example: Bearer XXXX securitySchemes: AuthorizationToken: type: http diff --git a/Specification/Generated/BrAPI-Genotyping.yaml b/Specification/Generated/BrAPI-Genotyping.yaml index 180d385a..c45f621c 100644 --- a/Specification/Generated/BrAPI-Genotyping.yaml +++ b/Specification/Generated/BrAPI-Genotyping.yaml @@ -31,7 +31,7 @@ paths: required: false schema: type: string - - name: expandHomozygote + - name: expandHomozygotes in: query description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) @@ -56,6 +56,7 @@ paths: required: false schema: type: string + - $ref: "#/components/parameters/pageToken" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" - $ref: "#/components/parameters/authorizationHeader" @@ -75,74 +76,12 @@ paths: summary: Get a filtered list of CallSet description: Get a list of CallSet parameters: - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - name: germplasmDbId in: query description: List of IDs which uniquely identify germplasm to search for required: false schema: type: string - - name: germplasmName - in: query - description: List of human readable names to identify germplasm to search - for - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - - name: studyDbId - in: query - description: List of study identifiers to search for - required: false - schema: - type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - - name: trialDbId - in: query - description: The ID which uniquely identifies a trial to search for - required: false - schema: - type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - name: sampleDbId in: query description: A list of IDs which uniquely identify `Samples` within the given @@ -150,12 +89,6 @@ paths: required: false schema: type: string - - name: sampleName - in: query - description: A list of human readable names associated with `Samples` - required: false - schema: - type: string - name: callSetDbId in: query description: A list of IDs which uniquely identify `CallSets` within the given @@ -176,7 +109,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -220,39 +152,18 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for required: false schema: type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - name: trialDbId in: query description: The ID which uniquely identifies a trial to search for required: false schema: type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - name: mapDbId in: query description: The ID which uniquely identifies a `GenomeMap` @@ -293,7 +204,7 @@ paths: /markerpositions: get: tags: - - MarkerPositions + - Genome Maps summary: Get a filtered list of MarkerPosition description: Get a list of MarkerPosition parameters: @@ -368,13 +279,6 @@ paths: required: false schema: type: string - - name: germplasmName - in: query - description: List of human readable names to identify germplasm to search - for - required: false - schema: - type: string - name: programDbId in: query description: "A BrAPI Program represents the high level organization or group\ @@ -385,39 +289,18 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for required: false schema: type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - name: trialDbId in: query description: The ID which uniquely identifies a trial to search for required: false schema: type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - name: observationUnitDbId in: query description: The ID which uniquely identifies an observation unit @@ -436,12 +319,6 @@ paths: required: false schema: type: string - - name: plateBarcode - in: query - description: A unique identifier physically attached to the plate - required: false - schema: - type: string - name: sampleDbId in: query description: The ID which uniquely identifies a sample @@ -460,13 +337,6 @@ paths: required: false schema: type: string - - name: germplasmDbId - in: query - description: The ID which uniquely identifies a germplasm - required: false - schema: - type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -492,7 +362,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/PlateNewRequest" + type: array + items: + $ref: "#/components/schemas/PlateNewRequest" responses: "200": $ref: "#/components/responses/PlateListResponse" @@ -521,19 +393,6 @@ paths: required: false schema: type: string - - name: germplasmDbId - in: query - description: List of IDs which uniquely identify germplasm to search for - required: false - schema: - type: string - - name: germplasmName - in: query - description: List of human readable names to identify germplasm to search - for - required: false - schema: - type: string - name: programDbId in: query description: "A BrAPI Program represents the high level organization or group\ @@ -544,39 +403,18 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for required: false schema: type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - name: trialDbId in: query description: The ID which uniquely identifies a trial to search for required: false schema: type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - name: accession in: query description: "If specified, return the references for which the `accession`\ @@ -615,6 +453,7 @@ paths: required: false schema: type: boolean + format: boolean - name: minLength in: query description: The minimum length of this `References` sequence. @@ -629,7 +468,6 @@ paths: schema: type: integer format: int32 - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -663,19 +501,6 @@ paths: required: false schema: type: string - - name: germplasmDbId - in: query - description: List of IDs which uniquely identify germplasm to search for - required: false - schema: - type: string - - name: germplasmName - in: query - description: List of human readable names to identify germplasm to search - for - required: false - schema: - type: string - name: programDbId in: query description: "A BrAPI Program represents the high level organization or group\ @@ -686,39 +511,18 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for required: false schema: type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - name: trialDbId in: query description: The ID which uniquely identifies a trial to search for required: false schema: type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - name: accession in: query description: "If set, return the reference sets for which the `accession`\ @@ -746,7 +550,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -786,13 +589,6 @@ paths: required: false schema: type: string - - name: germplasmName - in: query - description: List of human readable names to identify germplasm to search - for - required: false - schema: - type: string - name: programDbId in: query description: "A BrAPI Program represents the high level organization or group\ @@ -803,39 +599,18 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for required: false schema: type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - name: trialDbId in: query description: The ID which uniquely identifies a trial to search for required: false schema: type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - name: observationUnitDbId in: query description: The ID which uniquely identifies an `ObservationUnit` @@ -872,13 +647,6 @@ paths: required: false schema: type: string - - name: germplasmDbId - in: query - description: The ID which uniquely identifies a `Germplasm` - required: false - schema: - type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -904,7 +672,21 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/SampleNewRequest" + type: object + additionalProperties: + $ref: "#/components/schemas/SampleNewRequest" + example: "{_1={additionalInfo={}, callSets=[{}], column=10,\ + \ externalReferences=[{}], germplasm={}, observationUnit={}, plate={},\ + \ program={}, row=00358167, sampleBarcode=6a6db74b, sampleDescription=3388964f,\ + \ sampleDbId=079d6d5e, sampleGroupId=70fcb311, sampleName=082a6b4c,\ + \ samplePUI=08863647, sampleTimestamp=2020-08-12T18:10:40.413Z, sampleType=0889ec7d,\ + \ study={}, takenBy=599da043, tissueType=4d105e22, trial={}, well=06bc78f3},\ + \ _2={additionalInfo={}, callSets=[{}], column=20, externalReferences=[{}],\ + \ germplasm={}, observationUnit={}, plate={}, program={}, row=00358168,\ + \ sampleBarcode=6a6db74c, sampleDescription=33889650, sampleDbId=079d6d5f,\ + \ sampleGroupId=70fcb312, sampleName=082a6b4d, samplePUI=08863648,\ + \ sampleTimestamp=2020-08-12T18:10:40.413Z, sampleType=0889ec7e, study={},\ + \ takenBy=599da044, tissueType=4d105e23, trial={}, well=06bc78f4}}" responses: "200": $ref: "#/components/responses/SampleListResponse" @@ -925,7 +707,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/SampleNewRequest" + type: array + items: + $ref: "#/components/schemas/SampleNewRequest" responses: "200": $ref: "#/components/responses/SampleListResponse" @@ -942,6 +726,54 @@ paths: summary: Get a filtered list of Variant description: Get a list of Variant parameters: + - name: referenceDbId + in: query + description: |- + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + required: false + schema: + type: string + - name: referenceSetDbId + in: query + description: The unique identifier representing a genotype `ReferenceSet` + required: false + schema: + type: string + - name: variantDbId + in: query + description: A list of IDs which uniquely identify `Variants` + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: A list of IDs which uniquely identify `VariantSets` + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/pageToken" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/VariantListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /variantsets: + get: + tags: + - VariantSets + summary: Get a filtered list of VariantSet + description: Get a list of VariantSet + parameters: - name: commonCropName in: query description: "The BrAPI Common Crop Name is the simple, generalized, widely\ @@ -964,15 +796,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for @@ -985,185 +808,30 @@ paths: required: false schema: type: string - - name: trialDbId + - name: callSetDbId in: query - description: The ID which uniquely identifies a trial to search for + description: The unique identifier representing a CallSet required: false schema: type: string - - name: trialName + - name: variantDbId in: query - description: The human readable name of a trial to search for + description: The unique identifier representing a Variant required: false schema: type: string - - name: callSetDbId + - name: variantSetDbId in: query - description: "**Deprecated in v2.1** Parameter unnecessary. Github issue number\ - \ #474 \n
Only return variant calls which belong to call sets with these\ - \ IDs. If unspecified, return all variants and no variant call objects." + description: The unique identifier representing a VariantSet required: false schema: type: string - - name: end + - name: referenceSetDbId in: query - description: "The end of the window (0-based, exclusive) for which overlapping\ - \ variants should be returned." - required: false - schema: - type: integer - format: int32 - - name: referenceDbId - in: query - description: |- - **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 -
Only return variants on this reference. - required: false - schema: - type: string - - name: referenceDbId - in: query - description: The unique identifier representing a genotype `Reference` - required: false - schema: - type: string - - name: referenceSetDbId - in: query - description: The unique identifier representing a genotype `ReferenceSet` - required: false - schema: - type: string - - name: start - in: query - description: "The beginning of the window (0-based, inclusive) for which overlapping\ - \ variants should be returned. Genomic positions are non-negative integers\ - \ less than reference length. Requests spanning the join of circular genomes\ - \ are represented as two requests one on each side of the join (position\ - \ 0)." - required: false - schema: - type: integer - format: int32 - - name: variantDbId - in: query - description: A list of IDs which uniquely identify `Variants` - required: false - schema: - type: string - - name: variantSetDbId - in: query - description: A list of IDs which uniquely identify `VariantSets` - required: false - schema: - type: string - - $ref: "#/components/parameters/externalReferenceID" - - $ref: "#/components/parameters/externalReferenceId" - - $ref: "#/components/parameters/externalReferenceSource" - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/VariantListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /variantsets: - get: - tags: - - VariantSets - summary: Get a filtered list of VariantSet - description: Get a list of VariantSet - parameters: - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - - name: studyDbId - in: query - description: List of study identifiers to search for - required: false - schema: - type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - - name: trialDbId - in: query - description: The ID which uniquely identifies a trial to search for - required: false - schema: - type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - - name: callSetDbId - in: query - description: The unique identifier representing a CallSet - required: false - schema: - type: string - - name: variantDbId - in: query - description: The unique identifier representing a Variant - required: false - schema: - type: string - - name: variantSetDbId - in: query - description: The unique identifier representing a VariantSet - required: false - schema: - type: string - - name: referenceDbId - in: query - description: The unique identifier representing a genotype Reference - required: false - schema: - type: string - - name: referenceSetDbId - in: query - description: The unique identifier representing a genotype ReferenceSet + description: The unique identifier representing a genotype ReferenceSet required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -1184,6 +852,15 @@ paths: - CallSets summary: Get the details of a specific CallSet description: Get details for a CallSet + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: callSetDbId + in: path + description: The ID which uniquely identifies a CallSet within the given database + server + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/CallSetSingleResponse" @@ -1193,35 +870,23 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /callsets/{callSetDbId}/calls: get: tags: - - Calls + - CallSets summary: Get a filtered list of Call description: Get a list of Call parameters: - name: callSetDbId - in: query - description: A list of IDs which uniquely identify `CallSets` within the given - database server - required: false - schema: - type: string - - name: variantDbId - in: query - description: A list of IDs which uniquely identify `Variant` within the given - database server - required: false - schema: - type: string - - name: variantSetDbId - in: query - description: A list of IDs which uniquely identify `VariantSets` within the - given database server - required: false + in: path + description: The ID which uniquely identifies a CallSet within the given database + server + required: true schema: type: string - - name: expandHomozygote + - name: expandHomozygotes in: query description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) @@ -1248,6 +913,7 @@ paths: type: string - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/pageToken" - $ref: "#/components/parameters/authorizationHeader" responses: "200": @@ -1258,12 +924,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /maps/{mapDbId}: get: tags: - GenomeMaps summary: Get the details of a specific GenomeMap description: Get details for a GenomeMap + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: mapDbId + in: path + description: The unique identifier for a `GenomeMap` + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/GenomeMapSingleResponse" @@ -1273,12 +949,49 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /maps/{mapDbId}/linkagegroups: + get: + tags: + - GenomeMaps + summary: Get a filtered list of LinkageGroup + description: Get a list of LinkageGroup + parameters: + - name: mapDbId + in: path + description: The unique identifier for a `GenomeMap` + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/LinkageGroupListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /plates/{plateDbId}: get: tags: - Plates summary: Get the details of a specific Plate description: Get details for a Plate + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: plateDbId + in: path + description: The ID which uniquely identifies a `Plate` + required: false + schema: + type: string responses: "200": $ref: "#/components/responses/PlateSingleResponse" @@ -1288,12 +1001,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /references/{referenceDbId}: get: tags: - References summary: Get the details of a specific Reference description: Get details for a Reference + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: referenceDbId + in: path + description: The unique identifier for a `Reference` + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/ReferenceSingleResponse" @@ -1303,12 +1026,75 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /references/{referenceDbId}/bases: + get: + tags: + - References + summary: Get the details of a specific ReferenceBases + description: Get details for a ReferenceBases + parameters: + - name: start + in: query + description: |- + The start position (0-based) of this query. Defaults to 0. + Genomic positions are non-negative integers less than reference length. + Requests spanning the join of circular genomes are represented as + two requests one on each side of the join (position 0). + required: false + schema: + type: integer + format: int32 + - name: end + in: query + description: "The end position (0-based, exclusive) of this query. Defaults\ + \ to the length of this `Reference`." + required: false + schema: + type: integer + format: int32 + - name: pageToken + in: query + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + required: false + schema: + type: string + - $ref: "#/components/parameters/authorizationHeader" + - name: referenceDbId + in: path + description: The unique identifier for a `Reference` + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/ReferenceBasesSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /referencesets/{referenceSetDbId}: get: tags: - ReferenceSets summary: Get the details of a specific ReferenceSet description: Get details for a ReferenceSet + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: referenceSetDbId + in: path + description: The unique identifier for a ReferenceSet + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/ReferenceSetSingleResponse" @@ -1318,12 +1104,24 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /samples/{sampleDbId}: get: tags: - Samples summary: Get the details of a specific Sample description: Get details for a Sample + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: sampleDbId + in: path + description: |- + The ID which uniquely identifies a `Sample` +
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample. + required: false + schema: + type: string responses: "200": $ref: "#/components/responses/SampleSingleResponse" @@ -1333,12 +1131,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /variants/{variantDbId}: get: tags: - Variants summary: Get the details of a specific Variant description: Get details for a Variant + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: variantDbId + in: path + description: The ID which uniquely identifies a `Variant` + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/VariantSingleResponse" @@ -1348,38 +1156,25 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /variants/{variantDbId}/calls: get: tags: - - Calls + - Variants summary: Get a filtered list of Call description: Get a list of Call parameters: - - name: callSetDbId - in: query - description: A list of IDs which uniquely identify `CallSets` within the given - database server - required: false + - name: variantDbId + in: path + description: The ID which uniquely identifies a `Variant` + required: true schema: type: string - - name: variantDbId + - name: expandHomozygotes in: query - description: A list of IDs which uniquely identify `Variant` within the given - database server - required: false - schema: - type: string - - name: variantSetDbId - in: query - description: A list of IDs which uniquely identify `VariantSets` within the - given database server - required: false - schema: - type: string - - name: expandHomozygote - in: query - description: Should homozygotes be expanded (true) or collapsed into a single - occurrence (false) + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) required: false schema: type: boolean @@ -1403,6 +1198,7 @@ paths: type: string - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/pageToken" - $ref: "#/components/parameters/authorizationHeader" responses: "200": @@ -1413,12 +1209,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /variantsets/{variantSetDbId}: get: tags: - VariantSets summary: Get the details of a specific VariantSet description: Get details for a VariantSet + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: variantSetDbId + in: path + description: The unique identifier for a VariantSet + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/VariantSetSingleResponse" @@ -1428,35 +1234,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /variantsets/{variantSetDbId}/calls: get: tags: - - Calls + - VariantSets summary: Get a filtered list of Call description: Get a list of Call parameters: - - name: callSetDbId - in: query - description: A list of IDs which uniquely identify `CallSets` within the given - database server - required: false - schema: - type: string - - name: variantDbId - in: query - description: A list of IDs which uniquely identify `Variant` within the given - database server - required: false - schema: - type: string - name: variantSetDbId - in: query - description: A list of IDs which uniquely identify `VariantSets` within the - given database server - required: false + in: path + description: The unique identifier for a VariantSet + required: true schema: type: string - - name: expandHomozygote + - name: expandHomozygotes in: query description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) @@ -1483,6 +1276,7 @@ paths: type: string - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/pageToken" - $ref: "#/components/parameters/authorizationHeader" responses: "200": @@ -1493,92 +1287,19 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /variantsets/{variantSetDbId}/callsets: get: tags: - - CallSets + - VariantSets summary: Get a filtered list of CallSet description: Get a list of CallSet parameters: - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - - name: germplasmDbId - in: query - description: List of IDs which uniquely identify germplasm to search for - required: false - schema: - type: string - - name: germplasmName - in: query - description: List of human readable names to identify germplasm to search - for - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - - name: studyDbId - in: query - description: List of study identifiers to search for - required: false - schema: - type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - - name: trialDbId - in: query - description: The ID which uniquely identifies a trial to search for - required: false - schema: - type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - - name: sampleDbId - in: query - description: A list of IDs which uniquely identify `Samples` within the given - database server - required: false - schema: - type: string - - name: sampleName - in: query - description: A list of human readable names associated with `Samples` - required: false + - name: variantSetDbId + in: path + description: The unique identifier for a VariantSet + required: true schema: type: string - name: callSetDbId @@ -1594,16 +1315,6 @@ paths: required: false schema: type: string - - name: variantSetDbId - in: query - description: A list of IDs which uniquely identify `VariantSets` within the - given database server - required: false - schema: - type: string - - $ref: "#/components/parameters/externalReferenceID" - - $ref: "#/components/parameters/externalReferenceId" - - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" - $ref: "#/components/parameters/authorizationHeader" @@ -1616,132 +1327,30 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /variantsets/{variantSetDbId}/variants: get: tags: - - Variants + - VariantSets summary: Get a filtered list of Variant description: Get a list of Variant parameters: - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - - name: studyDbId - in: query - description: List of study identifiers to search for - required: false - schema: - type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - - name: trialDbId - in: query - description: The ID which uniquely identifies a trial to search for - required: false - schema: - type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - - name: callSetDbId - in: query - description: "**Deprecated in v2.1** Parameter unnecessary. Github issue number\ - \ #474 \n
Only return variant calls which belong to call sets with these\ - \ IDs. If unspecified, return all variants and no variant call objects." - required: false - schema: - type: string - - name: end - in: query - description: "The end of the window (0-based, exclusive) for which overlapping\ - \ variants should be returned." - required: false - schema: - type: integer - format: int32 - - name: referenceDbId - in: query - description: |- - **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 -
Only return variants on this reference. - required: false - schema: - type: string - - name: referenceDbId - in: query - description: The unique identifier representing a genotype `Reference` - required: false - schema: - type: string - - name: referenceSetDbId - in: query - description: The unique identifier representing a genotype `ReferenceSet` - required: false + - name: variantSetDbId + in: path + description: The unique identifier for a VariantSet + required: true schema: type: string - - name: start - in: query - description: "The beginning of the window (0-based, inclusive) for which overlapping\ - \ variants should be returned. Genomic positions are non-negative integers\ - \ less than reference length. Requests spanning the join of circular genomes\ - \ are represented as two requests one on each side of the join (position\ - \ 0)." - required: false - schema: - type: integer - format: int32 - name: variantDbId in: query description: A list of IDs which uniquely identify `Variants` required: false schema: type: string - - name: variantSetDbId - in: query - description: A list of IDs which uniquely identify `VariantSets` - required: false - schema: - type: string - - $ref: "#/components/parameters/externalReferenceID" - - $ref: "#/components/parameters/externalReferenceId" - - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/pageToken" - $ref: "#/components/parameters/authorizationHeader" responses: "200": @@ -1752,6 +1361,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/allelematrix: post: tags: @@ -1765,6 +1376,13 @@ paths: \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/AlleleMatrixSearchRequest" responses: "200": $ref: "#/components/responses/AlleleMatrixListResponse" @@ -1788,6 +1406,13 @@ paths: \ `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.\ \
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CallSearchRequest" responses: "200": $ref: "#/components/responses/CallListResponse" @@ -1811,6 +1436,13 @@ paths: \ `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CallSetSearchRequest" responses: "200": $ref: "#/components/responses/CallSetListResponse" @@ -1825,7 +1457,7 @@ paths: /search/markerpositions: post: tags: - - MarkerPositions + - Genome Maps summary: Submit a search request for `MarkerPosition` description: "Submit a search request for `MarkerPosition`
\nSearch requests\ \ allow a client to send a complex query for data. However, the server may\ @@ -1835,6 +1467,13 @@ paths: \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/MarkerPositionSearchRequest" responses: "200": $ref: "#/components/responses/MarkerPositionListResponse" @@ -1858,6 +1497,13 @@ paths: \ `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.\ \
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PlateSearchRequest" responses: "200": $ref: "#/components/responses/PlateListResponse" @@ -1882,6 +1528,13 @@ paths: \ the results of the search.
\nReview the Search\ \ Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ReferenceSearchRequest" responses: "200": $ref: "#/components/responses/ReferenceListResponse" @@ -1906,6 +1559,13 @@ paths: \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ReferenceSetSearchRequest" responses: "200": $ref: "#/components/responses/ReferenceSetListResponse" @@ -1929,6 +1589,13 @@ paths: \ `GET /search/sample/{searchResultsDbId}` to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/SampleSearchRequest" responses: "200": $ref: "#/components/responses/SampleListResponse" @@ -1952,6 +1619,13 @@ paths: \ `GET /search/variant/{searchResultsDbId}` to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/VariantSearchRequest" responses: "200": $ref: "#/components/responses/VariantListResponse" @@ -1976,6 +1650,13 @@ paths: \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/VariantSetSearchRequest" responses: "200": $ref: "#/components/responses/VariantSetListResponse" @@ -2006,6 +1687,14 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/AlleleMatrixListResponse" @@ -2034,6 +1723,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/CallListResponse" @@ -2062,6 +1761,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/CallSetListResponse" @@ -2074,7 +1783,7 @@ paths: /search/markerpositions/{searchResultsDbId}: get: tags: - - MarkerPositions + - Genome Maps summary: "Submit a search request for `MarkerPosition`
\nSearch requests\ \ allow a client to send a complex query for data. However, the server may\ \ not respond with the search results immediately. \nIf a server needs more\ @@ -2091,6 +1800,16 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/MarkerPositionListResponse" @@ -2119,6 +1838,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/PlateListResponse" @@ -2147,6 +1876,16 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/ReferenceListResponse" @@ -2175,6 +1914,16 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/ReferenceSetListResponse" @@ -2203,6 +1952,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/SampleListResponse" @@ -2231,6 +1990,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/VariantListResponse" @@ -2259,6 +2028,16 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/VariantSetListResponse" @@ -2271,56 +2050,304 @@ paths: components: schemas: AdditionalInfo: - type: object - properties: - additionalProperties: - type: string + type: string + additionalProperties: + description: A free space containing any additional information related to + a particular object. description: "A free space containing any additional information related to\ \ a particular object. A data source may provide any JSON object, unrestricted\ \ by the BrAPI specification." + nullable: true AlleleMatrix: - required: - - callSetDbIds - - variantSetDbIds + type: object + properties: + dataMatrices: + type: array + description: "The 'dataMatrices' are an array of matrix objects that hold\ + \ the allele data and associated metadata. Each matrix should be the same\ + \ size and orientation, aligned with the \"callSetDbIds\" as columns and\ + \ the \"variantDbIds\" as rows." + nullable: true + items: + $ref: "#/components/schemas/DataMatrix" + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + nullable: true + pagination: + type: array + description: Pagination for the matrix + nullable: true + items: + $ref: "#/components/schemas/Pagination" + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + nullable: true + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + nullable: true + unknownString: + type: string + description: The string used as a representation for missing data. + nullable: true + description: "The AlleleMatrix object is used to describe a matrix of genotyping\ + \ results. This 2d array of data reduces the overall size of the response\ + \ for larger datasets, when compared to the Calls endpoints. This makes genotype\ + \ data retrieval faster and easier." + AlleleMatrixPagination: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension of + the matrix + format: int32 + example: 500 + AlleleMatrixRequest: type: object properties: callSetDbIds: type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + dataMatrixAbbreviations: + type: array + description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ + \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ + \ in the response." + items: + type: string + dataMatrixNames: + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." items: type: string expandHomozygotes: type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + germplasmDbIds: + type: array + description: A list of IDs which uniquely identify `Germplasm` within the + given database server + items: + type: string + germplasmNames: + type: array + description: A list of human readable `Germplasm` names + items: + type: string + germplasmPUIs: + type: array + description: A list of permanent unique identifiers associated with `Germplasm` + items: + type: string + pagination: + type: array + description: Pagination for the matrix + items: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension + of the matrix + format: int32 + example: 500 + positionRanges: + type: array + description: "The postion range to search\n
\nUses the format \":-\"\ + \ where is the chromosome name, is \nthe starting position\ + \ of the range, and is the ending position of the range" + items: + type: string + preview: + type: boolean + description: "Default Value = false\n
\nIf 'preview' is set to true,\ + \ then the server should only return the lists of 'callSetDbIds', \n'variantDbIds',\ + \ and 'variantSetDbIds'. The server should not return any matrix data.\ + \ This\nis intended to be a preview and give the client a sense of how\ + \ large the matrix returned will be\n
\nIf 'preview' is set to false\ + \ or not set (default), then the server should return all the matrix\n\ + data as requested." + example: true + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + items: + type: string sepPhased: type: string + description: The string used as a separator for phased allele calls. + example: '|' sepUnphased: type: string + description: The string used as a separator for unphased allele calls. + example: / unknownString: type: string + description: The string used as a representation for missing data. + example: "." variantDbIds: type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server items: type: string variantSetDbIds: type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server items: type: string - description: "The AlleleMatrix object is used to describe a matrix of genotyping\ - \ results. This 2d array of data reduces the overall size of the response\ - \ for larger datasets, when compared to the Calls endpoints. This makes genotype\ - \ data retrieval faster and easier." AlleleMatrixSearchRequest: type: object properties: - expandHomozygotes: - type: boolean + germplasmDbIds: + type: array + description: A list of IDs which uniquely identify `Germplasm` within the + given database server + items: + type: string preview: type: boolean + description: "Default Value = false\n
\nIf 'preview' is set to true,\ + \ then the server should only return the lists of 'callSetDbIds', \n'variantDbIds',\ + \ and 'variantSetDbIds'. The server should not return any matrix data.\ + \ This\nis intended to be a preview and give the client a sense of how\ + \ large the matrix returned will be\n
\nIf 'preview' is set to false\ + \ or not set (default), then the server should return all the matrix\n\ + data as requested." + example: true + germplasmNames: + type: array + description: A list of human readable `Germplasm` names + items: + type: string + pagination: + type: array + description: Pagination for the matrix + items: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension + of the matrix + format: int32 + example: 500 + unknownString: + type: string + description: The string used as a representation for missing data. + example: "." + germplasmPUIs: + type: array + description: A list of permanent unique identifiers associated with `Germplasm` + items: + type: string + positionRanges: + type: array + description: "The postion range to search\n
\nUses the format \":-\"\ + \ where is the chromosome name, is \nthe starting position\ + \ of the range, and is the ending position of the range" + items: + type: string + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string + dataMatrixAbbreviations: + type: array + description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ + \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ + \ in the response." + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server + items: + type: string + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + dataMatrixNames: + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." + items: + type: string sepPhased: type: string + description: The string used as a separator for phased allele calls. + example: '|' sepUnphased: type: string - unknownString: - type: string + description: The string used as a separator for unphased allele calls. + example: / description: "The AlleleMatrix object is used to describe a matrix of genotyping\ \ results. This 2d array of data reduces the overall size of the response\ \ for larger datasets, when compared to the Calls endpoints. This makes genotype\ @@ -2332,20 +2359,37 @@ components: properties: analysisDbId: type: string + description: Unique identifier for this analysis description + nullable: true analysisName: type: string + description: A human readable name for this analysis + nullable: true created: type: string + description: "The time at which this record was created, in ISO 8601 format." + format: date-time + nullable: true description: type: string + description: A human readable description of the analysis + nullable: true software: type: array + description: The software run to generate this analysis. + nullable: true items: type: string type: type: string + description: The type of analysis. + nullable: true updated: type: string + description: "The time at which this record was last updated, in ISO 8601\ + \ format." + format: date-time + nullable: true variantSetDbId: type: string variantSetName: @@ -2356,57 +2400,118 @@ components: Attribute: required: - attributeName - - method - - scale - - trait + - methodDbId + - methodName + - scaleDbId + - scaleName + - traitName type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" attributeCategory: type: string + description: General category for the attribute. very similar to Trait class. + example: Morphological attributeDbId: type: string + description: The ID which uniquely identifies this attribute within the + given database server attributeDescription: type: string + description: A human readable description of this attribute + example: Height of the plant measured in meters by a tape attributeName: type: string + description: A human readable name for this attribute + example: Plant Height 1 attributePUI: type: string + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + example: http://my-traits.com/trait/CO_123:0008012 commonCropName: type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true contextOfUse: type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true items: type: string defaultValue: type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" growthStage: type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true institution: type: string + description: Name of institution submitting the variable + nullable: true language: type: string - method: - $ref: "#/components/schemas/Method" + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string ontologyReference: $ref: "#/components/schemas/OntologyReference" - scale: - $ref: "#/components/schemas/Scale" + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string scientist: type: string + description: Name of scientist submitting the variable. + nullable: true status: type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true submissionTimestamp: type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true synonyms: type: array + description: Other variable names + nullable: true items: type: string - trait: - $ref: "#/components/schemas/Trait" + traitDbId: + type: string + traitName: + type: string + traitPUI: + type: string AvailableFormat: type: object properties: @@ -2414,6 +2519,7 @@ components: type: string description: "dataFormat defines the structure of the data within a file\ \ (ie DartSeq, VCF, Hapmap, tabular, etc)" + nullable: true enum: - DartSeq - VCF @@ -2422,12 +2528,16 @@ components: - JSON expandHomozygotes: type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + nullable: true fileFormat: type: string description: "fileFormat defines the MIME type of the file (ie text/csv,\ \ application/excel, application/zip). This should also be reflected in\ \ the Accept and ContentType HTTP headers for every relevant request and\ \ response." + nullable: true enum: - text/csv - text/tsv @@ -2436,12 +2546,23 @@ components: - application/json fileURL: type: string + description: A URL which indicates the location of the file version of this + VariantSet. Could be a static file URL or an API endpoint which generates + the file. + format: uri + nullable: true sepPhased: type: string + description: The string used as a separator for phased allele calls. + nullable: true sepUnphased: type: string + description: The string used as a separator for unphased allele calls. + nullable: true unknownString: type: string + description: The string used as a representation for missing data. + nullable: true variantSetDbId: type: string variantSetName: @@ -2462,10 +2583,23 @@ components: type: string callSetName: type: string + genotypeMetadata: + type: array + description: Genotype Metadata are additional layers of metadata associated + with each genotype. + nullable: true + items: + $ref: "#/components/schemas/GenotypeMetadata" genotypeValue: type: string + description: The value of this genotype call + nullable: true phaseSet: type: string + description: "If this field is populated, this variant call's genotype ordering\ + \ implies the phase of the bases and \nis consistent with any other variant\ + \ calls on the same contig which have the same phase set string." + nullable: true variantDbId: type: string variantSetDbId: @@ -2477,17 +2611,82 @@ components: \ as quality and phasing. For example, a call might assign a probability of\ \ 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name\ \ NA_12345." - CallSearchRequest: + CallRequest: type: object properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string expandHomozygotes: type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true sepPhased: type: string + description: The string used as a separator for phased allele calls. + example: '|' sepUnphased: type: string + description: The string used as a separator for unphased allele calls. + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + example: "." + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variant` within the + given database server + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string + CallSearchRequest: + type: object + properties: + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string unknownString: type: string + description: The string used as a representation for missing data. + example: "." + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variant` within the + given database server + items: + type: string + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + example: / description: "A `Call` represents the determination of genotype with respect\ \ to a particular `Variant`. \n\nIt may include associated information such\ \ as quality and phasing. For example, a call might assign a probability of\ @@ -2502,10 +2701,26 @@ components: $ref: "#/components/schemas/AdditionalInfo" callSetDbId: type: string + description: The ID which uniquely identifies a CallSet within the given + database server callSetName: type: string + description: The human readable name which identifies a germplasm within + the given database server + nullable: true created: type: string + description: The date this call set was created + format: date-time + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" sampleDbId: type: string sampleName: @@ -2520,35 +2735,209 @@ components: type: string updated: type: string + description: The time at which this call set was last updated + format: date-time + nullable: true + description: A CallSet is a collection of Calls that were generated by the same + analysis of the same Sample + CallSetRequest: + type: object + properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + callSetNames: + type: array + description: A list of human readable names associated with `CallSets` + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + items: + type: string + sampleNames: + type: array + description: A list of human readable names associated with `Samples` + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string variantSetDbIds: type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server items: type: string - description: A CallSet is a collection of Calls that were generated by the same - analysis of the same Sample CallSetSearchRequest: type: object - properties: {} + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string + callSetNames: + type: array + description: A list of human readable names associated with `CallSets` + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + sampleNames: + type: array + description: A list of human readable names associated with `Samples` + items: + type: string + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string description: A CallSet is a collection of Calls that were generated by the same analysis of the same Sample - Contact: - required: - - contactDbId + CommonCropNamesParameters: type: object properties: - contactDbId: - type: string - email: - type: string - instituteName: - type: string - name: - type: string - orcid: - type: string - type: - type: string - description: A persons contact information + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string ContentTypes: type: string enum: @@ -2568,52 +2957,152 @@ components: items: type: string format: uri - CrossParent: + CrossRequest: type: object properties: - germplasm: - $ref: "#/components/schemas/Germplasm" - observationUnitDbId: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string - parentType: - $ref: "#/components/schemas/ParentType" - description: The identifying information gor the parent material of a cross. - CrossType: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + CrossStatus: + type: string + enum: + - TODO + - DONE + - SKIPPED + CrossingProjectRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + includePotentialParents: + type: boolean + description: "If the parameter 'includePotentialParents' is false, the array\ + \ 'potentialParents' should be empty, null, or excluded from the response\ + \ object." + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + DataFormat: type: string - description: "The type of cross make. Accepted values for this field are 'BIPARENTAL',\ - \ 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED'\ - \ and 'DOUBLE_HAPLOID'." + description: "dataFormat defines the structure of the data within a file (ie\ + \ DartSeq, VCF, Hapmap, tabular, etc)" enum: - - BIPARENTAL - - SELF - - OPEN_POLLINATED - - BULK - - BULK_SELFED - - BULK_OPEN_POLLINATED - - DOUBLE_HAPLOID + - DartSeq + - VCF + - Hapmap + - tabular + - JSON DataMatrix: type: object properties: - alleleMatrix: - $ref: "#/components/schemas/AlleleMatrix" dataMatrix: type: array + description: "The two dimensional array of data, providing the allele matrix\ + \ or an additional layer of metadata associated with each genotype value.\ + \ Each matrix should be the same size and orientation, aligned with the\ + \ \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." + nullable: true items: type: array items: type: string dataMatrixAbbreviation: type: string + description: |- + The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word "GT" is reserved for the allele matrix. Examples of other metadata matrices include: "GQ", "RD", and "HQ" +
This maps to a FORMAT field in the VCF file standard. + nullable: true dataMatrixName: type: string + description: |- + The name of the field represented in this data matrix. The key word "Genotype" is reserved for the allele matrix. Examples of other metadata matrices include: "Genotype Quality", "Read Depth", and "Haplotype Quality" +
This maps to a FORMAT field in the VCF file standard. + nullable: true dataType: type: string description: The type of field represented in this data matrix. This is intended to help parse the data out of JSON. + nullable: true enum: - string - integer @@ -2622,32 +3111,84 @@ components: description: "A two dimensional array that holds allele data or associated metadata.\ \ Each matrix should be the same size and orientation, aligned with the \"\ callSetDbIds\" as columns and the \"variantDbIds\" as rows." - ExperimentalDesign: + DataType: + type: string + description: The type of field represented in this Genotype Field. This is intended + to help parse the data out of JSON. + enum: + - string + - integer + - float + - boolean + Dimension: + type: string + description: The dimension of the matrix being paginated + enum: + - CALLSETS + - VARIANTS + EventRequest: type: object properties: - PUI: - type: string - description: - type: string - studyDbId: - type: string - studyName: + dateRangeEnd: type: string - studyPUI: + description: Filter based on an Event start date. + format: date-time + dateRangeStart: type: string - description: The experimental and statistical design full description plus a - category PUI taken from crop research ontology or agronomy ontology + description: Filter based on an Event start date. + format: date-time + eventDbIds: + type: array + description: Filter based on an Event DbId. + items: + type: string + eventTypes: + type: array + description: Filter based on an Event Type + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string ExternalReference: type: object properties: referenceId: type: string + description: The external reference ID. Could be a simple string or a URI. + nullable: true referenceSource: type: string + description: An identifier for the source system or database of this reference + nullable: true + FileFormat: + type: string + description: "fileFormat defines the MIME type of the file (ie text/csv, application/excel,\ + \ application/zip). This should also be reflected in the Accept and ContentType\ + \ HTTP headers for every relevant request and response." + enum: + - text/csv + - text/tsv + - application/excel + - application/zip + - application/json GenomeMap: required: - commonCropName - mapDbId + - mapName - type type: object properties: @@ -2655,42 +3196,138 @@ components: $ref: "#/components/schemas/AdditionalInfo" comments: type: string + description: Additional comments about a `GenomeMap` + nullable: true commonCropName: type: string + description: The common name of the `Crop` documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true linkageGroupCount: type: integer + description: The number of linkage groups present in a `GenomeMap` format: int32 + nullable: true mapDbId: type: string + description: The unique identifier for a `GenomeMap` mapName: type: string + description: The human readable identifier for a `GenomeMap` mapPUI: type: string + description: The DOI or other permanent identifier for a `GenomeMap` + nullable: true markerCount: type: integer + description: The number of markers present in a `GenomeMap` format: int32 + nullable: true publishedDate: type: string + description: The date this `GenomeMap` was published + format: date-time + nullable: true scientificName: type: string + description: "Full scientific binomial format name. This includes Genus,\ + \ Species, and Sub-species" + nullable: true type: type: string + description: "The type of map this represents, usually \"Genetic\" or \"\ + Physical\"" unit: type: string + description: The units used to describe the data in a `GenomeMap` + nullable: true description: The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map. + GenomeMapRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + mapDbIds: + type: array + description: The ID which uniquely identifies a `GenomeMap` + items: + type: string + mapPUIs: + type: array + description: The DOI or other permanent identifier for a `GenomeMap` + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scientificName: + type: array + description: "Full scientific binomial format name. This includes Genus,\ + \ Species, and Sub-species" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + types: + type: array + description: "The type of map, usually \"Genetic\" or \"Physical\"" + items: + type: string GenotypeMetadata: type: object properties: - call: - $ref: "#/components/schemas/Call" dataType: type: string description: The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON. + nullable: true enum: - string - integer @@ -2698,10 +3335,21 @@ components: - boolean fieldAbbreviation: type: string + description: |- + The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: "GQ", "RD", and "HQ" +
This maps to a FORMAT field in the VCF file standard. + nullable: true fieldName: type: string + description: |- + The name of the field represented in this Genotype Field. Examples include: "Genotype Quality", "Read Depth", and "Haplotype Quality" +
This maps to a FORMAT field in the VCF file standard. + nullable: true fieldValue: type: string + description: The additional metadata value associated with this genotype + call + nullable: true description: Genotype Metadata are additional layers of metadata associated with each genotype. GeoJSON: @@ -2711,6 +3359,8 @@ components: $ref: "#/components/schemas/GeoJSONGeometry" type: type: string + description: The literal string "Feature" + example: Feature description: |- One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. @@ -2727,10 +3377,12 @@ components: properties: coordinates: type: array + description: A single position items: type: number type: type: string + description: The literal string "Point" description: |- Copied from RFC 7946 Section 3.1.1 @@ -2743,6 +3395,7 @@ components: properties: coordinates: type: array + description: An array of linear rings items: type: array items: @@ -2751,1537 +3404,4800 @@ components: type: number type: type: string + description: The literal string "Polygon" description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ \ precisely in that order and using decimal numbers. Altitude or elevation\ \ MAY be included as an optional third element." - GeoJSONSearchArea: + GeoJSONPoint: + required: + - coordinateDbIds + - type type: object properties: - geometry: - $ref: "#/components/schemas/GeoJSONGeometry" - germplasmOrigin: - $ref: "#/components/schemas/GermplasmOrigin" - imageDbId: - type: string - imageName: - type: string - observationDbId: - type: string - observationUnit: - $ref: "#/components/schemas/ObservationUnitPosition" + coordinates: + type: array + description: A single position + items: + type: number type: type: string - Germplasm: - required: - - commonCropName - - germplasmDbId - - germplasmName - - germplasmPUI - type: object - properties: - accessionNumber: - type: string - acquisitionDate: - type: string - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - biologicalStatusOfAccessionCode: - type: string - description: "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can\ - \ be used at 3 different levels of detail: either by using the general\ - \ codes such as 100, 200, 300, 400, or by using the more specific codes\ - \ such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild\ - \ \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace\ - \ \n400) Breeding/research material \n410) Breeders line \n411) Synthetic\ - \ population \n412) Hybrid \n413) Founder stock/base population \n414)\ - \ Inbred line (parent of hybrid cultivar) \n415) Segregating population\ - \ \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion\ - \ mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome\ - \ addition/substitution, aneuploids, amphiploids) \n423) Other genetic\ - \ stocks (e.g. mapping populations) \n500) Advanced or improved cultivar\ - \ (conventional breeding methods) \n600) GMO (by genetic engineering)\ - \ \n999) Other (Elaborate in REMARKS field)" - enum: - - "100" - - "110" - - "120" - - "130" - - "200" - - "300" - - "400" - - "410" - - "411" - - "412" - - "413" - - "414" - - "415" - - "416" - - "420" - - "421" - - "422" - - "423" - - "500" - - "600" - - "999" - biologicalStatusOfAccessionDescription: - type: string - breedingMethodDbId: - type: string - breedingMethodName: - type: string - collection: - type: string - commonCropName: - type: string - countryOfOriginCode: - type: string - defaultDisplayName: - type: string - documentationURL: - type: string - genus: - type: string - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - germplasmPreprocessing: - type: string - instituteCode: - type: string - instituteName: - type: string - pedigree: - type: string - sampleDbIds: + description: The literal string "Point" + description: |- + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + GeoJSONPolygon: + required: + - coordinateDbIds + - type + type: object + properties: + coordinates: type: array + description: An array of linear rings items: - type: string - seedSource: - type: string - seedSourceDescription: - type: string - species: - type: string - speciesAuthority: - type: string - subtaxa: - type: string - subtaxaAuthority: + type: array + items: + type: array + items: + type: number + type: type: string - description: "The conceptual identifiers and metadata describing a genetically\ - \ unique organism that is noteworthy in some way. Depending on context, a\ - \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ - \ Germplasm is conceptual data, not necessarily associated to a real physical\ - \ object, so Seed/Inventory Lots and Observation Units become physical instantiations\ - \ of a particular Germplasm. Note a Germplasm is unique and noteworthy, so\ - \ a Cross may or may not create a new Germplasm, since not every Cross is\ - \ unique or noteworthy." - GermplasmOrigin: + description: The literal string "Polygon" + description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ + \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ + \ The first two elements are longitude and latitude, or\neasting and northing,\ + \ precisely in that order and using decimal numbers. Altitude or elevation\ + \ MAY be included as an optional third element." + GeoJSONSearchArea: type: object properties: - coordinateUncertainty: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + germplasmOrigin: + $ref: "#/components/schemas/GermplasmOrigin" + imageDbId: type: string - germplasmDbId: + imageName: type: string - germplasmName: + observationDbId: type: string - germplasmPUI: + observationUnit: + $ref: "#/components/schemas/ObservationUnitPosition" + type: type: string - description: "Information for material (orchard, natural sites, ...). Geographic\ - \ identification of the plants from which seeds or cutting have been taken\ - \ to produce that germplasm." - GrowthFacility: + description: The literal string "Feature" + example: Feature + GermplasmAttributeRequest: type: object properties: - PUI: - type: string - description: - type: string + attributeCategories: + type: array + description: General category for the attribute. very similar to Trait class. + items: + type: string + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + items: + type: string + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + items: + type: string + attributePUIs: + type: array + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - description: Short description of the facility in which the study was carried - out. - ListType: - type: string - description: The type of objects that are referenced in a List - enum: - - germplasm - - markers - - variants - - programs - - trials - - studies - - observationUnits - - observations - - observationVariables - - samples - MarkerPosition: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + GermplasmAttributeValueRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - linkageGroupName: - type: string - mapDbId: - type: string - mapName: - type: string - mapPUI: - type: string - position: - type: integer - format: int32 - variantDbId: - type: string - description: A MarkerPosition describes a particular genetic marker at a specific - position on a GenomeMap. A collection of MarkerPositions make up the data - to represent a full GenomeMap. - MarkerPositionSearchRequest: + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + items: + type: string + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + items: + type: string + attributeValueDbIds: + type: array + description: List of Germplasm Attribute Value IDs to search for + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: List of scales to filter search results + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: List of trait unique ID to filter search results + items: + type: string + GermplasmParameters: type: object properties: - maxPosition: - type: integer - format: int32 - minPosition: - type: integer - format: int32 - description: A MarkerPosition describes a particular genetic marker at a specific - position on a GenomeMap. A collection of MarkerPositions make up the data - to represent a full GenomeMap. - MetadataField: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + GermplasmRequest: type: object properties: - dataType: - type: string - description: The type of field represented in this Genotype Field. This - is intended to help parse the data out of JSON. - enum: - - string - - integer - - float - - boolean - fieldAbbreviation: - type: string - fieldName: - type: string - variantSetDbId: - type: string - variantSetName: - type: string - description: "Indicates which types of genotyping data and metadata are available\ - \ in the VariantSet. \n
When possible, these field names and abbreviations\ - \ should follow the VCF standard " - Method: - required: - - methodDbId - - methodName - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - bibliographicalReference: - type: string - description: - type: string - formula: - type: string - methodClass: - type: string - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string - ontologyReferenceDbId: - type: string - description: "A description of the way an Observation should be collected. \n\ -
For example, an ObservationVariable might be defined with a Trait of \"\ - plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This\ - \ variable would be distinct from a variable with the Method \"estimation\"\ - \ or \"drone image processing\". " - ObservationUnitHierarchyLevel: + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + items: + type: string + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + items: + type: string + parentDbIds: + type: array + description: Search for Germplasm with these parents + items: + type: string + progenyDbIds: + type: array + description: Search for Germplasm with these children + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ImageRequest: type: object properties: - levelName: - type: string - levelOrder: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + descriptiveOntologyTerms: + type: array + description: "A list of terms to formally describe the image to search for.\ + \ Each item could be a simple Tag, an Ontology reference Id, or a full\ + \ ontology URL." + items: + type: string + imageDbIds: + type: array + description: A list of image Ids to search for + items: + type: string + imageFileNames: + type: array + description: Image file names to search for. + items: + type: string + imageFileSizeMax: type: integer + description: A maximum image file size to search for. format: int32 - description: "The exact level and level code of an observation unit. \n\nFor\ - \ more information on Observation Levels, please review the Observation\ - \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ - Type of observation unit in textual form, usually one of the following: study,\ - \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ - \ types is possible but not recommended. \nThe observation unit type can not\ - \ be used to indicate sub-plant levels. However, observations can still be\ - \ made on the sub-plant level, as long as the details are indicated in the\ - \ associated observed variable (see observed variables). \nAlternatively,\ - \ it is possible to use samples for more detailed tracing of sub-plant units,\ - \ attaching the observations to them instead.\" " - ObservationUnitLevel: - type: object - properties: - levelCode: - type: string - levelName: - type: string - levelOrder: + example: 20000000 + imageFileSizeMin: type: integer + description: A minimum image file size to search for. format: int32 - description: "The exact level and level code of an observation unit. \n\nFor\ - \ more information on Observation Levels, please review the Observation\ - \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ - Type of observation unit in textual form, usually one of the following: study,\ - \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ - \ types is possible but not recommended. \nThe observation unit type can not\ - \ be used to indicate sub-plant levels. However, observations can still be\ - \ made on the sub-plant level, as long as the details are indicated in the\ - \ associated observed variable (see observed variables). \nAlternatively,\ - \ it is possible to use samples for more detailed tracing of sub-plant units,\ - \ attaching the observations to them instead.\" " - ObservationUnitPosition: - type: object - properties: - entryType: - type: string - description: "The type of entry for this observation unit. ex. \"CHECK\"\ - , \"TEST\", \"FILLER\"" - enum: - - CHECK - - TEST - - FILLER - observationLevel: - $ref: "#/components/schemas/ObservationUnitLevel" - observationUnitDbId: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string - positionCoordinateX: - type: string - positionCoordinateXType: - $ref: "#/components/schemas/PositionCoordinateType" - positionCoordinateY: - type: string - positionCoordinateYType: - $ref: "#/components/schemas/PositionCoordinateType" - description: All positional and layout information related to this Observation - Unit - Ontology: - required: - - ontologyDbId - - ontologyName - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - authors: - type: string - copyright: - type: string - description: - type: string - documentationURL: - type: string - licence: - type: string - ontologyDbId: - type: string - ontologyName: - type: string - version: - type: string - description: The identifier and metadata needed to reference an external controlled - vocabulary - OntologyReference: - required: - - ontology - type: object - properties: - ontology: - $ref: "#/components/schemas/Ontology" - ontologyReferenceDbId: - type: string - version: - type: string - description: "MIAPPE V1.1 (DM-85) Variable accession number - Accession number\ - \ of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession\ - \ number - Accession number of the trait in a suitable controlled vocabulary\ - \ (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number\ - \ - Accession number of the method in a suitable controlled vocabulary (Crop\ - \ Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number -\ - \ Accession number of the scale in a suitable controlled vocabulary (Crop\ - \ Ontology)." - OntologyTerm: - type: object - properties: - term: - type: string - termURI: - type: string - description: A pointer to an ontology used by a genomic reference - Pagination: - type: object - properties: - alleleMatrix: - $ref: "#/components/schemas/AlleleMatrix" - dimension: - type: string - description: The dimension of the matrix being paginated - enum: - - CALLSETS - - VARIANTS - page: + example: 1000 + imageHeightMax: type: integer + description: A maximum image height to search for. format: int32 - pageSize: + example: 1080 + imageHeightMin: type: integer + description: A minimum image height to search for. format: int32 - totalCount: + example: 720 + imageLocation: + $ref: "#/components/schemas/GeoJSONSearchArea" + imageNames: + type: array + description: Human readable names to search for. + items: + type: string + imageTimeStampRangeEnd: + type: string + description: The latest timestamp to search for. + format: date-time + imageTimeStampRangeStart: + type: string + description: The earliest timestamp to search for. + format: date-time + imageWidthMax: type: integer + description: A maximum image width to search for. format: int32 - totalPages: + example: 1920 + imageWidthMin: type: integer + description: A minimum image width to search for. format: int32 - description: Pagination info for the matrix - ParentType: - type: string - description: "The type of parent used during crossing. Accepted values for this\ - \ field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn\ - \ a pedigree record, the 'parentType' describes each parent of a particular\ - \ germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe\ - \ how this germplasm was crossed to generate a particular progeny. \\nFor\ - \ example, given a record for germplasm A, having a progeny B and C. The 'parentType'\ - \ field for progeny B item refers \\nto the 'parentType' of A toward B. The\ - \ 'parentType' field for progeny C item refers to the 'parentType' of A toward\ - \ C.\\nIn this way, A could be a male parent to B, but a female parent to\ - \ C. " - enum: - - MALE - - FEMALE - - SELF - - POPULATION - - CLONAL - Plate: - required: - - plateDbId - - plateName + example: 1280 + mimeTypes: + type: array + description: A set of image file types to search for. + items: + type: string + observationDbIds: + type: array + description: A list of observation Ids this image is associated with to + search for + items: + type: string + observationUnitDbIds: + type: array + description: A set of observation unit identifiers to search for. + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + LinkageGroup: type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" - plateBarcode: - type: string - plateFormat: - type: string - description: "Enum for plate formats, usually \"PLATE_96\" for a 96 well\ - \ plate or \"TUBES\" for plateless format" - enum: - - PLATE_96 - - TUBES - plateName: - type: string - programDbId: - type: string - programName: - type: string - sampleType: - type: string - description: "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" - enum: - - DNA - - RNA - - TISSUE - - MIXED - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - trialDbId: - type: string - trialName: - type: string - trialPUI: + linkageGroupName: type: string - description: "A Plate represents the metadata for a collection of Samples. The\ - \ physical Plate being represented might be a plastic tray full of Samples,\ - \ or a group of Samples stored in individual containers ie bags, test tubes,\ - \ etc. Whatever the container is, the Samples in a Plate should be related\ - \ by the same physical space, though they may or may not be related as part\ - \ of the same experiment or analysis." - PlateNewRequest: - required: - - plateDbId - - plateName - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - plateBarcode: - type: string - plateDbId: - type: string - plateFormat: - type: string - description: "Enum for plate formats, usually \"PLATE_96\" for a 96 well\ - \ plate or \"TUBES\" for plateless format" - enum: - - PLATE_96 - - TUBES - plateName: - type: string - programDbId: - type: string - programName: - type: string - sampleType: - type: string - description: "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" - enum: - - DNA - - RNA - - TISSUE - - MIXED - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - trialDbId: - type: string - trialName: - type: string - trialPUI: - type: string - description: "A Plate represents the metadata for a collection of Samples. The\ - \ physical Plate being represented might be a plastic tray full of Samples,\ - \ or a group of Samples stored in individual containers ie bags, test tubes,\ - \ etc. Whatever the container is, the Samples in a Plate should be related\ - \ by the same physical space, though they may or may not be related as part\ - \ of the same experiment or analysis." - PlateSearchRequest: - type: object - properties: {} - description: "A Plate represents the metadata for a collection of Samples. The\ - \ physical Plate being represented might be a plastic tray full of Samples,\ - \ or a group of Samples stored in individual containers ie bags, test tubes,\ - \ etc. Whatever the container is, the Samples in a Plate should be related\ - \ by the same physical space, though they may or may not be related as part\ - \ of the same experiment or analysis." - PositionCoordinateType: - type: string - description: "The type of positional coordinate. Must be one of the following\ - \ values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location\ - \ Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84\ - \ geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW\ - \ - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical\ - \ counted number, could be independent or within a planted row \n\nGRID_ROW\ - \ - The row index number of a square grid overlay \n\nGRID_COL - The column\ - \ index number of a square grid overlay \n\nMEASURED_ROW - The distance in\ - \ meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters\ - \ from a defined 0-th column " - enum: - - LONGITUDE - - LATITUDE - - PLANTED_ROW - - PLANTED_INDIVIDUAL - - GRID_ROW - - GRID_COL - - MEASURED_ROW - - MEASURED_COL - Reference: - required: - - referenceDbId - - referenceName - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - isDerived: - type: boolean - length: + description: The Uniquely Identifiable name of a `LinkageGroup`
This + might be a chromosome identifier or the generic linkage group identifier + if the chromosome is not applicable. + nullable: true + example: Chromosome 3 + markerCount: type: integer + description: The number of markers associated with a `LinkageGroup`. format: int32 - md5checksum: - type: string - referenceDbId: - type: string - referenceName: - type: string - referenceSetDbId: - type: string - referenceSetName: - type: string - sourceDivergence: - type: number - sourceGermplasmDbIds: + nullable: true + example: 150 + maxPosition: + type: integer + description: The maximum position of a marker within a `LinkageGroup`. + format: int32 + nullable: true + example: 2500 + description: "a `LinkageGroup` is the generic term for a named section of a\ + \ `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage\ + \ Group." + ListRequest: + type: object + properties: + commonCropNames: type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." items: type: string - sourceURI: - type: string - species: - $ref: "#/components/schemas/OntologyTerm" - variantDbIds: + dateCreatedRangeEnd: + type: string + description: Define the end for an interval of time and only include Lists + that are created within this interval. + format: date-time + dateCreatedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are created within this interval. + format: date-time + dateModifiedRangeEnd: + type: string + description: Define the end for an interval of time and only include Lists + that are modified within this interval. + format: date-time + dateModifiedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are modified within this interval. + format: date-time + listDbIds: type: array + description: An array of primary database identifiers to identify a set + of Lists items: type: string - description: "A `Reference` is a canonical assembled contig, intended to act\ - \ as a reference coordinate space for other genomic annotations. A single\ - \ `Reference` might represent the human chromosome 1, for instance. `References`\ - \ are designed to be immutable." - ReferenceSearchRequest: + listNames: + type: array + description: An array of human readable names to identify a set of Lists + items: + type: string + listOwnerNames: + type: array + description: An array of names for the people or entities who are responsible + for a set of Lists + items: + type: string + listOwnerPersonDbIds: + type: array + description: An array of primary database identifiers to identify people + or entities who are responsible for a set of Lists + items: + type: string + listSources: + type: array + description: "An array of terms identifying lists from different sources\ + \ (ie 'USER', 'SYSTEM', etc)" + items: + type: string + listType: + $ref: "#/components/schemas/ListType" + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + LocationParameters: type: object properties: - isDerived: - type: boolean - maxLength: - type: integer - format: int32 - minLength: - type: integer - format: int32 - description: "A `Reference` is a canonical assembled contig, intended to act\ - \ as a reference coordinate space for other genomic annotations. A single\ - \ `Reference` might represent the human chromosome 1, for instance. `References`\ - \ are designed to be immutable." - ReferenceSet: - required: - - referenceSetDbId - - referenceSetName + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + LocationRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - assemblyPUI: - type: string - commonCropName: - type: string - description: - type: string - isDerived: - type: boolean - md5checksum: - type: string - referenceDbId: - type: string - referenceName: - type: string - referenceSetName: - type: string - sourceGermplasmDbIds: + abbreviations: type: array + description: A list of shortened human readable names for a set of Locations items: type: string - sourceURI: - type: string - species: - $ref: "#/components/schemas/OntologyTerm" - variantDbIds: + altitudeMax: + type: number + description: The maximum altitude to search for + example: 200 + altitudeMin: + type: number + description: The minimum altitude to search for + example: 20 + commonCropNames: type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." items: type: string - variantSetDbIds: + coordinates: + $ref: "#/components/schemas/GeoJSONSearchArea" + countryCodes: type: array + description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ + \ spec" items: type: string - description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ - \ a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common\ - \ coordinate space for comparing reference-aligned experimental data." - ReferenceSetNewRequest: - required: - - referenceSetDbId - - referenceSetDbId - - referenceSetName + countryNames: + type: array + description: The full name of the country to search for + items: + type: string + instituteAddresses: + type: array + description: The street address of the institute to search for + items: + type: string + instituteNames: + type: array + description: The name of the institute to search for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + locationTypes: + type: array + description: "The type of location this represents (ex. Breeding Location,\ + \ Storage Location, etc)" + items: + type: string + parentLocationDbIds: + type: array + description: "The unique identifier for a Location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + items: + type: string + parentLocationNames: + type: array + description: "A human readable name for a location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + MarkerPosition: type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" - assemblyPUI: - type: string - commonCropName: - type: string - description: - type: string - isDerived: - type: boolean - md5checksum: + linkageGroupName: type: string - referenceDbId: + description: |- + The Uniquely Identifiable name of a `LinkageGroup` +
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable. + nullable: true + mapDbId: type: string - referenceName: + mapName: type: string - referenceSetDbId: + mapPUI: type: string - referenceSetName: + position: + type: integer + description: The position of a marker or variant within a `LinkageGroup` + format: int32 + nullable: true + variantDbId: type: string - sourceGermplasmDbIds: + description: A MarkerPosition describes a particular genetic marker at a specific + position on a GenomeMap. A collection of MarkerPositions make up the data + to represent a full GenomeMap. + MarkerPositionRequest: + type: object + properties: + linkageGroupNames: type: array + description: A list of Uniquely Identifiable linkage group names items: type: string - sourceURI: - type: string - species: - $ref: "#/components/schemas/OntologyTerm" - variantDbIds: + mapDbIds: type: array + description: A list of IDs which uniquely identify `GenomeMaps` within the + given database server items: type: string - variantSetDbIds: + maxPosition: + type: integer + description: The maximum position of markers in a given map + format: int32 + example: 4000 + minPosition: + type: integer + description: The minimum position of markers in a given map + format: int32 + example: 250 + variantDbIds: type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server items: type: string - description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ - \ a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common\ - \ coordinate space for comparing reference-aligned experimental data." - ReferenceSetSearchRequest: - type: object - properties: {} - description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ - \ a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common\ - \ coordinate space for comparing reference-aligned experimental data." - Sample: - required: - - sampleDbId - - sampleName + MarkerPositionSearchRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - callSetDbIds: + linkageGroupNames: type: array + description: A list of Uniquely Identifiable linkage group names items: type: string - column: - type: integer - format: int32 - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - observationUnitDbId: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string - plateDbId: - type: string - plateName: - type: string - programDbId: - type: string - programName: - type: string - row: - type: string - sampleBarcode: - type: string - sampleDescription: - type: string - sampleGroupId: - type: string - sampleName: - type: string - samplePUI: - type: string - sampleTimestamp: - type: string - sampleType: - type: string - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - takenBy: - type: string - tissueType: - type: string - trialDbId: - type: string - trialName: - type: string - trialPUI: - type: string - well: - type: string - description: "The identifiers and metadata associated with a physical piece\ - \ of biological material collected from the field for external analysis. A\ - \ Sample can take many forms (leaf clipping, seed, DNA, etc) and might be\ - \ used for a variety of analysis procedures (spectra, genotyping, etc)." - SampleNewRequest: - required: - - sampleDbId - - sampleName - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - callSetDbIds: + variantDbIds: type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server items: type: string - column: + mapDbIds: + type: array + description: A list of IDs which uniquely identify `GenomeMaps` within the + given database server + items: + type: string + maxPosition: type: integer + description: The maximum position of markers in a given map format: int32 - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - observationUnitDbId: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string - plateDbId: - type: string - plateName: - type: string - programDbId: - type: string - programName: - type: string - row: - type: string - sampleBarcode: - type: string - sampleDbId: - type: string - sampleDescription: - type: string - sampleGroupId: - type: string - sampleName: - type: string - samplePUI: - type: string - sampleTimestamp: - type: string - sampleType: - type: string - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - takenBy: - type: string - tissueType: - type: string - trialDbId: - type: string - trialName: - type: string - trialPUI: - type: string - well: - type: string - description: "The identifiers and metadata associated with a physical piece\ - \ of biological material collected from the field for external analysis. A\ - \ Sample can take many forms (leaf clipping, seed, DNA, etc) and might be\ - \ used for a variety of analysis procedures (spectra, genotyping, etc)." - SampleSearchRequest: - type: object - properties: {} - description: "The identifiers and metadata associated with a physical piece\ - \ of biological material collected from the field for external analysis. A\ - \ Sample can take many forms (leaf clipping, seed, DNA, etc) and might be\ - \ used for a variety of analysis procedures (spectra, genotyping, etc)." - Scale: - required: - - scaleDbId - - scaleName - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - dataType: - type: string - description: |- -

Class of the scale, entries can be

-

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

-

"Date" - The date class is for events expressed in a time format, See ISO 8601

-

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

-

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

-

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

-

"Ordinal" - Ordinal scales are scales composed of ordered categories

-

"Text" - A free text is used to express the trait.

- enum: - - Code - - Date - - Duration - - Nominal - - Numerical - - Ordinal - - Text - decimalPlaces: + example: 4000 + minPosition: type: integer + description: The minimum position of markers in a given map format: int32 - ontologyReferenceDbId: - type: string - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string - units: - type: string - validValues: - $ref: "#/components/schemas/ValidValues" - description: "A Scale describes the units and acceptable values for an ObservationVariable.\ - \ \n
For example, an ObservationVariable might be defined with a Trait\ - \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ - . This variable would be distinct from a variable with the Scale \"inches\"\ - \ or \"pixels\"." - Trait: - required: - - traitName - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - attribute: - type: string - attributePUI: - type: string - entity: - type: string - entityPUI: - type: string - mainAbbreviation: - type: string - ontologyReferenceDbId: - type: string - status: - type: string - traitClass: - type: string - traitDbId: - type: string - traitDescription: - type: string - traitName: - type: string - traitPUI: - type: string - description: "A Trait describes what property is being observed. \n
For example,\ - \ an ObservationVariable might be defined with a Trait of \"plant height\"\ - , a Scale of \"meters\", and a Method of \"tape measure\". This variable would\ - \ be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\"\ - . " - TraitDataType: - type: string - description: |- -

Class of the scale, entries can be

-

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

-

"Date" - The date class is for events expressed in a time format, See ISO 8601

-

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

-

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

-

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

-

"Ordinal" - Ordinal scales are scales composed of ordered categories

-

"Text" - A free text is used to express the trait.

- enum: - - Code - - Date - - Duration - - Nominal - - Numerical - - Ordinal - - Text - ValidValues: + example: 250 + description: A MarkerPosition describes a particular genetic marker at a specific + position on a GenomeMap. A collection of MarkerPositions make up the data + to represent a full GenomeMap. + MetadataField: type: object properties: - maximumValue: + dataType: type: string - minimumValue: + description: The type of field represented in this Genotype Field. This + is intended to help parse the data out of JSON. + nullable: true + enum: + - string + - integer + - float + - boolean + fieldAbbreviation: type: string - scaleDbId: + description: "The abbreviated code of the field represented in this Genotype\ + \ Field. These codes should match the VCF standard when possible. Examples\ + \ include: \"GQ\", \"RD\", and \"HQ\"" + nullable: true + fieldName: type: string - scaleName: + description: "The name of the field represented in this Genotype Field.\ + \ Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype\ + \ Quality\"" + nullable: true + variantSetDbId: type: string - scalePUI: + variantSetName: type: string - description: Metadata describing the acceptable values for this Scale - Variable: - required: - - method - - scale - - trait + description: "Indicates which types of genotyping data and metadata are available\ + \ in the VariantSet. \n
When possible, these field names and abbreviations\ + \ should follow the VCF standard " + MethodRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - contextOfUse: + commonCropNames: type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." items: type: string - defaultValue: - type: string - documentationURL: - type: string - growthStage: - type: string - institution: - type: string - language: - type: string - method: - $ref: "#/components/schemas/Method" - ontologyReference: - $ref: "#/components/schemas/OntologyReference" - scale: - $ref: "#/components/schemas/Scale" - scientist: - type: string - status: - type: string - submissionTimestamp: - type: string - synonyms: + methodDbIds: type: array + description: The unique identifier for a method. items: type: string - trait: - $ref: "#/components/schemas/Trait" - description: "A unique combination of Trait, Method, and Scale to define a clear\ - \ context for an Observation." - Variant: - required: - - variantDbId + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + ObservationRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - created: - type: string - end: - type: integer - format: int32 - filtersApplied: - type: boolean - filtersPassed: - type: boolean - referenceBases: - type: string - referenceDbId: - type: string - referenceName: - type: string - referenceSetDbId: - type: string - referenceSetName: - type: string - start: - type: integer - format: int32 - svlen: - type: integer - format: int32 - updated: - type: string - variantDbId: - type: string - variantSetDbId: - type: string - variantSetName: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationDbIds: + type: array + description: The unique id of an Observation + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationTimeStampRangeEnd: type: string - variantType: + description: Timestamp range end + format: date-time + observationTimeStampRangeStart: type: string - description: "A `Variant` represents a change in DNA sequence relative to some\ - \ reference. For example, a variant could represent a classic marker, a SNP,\ - \ or an insertion. This is equivalent to a row in VCF." - VariantSearchRequest: + description: Timestamp range start + format: date-time + observationUnitDbIds: + type: array + description: The unique id of an Observation Unit + items: + type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ObservationUnitHierarchyLevel: type: object properties: - end: - type: integer - format: int32 - referenceDbId: + levelName: type: string - start: + description: "A name for this level \n\n**Standard Level Names: study, field,\ + \ entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\ + \nFor more information on Observation Levels, please review the Observation Levels documentation. " + nullable: true + levelOrder: type: integer + description: "`levelOrder` defines where that level exists in the hierarchy\ + \ of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy\ + \ (ie field -> 1) and higher numbers are at the bottom of the hierarchy\ + \ (ie plant -> 9). \n\nFor more information on Observation Levels, please\ + \ review the Observation Levels documentation. " format: int32 - description: "A `Variant` represents a change in DNA sequence relative to some\ - \ reference. For example, a variant could represent a classic marker, a SNP,\ - \ or an insertion. This is equivalent to a row in VCF." - VariantSet: - required: - - variantSetDbId + nullable: true + description: "The exact level and level code of an observation unit. \n\nFor\ + \ more information on Observation Levels, please review the Observation\ + \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ + Type of observation unit in textual form, usually one of the following: study,\ + \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ + \ types is possible but not recommended. \nThe observation unit type can not\ + \ be used to indicate sub-plant levels. However, observations can still be\ + \ made on the sub-plant level, as long as the details are indicated in the\ + \ associated observed variable (see observed variables). \nAlternatively,\ + \ it is possible to use samples for more detailed tracing of sub-plant units,\ + \ attaching the observations to them instead.\" " + ObservationUnitRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - analysiDbIds: + commonCropNames: type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." items: type: string - callSetCount: - type: integer - format: int32 - referenceSetDbId: - type: string - referenceSetName: - type: string - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - variantCount: - type: integer - format: int32 - variantSetDbId: - type: string - variantSetName: - type: string - description: A VariantSet is a collection of variants and variant calls intended - to be analyzed together. - VariantSetSearchRequest: - type: object - properties: {} - description: A VariantSet is a collection of variants and variant calls intended - to be analyzed together. - basePagination: - required: - - currentPage - - pageSize - type: object - properties: - currentPage: - type: integer - description: The index number for the returned page of data. This should - always match the requested page number or the default page (0). - example: 0 - default: 0 - pageSize: - type: integer - description: "The number of data elements returned, aka the size of the\ - \ current page. If the requested page does not have enough elements to\ - \ fill a page at the requested page size, this field should indicate the\ - \ actual number of elements returned." - example: 1000 - default: 1000 - totalCount: - type: integer - description: The total number of elements that are available on the server - and match the requested query parameters. - example: 10 - totalPages: - type: integer - description: "The total number of pages of elements available on the server.\ - \ This should be calculated with the following formula. \n
totalPages\ - \ = CEILING( totalCount / requested_page_size)" - example: 1 - description: "The pagination object is applicable only when the payload contains\ - \ a \"data\" key. It describes the pagination of the data contained in the\ - \ \"data\" array, as a way to identify which subset of data is being returned.\ - \ \n
Pages are zero indexed, so the first page will be page 0 (zero)." - dataFile: - required: - - fileURL - type: object - properties: - fileURL: - type: string - description: The absolute URL where the file is located - format: uri - example: https://wiki.brapi.org/examples/datafile.xlsx - fileName: - type: string - description: The name of the file - example: datafile.xlsx - fileSize: - type: integer - description: The size of the file in bytes - example: 4398 - fileDescription: - type: string - description: A human readable description of the file contents - example: This is an Excel data file - fileType: - type: string - description: The type or format of the file. Preferably MIME Type. - example: application/vnd.ms-excel - fileMD5Hash: - type: string - description: The MD5 Hash of the file contents to be used as a check sum - example: c2365e900c81a89cf74d83dab60df146 - description: A dataFile contains a URL and the relevant file metadata to represent - a file - metadata: - allOf: - - $ref: "#/components/schemas/metadataBase" - - type: object - properties: - pagination: - $ref: "#/components/schemas/basePagination" - metadataBase: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + includeObservations: + type: boolean + description: "Use this parameter to include a list of observations embedded\ + \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ + \ your own risk. It may return large, unpaginated lists of observation\ + \ data. Only set this value to True if you are sure you need to." + example: false + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationUnitDbIds: + type: array + description: The unique id of an observation unit + items: + type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitNames: + type: array + description: The human readable identifier for an Observation Unit + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ObservationVariableParameters: type: object properties: - datafiles: + observationVariableDbIds: type: array - description: "The datafiles contains a list of file URLs and metadata. \n\ - These files contain additional information related to the returned object\ - \ and can be retrieved by a subsequent call. \nThis could be a supplementary\ - \ data file, an informational file, the uploaded file where the data originated\ - \ from, a generated file representing the whole dataset in a particular\ - \ format, or any other related file. " - example: [] + description: The DbIds of Variables to search for items: - $ref: "#/components/schemas/dataFile" - status: + type: string + observationVariableNames: type: array - description: "The status field contains a list of informational status messages\ - \ from the server. \nIf no status is reported, an empty list should be\ - \ returned. See Error Reporting for more information." + description: The names of Variables to search for items: - $ref: "#/components/schemas/status" - description: "An object in the BrAPI standard response model that describes\ - \ some information about the service call being performed. This includes supplementary\ - \ data, status log messages, and pagination information." - metadataTokenPagination: - allOf: - - $ref: "#/components/schemas/metadataBase" - - type: object - properties: - pagination: - $ref: "#/components/schemas/tokenPagination" - status: - required: - - message - - messageType + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + ObservationVariableRequest: type: object properties: - message: - type: string - description: A short message concerning the status of this request/response - example: "Request accepted, response successful" - messageType: - type: string - description: The logging level for the attached message - example: INFO - enum: - - DEBUG - - ERROR - - WARNING - - INFO - description: An array of status messages to convey technical logging information - from the server to the client. - tokenPagination: - allOf: - - $ref: "#/components/schemas/basePagination" - - required: - - nextPageToken - type: object - properties: - nextPageToken: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: type: string - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The string token used to query the next page of data." - example: cb668f63 - deprecated: true - currentPageToken: + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodDbIds: + type: array + description: List of methods to filter search results + items: type: string - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The string token used to query the current page of data." - example: 48bc6ac1 - deprecated: true - prevPageToken: + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: type: string - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The string token used to query the previous page of data." - example: 9659857e - deprecated: true - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The pagination object is applicable only when the payload contains\ - \ a \"data\" key. It describes the pagination of the data contained in the\ - \ \"data\" array, as a way to identify which subset of data is being returned.\ - \ \n
Tokenized pages are for large data sets which can not be efficiently\ - \ broken into indexed pages. Use the nextPageToken and prevPageToken to\ - \ construct an additional query and move to the next or previous page respectively.\ - \ " - example: - currentPage: 0 - pageSize: 1000 - totalCount: 10 - totalPages: 1 - responses: - SeedLotSingleResponse: - description: OK - content: - application/json: - schema: - title: SeedLotSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/SeedLot" - VariantSingleResponse: - description: OK - content: - application/json: - schema: - title: VariantSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/Variant" - "202AcceptedSearchResponse": - description: Accepted - content: - application/json: - schema: - title: 202AcceptedSearchResponse - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - type: object - properties: - searchResultsDbId: - type: string - example: 551ae08c - StudySingleResponse: - description: OK - content: - application/json: - schema: - title: StudySingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/Study" - MarkerPositionListResponse: - description: OK - content: - application/json: - schema: - title: MarkerPositionListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/MarkerPosition" - TrialListResponse: - description: OK - content: - application/json: - schema: - title: TrialListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Trial" - SeedLotListResponse: - description: OK - content: - application/json: - schema: - title: SeedLotListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/SeedLot" - VariantSetListResponse: - description: OK - content: - application/json: - schema: - title: VariantSetListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/VariantSet" - SampleSingleResponse: - description: OK - content: - application/json: - schema: - title: SampleSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/Sample" - CallSetListResponse: - description: OK - content: - application/json: - schema: - title: CallSetListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/CallSet" - CallSetSingleResponse: - description: OK - content: - application/json: - schema: - title: CallSetSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/CallSet" - VariantSetSingleResponse: - description: OK + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + OntologyParameters: + type: object + properties: + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + OntologyRequest: + type: object + properties: + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + ontologyNames: + type: array + description: The human readable identifier for an ontology definition. + items: + type: string + OntologyTerm: + type: object + properties: + term: + type: string + description: Ontology term - the label of the ontology term the termId is + pointing to. + nullable: true + termURI: + type: string + description: Ontology term identifier - the CURIE for an ontology term. + It differs from the standard GA4GH schema's :ref:`id ` in that it is a + CURIE pointing to an information resource outside of the scope of the + schema or its resource implementation. + nullable: true + description: A pointer to an ontology used by a genomic reference + Pagination: + type: object + properties: + dimension: + type: string + description: The dimension of the matrix being paginated + nullable: true + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + nullable: true + pageSize: + type: integer + description: the maximum number of elements per page in this dimension of + the matrix + format: int32 + nullable: true + totalCount: + type: integer + description: The total number of elements that are available on the server + and match the requested query parameters. + format: int32 + nullable: true + totalPages: + type: integer + description: "The total number of pages of elements available on the server.\ + \ This should be calculated with the following formula. \n
totalPages\ + \ = CEILING( totalCount / requested_page_size)" + format: int32 + nullable: true + description: Pagination info for the matrix + PedigreeNodeRequest: + type: object + properties: + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + items: + type: string + includeFullTree: + type: boolean + description: "If this parameter is true, recursively include ALL of the\ + \ nodes available in this pedigree tree" + example: true + includeParents: + type: boolean + description: "If this parameter is true, include the array of parents in\ + \ the response" + example: true + includeProgeny: + type: boolean + description: "If this parameter is true, include the array of progeny in\ + \ the response" + example: true + includeSiblings: + type: boolean + description: "If this parameter is true, include the array of siblings in\ + \ the response" + example: true + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + items: + type: string + pedigreeDepth: + type: integer + description: "Recursively include this number of levels up the tree in the\ + \ response (parents, grand-parents, great-grand-parents, etc)" + format: int32 + example: 3 + progenyDepth: + type: integer + description: "Recursively include this number of levels down the tree in\ + \ the response (children, grand-children, great-grand-children, etc)" + format: int32 + example: 3 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + PersonRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + emailAddresses: + type: array + description: email address for this person + items: + type: string + firstNames: + type: array + description: Persons first name + items: + type: string + lastNames: + type: array + description: Persons last name + items: + type: string + mailingAddresses: + type: array + description: physical address of this person + items: + type: string + middleNames: + type: array + description: Persons middle name + items: + type: string + personDbIds: + type: array + description: Unique ID for this person + items: + type: string + phoneNumbers: + type: array + description: phone number of this person + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + userIDs: + type: array + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + items: + type: string + PlannedCrossRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + plannedCrossDbIds: + type: array + description: Search for Planned Cross with this unique id + items: + type: string + plannedCrossNames: + type: array + description: Search for Planned Cross with this human readable name + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + statuses: + type: array + description: "The status of this planned cross. Is it waiting to be performed\ + \ ('TODO'), has it been completed successfully ('DONE'), or has it not\ + \ been done on purpose ('SKIPPED')." + items: + type: string + enum: + - TODO + - DONE + - SKIPPED + Plate: + allOf: + - $ref: "#/components/schemas/PlateNewRequest" + - type: object + properties: + plateDbId: + type: string + description: The ID which uniquely identifies a `Plate` + description: "A Plate represents the metadata for a collection of Samples.\ + \ The physical Plate being represented might be a plastic tray full of Samples,\ + \ or a group of Samples stored in individual containers ie bags, test tubes,\ + \ etc. Whatever the container is, the Samples in a Plate should be related\ + \ by the same physical space, though they may or may not be related as part\ + \ of the same experiment or analysis." + PlateFormat: + type: string + description: "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate\ + \ or \"TUBES\" for plateless format" + enum: + - PLATE_96 + - TUBES + PlateNewRequest: + required: + - plateName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + plateBarcode: + type: string + description: A unique identifier physically attached to a `Plate` + nullable: true + plateFormat: + type: string + description: "Enum for plate formats, usually \"PLATE_96\" for a 96 well\ + \ plate or \"TUBES\" for plateless format" + nullable: true + enum: + - PLATE_96 + - TUBES + plateName: + type: string + description: A human readable name for a `Plate` + programDbId: + type: string + programName: + type: string + sampleType: + type: string + description: "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" + nullable: true + enum: + - DNA + - RNA + - TISSUE + - MIXED + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + description: "A Plate represents the metadata for a collection of Samples. The\ + \ physical Plate being represented might be a plastic tray full of Samples,\ + \ or a group of Samples stored in individual containers ie bags, test tubes,\ + \ etc. Whatever the container is, the Samples in a Plate should be related\ + \ by the same physical space, though they may or may not be related as part\ + \ of the same experiment or analysis." + PlateRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit + items: + type: string + plateBarcodes: + type: array + description: A unique identifier physically attached to the plate + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a plate of samples + items: + type: string + plateNames: + type: array + description: The human readable name of a plate of samples + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a sample + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related Samples + items: + type: string + sampleNames: + type: array + description: The human readable name of the sample + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + PlateSearchRequest: + type: object + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit + items: + type: string + plateBarcodes: + type: array + description: A unique identifier physically attached to the plate + items: + type: string + plateNames: + type: array + description: The human readable name of a plate of samples + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a sample + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a plate of samples + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related Samples + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + sampleNames: + type: array + description: The human readable name of the sample + items: + type: string + description: "A Plate represents the metadata for a collection of Samples. The\ + \ physical Plate being represented might be a plastic tray full of Samples,\ + \ or a group of Samples stored in individual containers ie bags, test tubes,\ + \ etc. Whatever the container is, the Samples in a Plate should be related\ + \ by the same physical space, though they may or may not be related as part\ + \ of the same experiment or analysis." + ProgramParameters: + type: object + properties: + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + ProgramRequest: + type: object + properties: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Programs + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + leadPersonDbIds: + type: array + description: The person DbIds of the program leader to search for + items: + type: string + leadPersonNames: + type: array + description: The names of the program leader to search for + items: + type: string + objectives: + type: array + description: A program objective to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + programTypes: + type: array + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding " + items: + type: string + description: |- + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding. + enum: + - STANDARD + - PROJECT + Reference: + required: + - referenceDbId + - referenceName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + description: Common name for the crop + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + isDerived: + type: boolean + description: "A sequence X is said to be derived from source sequence Y,\ + \ if X and Y are of the same length and the per-base sequence divergence\ + \ at A/C/G/T bases is sufficiently small. Two sequences derived from the\ + \ same official sequence share the same coordinates and annotations, and\ + \ can be replaced with the official sequence for certain use cases." + nullable: true + length: + type: integer + description: The length of this `Reference` sequence. + format: int32 + nullable: true + md5checksum: + type: string + description: "The MD5 checksum uniquely representing this `Reference` as\ + \ a lower-case hexadecimal string, calculated as the MD5 of the upper-case\ + \ sequence excluding all whitespace characters (this is equivalent to\ + \ SQ:M5 in SAM)." + nullable: true + referenceDbId: + type: string + description: The unique identifier for a `Reference` + referenceName: + type: string + description: The human readable name of a `Reference` within a `ReferenceSet`. + referenceSetDbId: + type: string + referenceSetName: + type: string + sourceAccessions: + type: array + description: "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ)\ + \ which must include a version number, e.g. `GCF_000001405.26`." + nullable: true + items: + type: string + sourceDivergence: + type: number + description: The `sourceDivergence` is the fraction of non-indel bases that + do not match the `Reference` this message was derived from. + nullable: true + sourceGermplasmDbIds: + type: array + description: All known corresponding Germplasm + nullable: true + items: + type: string + sourceURI: + type: string + description: "The URI from which the sequence was obtained. Specifies a\ + \ FASTA format file/string with one name, sequence pair. In most cases,\ + \ clients should call the `getReferenceBases()` method to obtain sequence\ + \ bases for a `Reference` instead of attempting to retrieve this URI." + nullable: true + species: + $ref: "#/components/schemas/OntologyTerm" + variantDbIds: + type: array + description: variants + nullable: true + items: + type: string + description: "A `Reference` is a canonical assembled contig, intended to act\ + \ as a reference coordinate space for other genomic annotations. A single\ + \ `Reference` might represent the human chromosome 1, for instance. `References`\ + \ are designed to be immutable." + ReferenceBases: + type: object + properties: + nextPageToken: + type: string + description: "The continuation token, which is used to page through large\ + \ result sets. Provide this value in a subsequent request to return the\ + \ next page of results. This field will be empty if there are not any\ + \ additional results." + nullable: true + example: 3a3d658a + offset: + type: integer + description: The offset position (0-based) of the given sequence from the + start of this `Reference`. This value will differ for each page in a request. + format: int32 + nullable: true + example: 20000 + sequence: + type: string + description: "A sub-string of the bases that make up this reference. Bases\ + \ are represented as IUPAC-IUB codes; this string matches the regular\ + \ expression `[ACGTMRWSYKVHDBN]*`." + nullable: true + example: TAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATAT + description: A string representation of the `Reference` base alleles. + ReferenceBasesRequest: + type: object + properties: + end: + type: integer + description: "The end position (0-based, exclusive) of this query. Defaults\ + \ to the length of this `Reference`." + format: int32 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + start: + type: integer + description: |- + The start position (0-based) of this query. Defaults to 0. + Genomic positions are non-negative integers less than reference length. + Requests spanning the join of circular genomes are represented as + two requests one on each side of the join (position 0). + format: int32 + ReferenceRequest: + type: object + properties: + accessions: + type: array + description: "If specified, return the references for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + isDerived: + type: boolean + description: "A sequence X is said to be derived from source sequence Y,\ + \ if X and Y are of the same length and the per-base sequence divergence\ + \ at A/C/G/T bases is sufficiently small. Two sequences derived from the\ + \ same official sequence share the same coordinates and annotations, and\ + \ can be replaced with the official sequence for certain use cases." + format: boolean + maxLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 90000 + md5checksums: + type: array + description: "If specified, return the references for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + minLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 4000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: A list of IDs which uniquely identify `References` within the + given database server + items: + type: string + referenceSetDbIds: + type: array + description: A list of IDs which uniquely identify `ReferenceSets` within + the given database server + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ReferenceSearchRequest: + type: object + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + isDerived: + type: boolean + description: "A sequence X is said to be derived from source sequence Y,\ + \ if X and Y are of the same length and the per-base sequence divergence\ + \ at A/C/G/T bases is sufficiently small. Two sequences derived from the\ + \ same official sequence share the same coordinates and annotations, and\ + \ can be replaced with the official sequence for certain use cases." + format: boolean + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + minLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 4000 + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + referenceSetDbIds: + type: array + description: A list of IDs which uniquely identify `ReferenceSets` within + the given database server + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + md5checksums: + type: array + description: "If specified, return the references for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + referenceDbIds: + type: array + description: A list of IDs which uniquely identify `References` within the + given database server + items: + type: string + accessions: + type: array + description: "If specified, return the references for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + maxLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 90000 + description: "A `Reference` is a canonical assembled contig, intended to act\ + \ as a reference coordinate space for other genomic annotations. A single\ + \ `Reference` might represent the human chromosome 1, for instance. `References`\ + \ are designed to be immutable." + ReferenceSet: + allOf: + - $ref: "#/components/schemas/ReferenceSetNewRequest" + - required: + - referenceSetDbId + type: object + properties: + referenceSetDbId: + type: string + description: The unique identifier for a ReferenceSet + description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ + \ a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common\ + \ coordinate space for comparing reference-aligned experimental data." + ReferenceSetNewRequest: + required: + - referenceSetName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + assemblyPUI: + type: string + description: "The remaining information is about the source of the sequences\ + \ Public id of this reference set, such as `GRCH_37`." + nullable: true + commonCropName: + type: string + description: Common name for the crop + nullable: true + description: + type: string + description: Optional free text description of this reference set. + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + isDerived: + type: boolean + description: "A reference set may be derived from a source if it contains\ + \ additional sequences, or some of the sequences within it are derived\ + \ (see the definition of `isDerived` in `Reference`)." + nullable: true + md5checksum: + type: string + description: |- + Order-independent MD5 checksum which identifies this `ReferenceSet`. + + To compute this checksum, make a list of `Reference.md5checksum` for all + `Reference` s in this set. Then sort that list, and take the MD5 hash of + all the strings concatenated together. Express the hash as a lower-case + hexadecimal string. + nullable: true + referenceDbId: + type: string + referenceName: + type: string + referenceSetName: + type: string + description: The human readable name of a ReferenceSet + sourceAccessions: + type: array + description: "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ)\ + \ ideally with a version number, e.g. `NC_000001.11`." + nullable: true + items: + type: string + sourceGermplasmDbIds: + type: array + description: All known corresponding Germplasm + nullable: true + items: + type: string + sourceURI: + type: string + description: Specifies a FASTA format file/string. + nullable: true + species: + $ref: "#/components/schemas/OntologyTerm" + variantDbIds: + type: array + description: variants + nullable: true + items: + type: string + variantSetDbIds: + type: array + description: variantSets + nullable: true + items: + type: string + description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ + \ a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common\ + \ coordinate space for comparing reference-aligned experimental data." + ReferenceSetRequest: + type: object + properties: + accessions: + type: array + description: "If set, return the reference sets for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + assemblyPUIs: + type: array + description: "If set, return the reference sets for which the `assemblyId`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + md5checksums: + type: array + description: "If set, return the reference sets for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceSetDbIds: + type: array + description: The `ReferenceSets` to search. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ReferenceSetSearchRequest: + type: object + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + referenceSetDbIds: + type: array + description: The `ReferenceSets` to search. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + md5checksums: + type: array + description: "If set, return the reference sets for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + assemblyPUIs: + type: array + description: "If set, return the reference sets for which the `assemblyId`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + accessions: + type: array + description: "If set, return the reference sets for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ + \ a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common\ + \ coordinate space for comparing reference-aligned experimental data." + Sample: + allOf: + - $ref: "#/components/schemas/SampleNewRequest" + - type: object + properties: + sampleDbId: + type: string + description: |- + The ID which uniquely identifies a `Sample` +
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample. + nullable: true + description: "The identifiers and metadata associated with a physical piece\ + \ of biological material collected from the field for external analysis.\ + \ A Sample can take many forms (leaf clipping, seed, DNA, etc) and might\ + \ be used for a variety of analysis procedures (spectra, genotyping, etc)." + SampleNewRequest: + required: + - sampleName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + callSetDbIds: + type: array + description: "" + nullable: true + items: + type: string + column: + type: integer + description: The Column identifier for this `Sample` location in the `Plate` + format: int32 + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + observationUnitDbId: + type: string + observationUnitName: + type: string + observationUnitPUI: + type: string + plateDbId: + type: string + plateName: + type: string + programDbId: + type: string + programName: + type: string + row: + type: string + description: The Row identifier for this `Sample` location in the `Plate` + nullable: true + sampleBarcode: + type: string + description: A unique identifier physically attached to the `Sample` + nullable: true + sampleDescription: + type: string + description: |- + Description of a `Sample` +
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing. + nullable: true + sampleGroupId: + type: string + description: The ID which uniquely identifies a group of `Samples` + nullable: true + sampleName: + type: string + description: The human readable name of the `Sample` + samplePUI: + type: string + description: "A permanent unique identifier for the `Sample` (DOI, URL,\ + \ UUID, etc)\n
MIAPPE V1.1 (DM-81) External ID - An identifier for\ + \ the sample in a persistent repository, comprising the name of the repository\ + \ and the accession number of the observation unit therein. Submission\ + \ to the EBI Biosamples repository is recommended. URI are recommended\ + \ when possible. " + nullable: true + sampleTimestamp: + type: string + description: |- + The date and time a `Sample` was collected from the field +
MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested + format: date-time + nullable: true + sampleType: + type: string + description: "The type of `Sample` taken. ex. 'DNA', 'RNA', 'Tissue', etc" + nullable: true + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + takenBy: + type: string + description: The name or identifier of the entity which took the `Sample` + from the field + nullable: true + tissueType: + type: string + description: |- + The type of tissue sampled. ex. 'Leaf', 'Root', etc. +
MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology). + nullable: true + trialDbId: + type: string + trialName: + type: string + trialPUI: + type: string + well: + type: string + description: "The Well identifier for this `Sample` location in the `Plate`.\ + \ Usually a concatenation of Row and Column, or just a number if the `Samples`\ + \ are not part of an ordered `Plate`." + nullable: true + description: "The identifiers and metadata associated with a physical piece\ + \ of biological material collected from the field for external analysis. A\ + \ Sample can take many forms (leaf clipping, seed, DNA, etc) and might be\ + \ used for a variety of analysis procedures (spectra, genotyping, etc)." + SampleRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an `ObservationUnit` + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a `Plate` of `Samples` + items: + type: string + plateNames: + type: array + description: The human readable name of a `Plate` of `Samples` + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a `Sample` + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related `Samples` + items: + type: string + sampleNames: + type: array + description: The human readable name of the `Sample` + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + SampleSearchRequest: + type: object + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an `ObservationUnit` + items: + type: string + plateNames: + type: array + description: The human readable name of a `Plate` of `Samples` + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a `Sample` + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a `Plate` of `Samples` + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related `Samples` + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + sampleNames: + type: array + description: The human readable name of the `Sample` + items: + type: string + description: "The identifiers and metadata associated with a physical piece\ + \ of biological material collected from the field for external analysis. A\ + \ Sample can take many forms (leaf clipping, seed, DNA, etc) and might be\ + \ used for a variety of analysis procedures (spectra, genotyping, etc)." + SampleType: + type: string + description: "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" + enum: + - DNA + - RNA + - TISSUE + - MIXED + ScaleRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a scale. + items: + type: string + SeasonRequest: + type: object + properties: + seasonDbIds: + type: array + description: "The unique identifier for a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'." + items: + type: string + seasonNames: + type: array + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + items: + type: string + seasons: + type: array + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + items: + type: string + years: + type: array + description: The 4 digit year of a season. Example "2017" + items: + type: string + SeedLotRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seedLotDbIds: + type: array + description: Unique id for a seed lot on this server + items: + type: string + SortBy: + type: string + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + SortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + StudyParameters: + type: object + properties: + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + StudyRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Study is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: The ID which uniquely identifies a season + items: + type: string + sortBy: + type: string + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + studyCodes: + type: array + description: A short human readable code for a study + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + studyPUIs: + type: array + description: "Permanent unique identifier associated with study data. For\ + \ example, a URI or DOI" + items: + type: string + studyTypes: + type: array + description: "The type of study being performed. ex. \"Yield Trial\", etc" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + TraitDataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + TraitRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a trait. + items: + type: string + TrialParameters: + type: object + properties: + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + TrialRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Trial is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + contactDbIds: + type: array + description: List of contact entities associated with this trial + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + searchDateRangeEnd: + type: string + description: "The end of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + searchDateRangeStart: + type: string + description: "The start of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + sortBy: + type: string + description: Name of the field to sort by. + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + trialPUIs: + type: array + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + items: + type: string + Variable: + required: + - methodDbId + - methodName + - scaleDbId + - scaleName + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true + contextOfUse: + type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true + items: + type: string + defaultValue: + type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true + documentationURL: + type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + growthStage: + type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true + institution: + type: string + description: Name of institution submitting the variable + nullable: true + language: + type: string + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + scientist: + type: string + description: Name of scientist submitting the variable. + nullable: true + status: + type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true + submissionTimestamp: + type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true + synonyms: + type: array + description: Other variable names + nullable: true + items: + type: string + traitDbId: + type: string + traitName: + type: string + traitPUI: + type: string + description: "A unique combination of Trait, Method, and Scale to define a clear\ + \ context for an Observation." + VariableBaseClassParameters: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + Variant: + required: + - variantDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + analysis: + type: array + description: Set of Analysis descriptors for this VariantSet + nullable: true + items: + type: string + ciend: + type: array + description: "Similar to \"cipos\", but for the variant's end position (which\ + \ is derived from start + svlen)." + nullable: true + items: + type: integer + format: int32 + cipos: + type: array + description: |- + In the case of structural variants, start and end of the variant may not + be known with an exact base position. "cipos" provides an interval with + high confidence for the start position. The interval is provided by 0 or + 2 signed integers which are added to the start position. + Based on the use in VCF v4.2 + nullable: true + items: + type: integer + format: int32 + created: + type: string + description: The timestamp when this variant was created. + format: date-time + nullable: true + end: + type: integer + description: "This field is optional and may be ignored if there is no relevant\ + \ map or reference to be associated with.\n
The end position (exclusive),\ + \ resulting in [start, end) closed-open interval. This is typically calculated\ + \ \nby `start + referenceBases.length`." + format: int32 + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + filtersApplied: + type: boolean + description: True if filters were applied for this variant. VCF column 7 + "FILTER" any value other than the missing value. + nullable: true + filtersFailed: + type: array + description: Zero or more filters that failed for this variant. VCF column + 7 "FILTER" shared across all alleles in the same VCF record. + nullable: true + items: + type: string + filtersPassed: + type: boolean + description: True if all filters for this variant passed. VCF column 7 "FILTER" + value PASS. + nullable: true + referenceBases: + type: string + description: The reference bases for this variant. They start at the given + start position. + nullable: true + referenceDbId: + type: string + referenceName: + type: string + referenceSetDbId: + type: string + referenceSetName: + type: string + start: + type: integer + description: "This field is optional and may be ignored if there is no relevant\ + \ map or reference to be associated with.\n
The start position at\ + \ which this variant occurs (0-based). This corresponds to the first base\ + \ of the string \nof reference bases. Genomic positions are non-negative\ + \ integers less than reference length. Variants spanning \nthe join of\ + \ circular genomes are represented as two variants one on each side of\ + \ the join (position 0)." + format: int32 + nullable: true + svlen: + type: integer + description: Length of the - if labeled as such in variant_type - structural + variation. Based on the use in VCF v4.2 + format: int32 + nullable: true + updated: + type: string + description: The time at which this variant was last updated. + format: date-time + nullable: true + variantDbId: + type: string + description: The ID which uniquely identifies a `Variant` + variantNames: + type: array + description: A human readable name associated with a `Variant` + nullable: true + items: + type: string + variantSetDbId: + type: string + variantSetName: + type: string + variantType: + type: string + description: |- + The "variant_type" is used to denote e.g. structural variants. + Examples: + DUP : duplication of sequence following "start" + DEL : deletion of sequence following "start" + nullable: true + description: "A `Variant` represents a change in DNA sequence relative to some\ + \ reference. For example, a variant could represent a classic marker, a SNP,\ + \ or an insertion. This is equivalent to a row in VCF." + VariantRequest: + type: object + properties: + callSetDbIds: + type: array + description: "**Deprecated in v2.1** Parameter unnecessary. Github issue\ + \ number #474 \n
Only return variant calls which belong to call sets\ + \ with these IDs. If unspecified, return all variants and no variant call\ + \ objects." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + end: + type: integer + description: "The end of the window (0-based, exclusive) for which overlapping\ + \ variants should be returned." + format: int32 + example: 1500 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbId: + type: string + description: |- + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + example: 120a2d5c + referenceDbIds: + type: array + description: The unique identifier representing a genotype `Reference` + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype `ReferenceSet` + items: + type: string + start: + type: integer + description: "The beginning of the window (0-based, inclusive) for which\ + \ overlapping variants should be returned. Genomic positions are non-negative\ + \ integers less than reference length. Requests spanning the join of circular\ + \ genomes are represented as two requests one on each side of the join\ + \ (position 0)." + format: int32 + example: 100 + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` + items: + type: string + VariantSearchRequest: + type: object + properties: + referenceDbId: + type: string + description: |- + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + example: 120a2d5c + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + start: + type: integer + description: "The beginning of the window (0-based, inclusive) for which\ + \ overlapping variants should be returned. Genomic positions are non-negative\ + \ integers less than reference length. Requests spanning the join of circular\ + \ genomes are represented as two requests one on each side of the join\ + \ (position 0)." + format: int32 + example: 100 + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype `ReferenceSet` + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + referenceDbIds: + type: array + description: The unique identifier representing a genotype `Reference` + items: + type: string + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` + items: + type: string + end: + type: integer + description: "The end of the window (0-based, exclusive) for which overlapping\ + \ variants should be returned." + format: int32 + example: 1500 + callSetDbIds: + type: array + description: "**Deprecated in v2.1** Parameter unnecessary. Github issue\ + \ number #474 \n
Only return variant calls which belong to call sets\ + \ with these IDs. If unspecified, return all variants and no variant call\ + \ objects." + items: + type: string + description: "A `Variant` represents a change in DNA sequence relative to some\ + \ reference. For example, a variant could represent a classic marker, a SNP,\ + \ or an insertion. This is equivalent to a row in VCF." + VariantSet: + required: + - variantSetDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + analysis: + type: array + description: Set of Analysis descriptors for this VariantSet + nullable: true + items: + $ref: "#/components/schemas/Analysis" + callSetCount: + type: integer + description: The number of CallSets included in this VariantSet + format: int32 + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + metadataFields: + type: array + description: "The 'metadataField' indicates which types of genotyping data\ + \ and metadata are available in the VariantSet. \n
When possible,\ + \ these field names and abbreviations should follow the VCF standard " + nullable: true + items: + $ref: "#/components/schemas/MetadataField" + referenceSetDbId: + type: string + referenceSetName: + type: string + studyDbId: + type: string + studyName: + type: string + studyPUI: + type: string + variantCount: + type: integer + description: The number of Variants included in this VariantSet + format: int32 + nullable: true + variantSetDbId: + type: string + description: The unique identifier for a VariantSet + variantSetName: + type: string + description: The human readable name for a VariantSet + nullable: true + description: A VariantSet is a collection of variants and variant calls intended + to be analyzed together. + VariantSetRequest: + type: object + properties: + callSetDbIds: + type: array + description: The unique identifier representing a CallSet + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: The unique identifier representing a genotype Reference + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype ReferenceSet + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantDbIds: + type: array + description: The unique identifier representing a Variant + items: + type: string + variantSetDbIds: + type: array + description: The unique identifier representing a VariantSet + items: + type: string + VariantSetSearchRequest: + type: object + properties: + variantSetDbIds: + type: array + description: The unique identifier representing a VariantSet + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + referenceDbIds: + type: array + description: The unique identifier representing a genotype Reference + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + variantDbIds: + type: array + description: The unique identifier representing a Variant + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + callSetDbIds: + type: array + description: The unique identifier representing a CallSet + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype ReferenceSet + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + description: A VariantSet is a collection of variants and variant calls intended + to be analyzed together. + basePagination: + required: + - currentPage + - pageSize + type: object + properties: + currentPage: + type: integer + description: The index number for the returned page of data. This should + always match the requested page number or the default page (0). + example: 0 + default: 0 + pageSize: + type: integer + description: "The number of data elements returned, aka the size of the\ + \ current page. If the requested page does not have enough elements to\ + \ fill a page at the requested page size, this field should indicate the\ + \ actual number of elements returned." + example: 1000 + default: 1000 + totalCount: + type: integer + description: The total number of elements that are available on the server + and match the requested query parameters. + example: 10 + totalPages: + type: integer + description: "The total number of pages of elements available on the server.\ + \ This should be calculated with the following formula. \n
totalPages\ + \ = CEILING( totalCount / requested_page_size)" + example: 1 + description: "The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Pages are zero indexed, so the first page will be page 0 (zero)." + dataFile: + required: + - fileURL + type: object + properties: + fileURL: + type: string + description: The absolute URL where the file is located + format: uri + example: https://wiki.brapi.org/examples/datafile.xlsx + fileName: + type: string + description: The name of the file + example: datafile.xlsx + fileSize: + type: integer + description: The size of the file in bytes + example: 4398 + fileDescription: + type: string + description: A human readable description of the file contents + example: This is an Excel data file + fileType: + type: string + description: The type or format of the file. Preferably MIME Type. + example: application/vnd.ms-excel + fileMD5Hash: + type: string + description: The MD5 Hash of the file contents to be used as a check sum + example: c2365e900c81a89cf74d83dab60df146 + description: A dataFile contains a URL and the relevant file metadata to represent + a file + metadata: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/basePagination" + metadataBase: + type: object + properties: + datafiles: + type: array + description: "The datafiles contains a list of file URLs and metadata. \n\ + These files contain additional information related to the returned object\ + \ and can be retrieved by a subsequent call. \nThis could be a supplementary\ + \ data file, an informational file, the uploaded file where the data originated\ + \ from, a generated file representing the whole dataset in a particular\ + \ format, or any other related file. " + example: [] + items: + $ref: "#/components/schemas/dataFile" + status: + type: array + description: "The status field contains a list of informational status messages\ + \ from the server. \nIf no status is reported, an empty list should be\ + \ returned. See Error Reporting for more information." + items: + $ref: "#/components/schemas/status" + description: "An object in the BrAPI standard response model that describes\ + \ some information about the service call being performed. This includes supplementary\ + \ data, status log messages, and pagination information." + metadataTokenPagination: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/tokenPagination" + status: + required: + - message + - messageType + type: object + properties: + message: + type: string + description: A short message concerning the status of this request/response + example: "Request accepted, response successful" + messageType: + type: string + description: The logging level for the attached message + example: INFO + enum: + - DEBUG + - ERROR + - WARNING + - INFO + description: An array of status messages to convey technical logging information + from the server to the client. + tokenPagination: + allOf: + - $ref: "#/components/schemas/basePagination" + - required: + - nextPageToken + type: object + properties: + nextPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the next page of data." + example: cb668f63 + deprecated: true + currentPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the current page of data." + example: 48bc6ac1 + deprecated: true + prevPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the previous page of data." + example: 9659857e + deprecated: true + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken to\ + \ construct an additional query and move to the next or previous page respectively.\ + \ " + example: + currentPage: 0 + pageSize: 1000 + totalCount: 10 + totalPages: 1 + responses: + "401Unauthorized": + description: Unauthorized content: application/json: schema: - title: VariantSetSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/VariantSet" - ReferenceSetSingleResponse: + type: string + example: ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization + token + VariantSingleResponse: description: OK content: application/json: schema: - title: ReferenceSetSingleResponse + title: VariantSingleResponse required: - metadata - result @@ -4292,16 +8208,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/ReferenceSet" - CrossListResponse: - description: OK + $ref: "#/components/schemas/Variant" + "202AcceptedSearchResponse": + description: Accepted content: application/json: schema: - title: CrossListResponse - required: - - metadata - - result + title: 202AcceptedSearchResponse type: object properties: '@context': @@ -4309,20 +8222,17 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data type: object properties: - data: - type: array - items: - $ref: "#/components/schemas/Cross" - PlateListResponse: + searchResultsDbId: + type: string + example: 551ae08c + StudyStudyTypeListResponse: description: OK content: application/json: schema: - title: PlateListResponse + title: StudyStudyTypeListResponse required: - metadata - result @@ -4340,13 +8250,13 @@ components: data: type: array items: - $ref: "#/components/schemas/Plate" - SeasonListResponse: + type: string + StudySingleResponse: description: OK content: application/json: schema: - title: SeasonListResponse + title: StudySingleResponse required: - metadata - result @@ -4357,20 +8267,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Season" - ReferenceListResponse: + $ref: "#/components/schemas/Study" + MarkerPositionListResponse: description: OK content: application/json: schema: - title: ReferenceListResponse + title: MarkerPositionListResponse required: - metadata - result @@ -4388,13 +8291,13 @@ components: data: type: array items: - $ref: "#/components/schemas/Reference" - AlleleMatrixListResponse: + $ref: "#/components/schemas/MarkerPosition" + TrialListResponse: description: OK content: application/json: schema: - title: AlleleMatrixListResponse + title: TrialListResponse required: - metadata - result @@ -4412,30 +8315,13 @@ components: data: type: array items: - $ref: "#/components/schemas/AlleleMatrix" - GenomeMapSingleResponse: - description: OK - content: - application/json: - schema: - title: GenomeMapSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/GenomeMap" - PersonListResponse: + $ref: "#/components/schemas/Trial" + SampleListResponse: description: OK content: application/json: schema: - title: PersonListResponse + title: SampleListResponse required: - metadata - result @@ -4453,13 +8339,13 @@ components: data: type: array items: - $ref: "#/components/schemas/Person" - PlannedCrossListResponse: + $ref: "#/components/schemas/Sample" + VariantSetListResponse: description: OK content: application/json: schema: - title: PlannedCrossListResponse + title: VariantSetListResponse required: - metadata - result @@ -4477,13 +8363,13 @@ components: data: type: array items: - $ref: "#/components/schemas/PlannedCross" - LocationListResponse: + $ref: "#/components/schemas/VariantSet" + SampleSingleResponse: description: OK content: application/json: schema: - title: LocationListResponse + title: SampleSingleResponse required: - metadata - result @@ -4494,28 +8380,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Location" - "403Forbidden": - description: Forbidden - content: - application/json: - schema: - type: string - example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to - perform this action - ProgramListResponse: + $ref: "#/components/schemas/Sample" + ReferenceSetListResponse: description: OK content: application/json: schema: - title: ProgramListResponse + title: ReferenceSetListResponse required: - metadata - result @@ -4533,49 +8404,30 @@ components: data: type: array items: - $ref: "#/components/schemas/Program" - ListListResponse: + $ref: "#/components/schemas/ReferenceSet" + TrialSingleResponse: description: OK content: - application/json: - schema: - title: ListListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/List" - "400BadRequest": - description: Bad Request - content: - application/json: - schema: - type: string - example: |- - ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object - - ERROR - 2018-10-08T18:15:11Z - Invalid query parameter - - ERROR - 2018-10-08T18:15:11Z - Required parameter is missing - CrossingProjectListResponse: + application/json: + schema: + title: TrialSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Trial" + CallSetListResponse: description: OK content: application/json: schema: - title: CrossingProjectListResponse + title: CallSetListResponse required: - metadata - result @@ -4593,13 +8445,13 @@ components: data: type: array items: - $ref: "#/components/schemas/CrossingProject" - GermplasmAttributeSingleResponse: + $ref: "#/components/schemas/CallSet" + CallSetSingleResponse: description: OK content: application/json: schema: - title: GermplasmAttributeSingleResponse + title: CallSetSingleResponse required: - metadata - result @@ -4610,21 +8462,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/GermplasmAttribute" - "401Unauthorized": - description: Unauthorized - content: - application/json: - schema: - type: string - example: ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization - token - GermplasmAttributeListResponse: + $ref: "#/components/schemas/CallSet" + VariantSetSingleResponse: description: OK content: application/json: schema: - title: GermplasmAttributeListResponse + title: VariantSetSingleResponse required: - metadata - result @@ -4635,20 +8479,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/GermplasmAttribute" - GermplasmListResponse: + $ref: "#/components/schemas/VariantSet" + SeasonSingleResponse: description: OK content: application/json: schema: - title: GermplasmListResponse + title: SeasonSingleResponse required: - metadata - result @@ -4659,20 +8496,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Germplasm" - CrossingProjectSingleResponse: + $ref: "#/components/schemas/Season" + ReferenceSingleResponse: description: OK content: application/json: schema: - title: CrossingProjectSingleResponse + title: ReferenceSingleResponse required: - metadata - result @@ -4683,13 +8513,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/CrossingProject" - SampleListResponse: + $ref: "#/components/schemas/Reference" + ReferenceSetSingleResponse: description: OK content: application/json: schema: - title: SampleListResponse + title: ReferenceSetSingleResponse required: - metadata - result @@ -4700,20 +8530,21 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Sample" - ReferenceSetListResponse: + $ref: "#/components/schemas/ReferenceSet" + "404NotFound": + description: Not Found + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not + found + StudyListResponse: description: OK content: application/json: schema: - title: ReferenceSetListResponse + title: StudyListResponse required: - metadata - result @@ -4731,13 +8562,13 @@ components: data: type: array items: - $ref: "#/components/schemas/ReferenceSet" - TrialSingleResponse: + $ref: "#/components/schemas/Study" + LinkageGroupListResponse: description: OK content: application/json: schema: - title: TrialSingleResponse + title: LinkageGroupListResponse required: - metadata - result @@ -4748,13 +8579,20 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Trial" - GermplasmSingleResponse: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/LinkageGroup" + CallListResponse: description: OK content: application/json: schema: - title: GermplasmSingleResponse + title: CallListResponse required: - metadata - result @@ -4765,13 +8603,20 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Germplasm" - SeasonSingleResponse: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Call" + LocationSingleResponse: description: OK content: application/json: schema: - title: SeasonSingleResponse + title: LocationSingleResponse required: - metadata - result @@ -4782,13 +8627,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Season" - ReferenceSingleResponse: + $ref: "#/components/schemas/Location" + PlateListResponse: description: OK content: application/json: schema: - title: ReferenceSingleResponse + title: PlateListResponse required: - metadata - result @@ -4799,21 +8644,20 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Reference" - "404NotFound": - description: Not Found - content: - application/json: - schema: - type: string - example: ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not - found - StudyListResponse: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Plate" + SeasonListResponse: description: OK content: application/json: schema: - title: StudyListResponse + title: SeasonListResponse required: - metadata - result @@ -4831,13 +8675,13 @@ components: data: type: array items: - $ref: "#/components/schemas/Study" - BreedingMethodSingleResponse: + $ref: "#/components/schemas/Season" + ReferenceBasesSingleResponse: description: OK content: application/json: schema: - title: BreedingMethodSingleResponse + title: ReferenceBasesSingleResponse required: - metadata - result @@ -4848,13 +8692,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/BreedingMethod" - CallListResponse: + $ref: "#/components/schemas/ReferenceBases" + PersonSingleResponse: description: OK content: application/json: schema: - title: CallListResponse + title: PersonSingleResponse required: - metadata - result @@ -4865,20 +8709,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Call" - LocationSingleResponse: + $ref: "#/components/schemas/Person" + ReferenceListResponse: description: OK content: application/json: schema: - title: LocationSingleResponse + title: ReferenceListResponse required: - metadata - result @@ -4889,13 +8726,20 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Location" - PersonSingleResponse: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Reference" + AlleleMatrixListResponse: description: OK content: application/json: schema: - title: PersonSingleResponse + title: AlleleMatrixListResponse required: - metadata - result @@ -4906,7 +8750,14 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Person" + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/AlleleMatrix" VariantListResponse: description: OK content: @@ -4948,12 +8799,29 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/Plate" - GermplasmAttributeValueListResponse: + GenomeMapSingleResponse: + description: OK + content: + application/json: + schema: + title: GenomeMapSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GenomeMap" + PersonListResponse: description: OK content: application/json: schema: - title: GermplasmAttributeValueListResponse + title: PersonListResponse required: - metadata - result @@ -4971,13 +8839,13 @@ components: data: type: array items: - $ref: "#/components/schemas/GermplasmAttributeValue" - BreedingMethodListResponse: + $ref: "#/components/schemas/Person" + LocationListResponse: description: OK content: application/json: schema: - title: BreedingMethodListResponse + title: LocationListResponse required: - metadata - result @@ -4995,13 +8863,21 @@ components: data: type: array items: - $ref: "#/components/schemas/BreedingMethod" - GermplasmAttributeValueSingleResponse: + $ref: "#/components/schemas/Location" + "403Forbidden": + description: Forbidden + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to + perform this action + ProgramListResponse: description: OK content: application/json: schema: - title: GermplasmAttributeValueSingleResponse + title: ProgramListResponse required: - metadata - result @@ -5012,13 +8888,20 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/GermplasmAttributeValue" - GenomeMapListResponse: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Program" + ListListResponse: description: OK content: application/json: schema: - title: GenomeMapListResponse + title: ListListResponse required: - metadata - result @@ -5036,13 +8919,25 @@ components: data: type: array items: - $ref: "#/components/schemas/GenomeMap" - PedigreeNodeListResponse: + $ref: "#/components/schemas/List" + "400BadRequest": + description: Bad Request + content: + application/json: + schema: + type: string + example: |- + ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object + + ERROR - 2018-10-08T18:15:11Z - Invalid query parameter + + ERROR - 2018-10-08T18:15:11Z - Required parameter is missing + GenomeMapListResponse: description: OK content: application/json: schema: - title: PedigreeNodeListResponse + title: GenomeMapListResponse required: - metadata - result @@ -5060,7 +8955,7 @@ components: data: type: array items: - $ref: "#/components/schemas/PedigreeNode" + $ref: "#/components/schemas/GenomeMap" ListSingleResponse: description: OK content: @@ -5159,6 +9054,18 @@ components: schema: type: integer example: 1000 + authorizationHeader: + name: Authorization + in: header + description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ + \ {token_string} " + required: false + style: simple + explode: false + schema: + pattern: ^Bearer .*$ + type: string + example: Bearer XXXX page: name: page in: query @@ -5187,18 +9094,6 @@ components: schema: type: string example: 33c27874 - authorizationHeader: - name: Authorization - in: header - description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ - \ {token_string} " - required: false - style: simple - explode: false - schema: - pattern: ^Bearer .*$ - type: string - example: Bearer XXXX securitySchemes: AuthorizationToken: type: http diff --git a/Specification/Generated/BrAPI-Germplasm.yaml b/Specification/Generated/BrAPI-Germplasm.yaml index 59d8621c..ca169260 100644 --- a/Specification/Generated/BrAPI-Germplasm.yaml +++ b/Specification/Generated/BrAPI-Germplasm.yaml @@ -9,7 +9,10 @@ paths: - Germplasm summary: Get a filtered list of BreedingMethod description: Get a list of BreedingMethod - parameters: [] + parameters: + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/BreedingMethodListResponse" @@ -48,15 +51,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: crossingProjectDbId in: query description: Search for Crossing Projects with this unique id @@ -81,7 +75,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -107,7 +100,16 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/CrossNewRequest" + type: object + additionalProperties: + $ref: "#/components/schemas/CrossNewRequest" + example: "{_1={additionalInfo={}, crossAttributes=[{}], crossDbId=15187888,\ + \ crossName=15a57676, crossType={}, crossingProject={}, externalReferences=[{}],\ + \ parent1={}, parent2={}, plannedCross={}, pollinationEvents=[{}],\ + \ observationUnits=[{}]}, _2={additionalInfo={}, crossAttributes=[{}],\ + \ crossDbId=15187889, crossName=15a57677, crossType={}, crossingProject={},\ + \ externalReferences=[{}], parent1={}, parent2={}, plannedCross={},\ + \ pollinationEvents=[{}], observationUnits=[{}]}}" responses: "200": $ref: "#/components/responses/CrossListResponse" @@ -128,7 +130,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/CrossNewRequest" + type: array + items: + $ref: "#/components/schemas/CrossNewRequest" responses: "200": $ref: "#/components/responses/CrossListResponse" @@ -167,15 +171,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: crossingProjectDbId in: query description: Search for Crossing Projects with this unique id @@ -188,7 +183,7 @@ paths: required: false schema: type: string - - name: includePotentialParent + - name: includePotentialParents in: query description: "If the parameter 'includePotentialParents' is false, the array\ \ 'potentialParents' should be empty, null, or excluded from the response\ @@ -196,7 +191,6 @@ paths: required: false schema: type: boolean - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -222,7 +216,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/CrossingProjectNewRequest" + type: array + items: + $ref: "#/components/schemas/CrossingProjectNewRequest" responses: "200": $ref: "#/components/responses/CrossingProjectListResponse" @@ -274,39 +270,18 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for required: false schema: type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - name: trialDbId in: query description: The ID which uniquely identifies a trial to search for required: false schema: type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - name: germplasmPUI in: query description: List of Permanent Unique Identifiers to identify germplasm @@ -329,24 +304,6 @@ paths: required: false schema: type: string - - name: familyCode - in: query - description: A familyCode representing the family this germplasm belongs to. - required: false - schema: - type: string - - name: instituteCode - in: query - description: "The code for the institute that maintains the material. \n
\ - \ MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession\ - \ is maintained. The codes consist of the 3-letter ISO 3166 country code\ - \ of the country where the institute is located plus a number (e.g. PER001).\ - \ The current set of institute codes is available from http://www.fao.org/wiews.\ - \ For those institutes not yet having an FAO Code, or for those with \"\ - obsolete\" codes, see \"Common formatting rules (v)\"." - required: false - schema: - type: string - name: binomialName in: query description: List of the full binomial name (scientific name) to identify @@ -354,13 +311,13 @@ paths: required: false schema: type: string - - name: genu + - name: genus in: query description: List of Genus names to identify germplasm required: false schema: type: string - - name: specy + - name: species in: query description: List of Species names to identify germplasm required: false @@ -384,7 +341,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -410,7 +366,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/GermplasmNewRequest" + type: array + items: + $ref: "#/components/schemas/GermplasmNewRequest" responses: "200": $ref: "#/components/responses/GermplasmListResponse" @@ -543,7 +501,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -569,7 +526,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/GermplasmAttributeNewRequest" + type: array + items: + $ref: "#/components/schemas/GermplasmAttributeNewRequest" responses: "200": $ref: "#/components/responses/GermplasmAttributeListResponse" @@ -604,13 +563,6 @@ paths: required: false schema: type: string - - name: germplasmName - in: query - description: List of human readable names to identify germplasm to search - for - required: false - schema: - type: string - name: programDbId in: query description: "A BrAPI Program represents the high level organization or group\ @@ -621,15 +573,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: attributeValueDbId in: query description: List of Germplasm Attribute Value IDs to search for @@ -648,43 +591,6 @@ paths: required: false schema: type: string - - name: ontologyDbId - in: query - description: List of ontology IDs to search for - required: false - schema: - type: string - - name: methodDbId - in: query - description: List of methods to filter search results - required: false - schema: - type: string - - name: scaleDbId - in: query - description: List of scales to filter search results - required: false - schema: - type: string - - name: traitDbId - in: query - description: List of trait unique ID to filter search results - required: false - schema: - type: string - - name: traitClass - in: query - description: List of trait classes to filter search results - required: false - schema: - type: string - - name: dataType - in: query - description: List of scale data types to filter search results - required: false - schema: - $ref: "#/components/schemas/TraitDataType" - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -710,7 +616,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/GermplasmAttributeValueNewRequest" + type: array + items: + $ref: "#/components/schemas/GermplasmAttributeValueNewRequest" responses: "200": $ref: "#/components/responses/GermplasmAttributeValueListResponse" @@ -762,39 +670,18 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for required: false schema: type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - name: trialDbId in: query description: The ID which uniquely identifies a trial to search for required: false schema: type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - name: germplasmPUI in: query description: List of Permanent Unique Identifiers to identify germplasm @@ -823,18 +710,6 @@ paths: required: false schema: type: string - - name: instituteCode - in: query - description: "The code for the institute that maintains the material. \n
\ - \ MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession\ - \ is maintained. The codes consist of the 3-letter ISO 3166 country code\ - \ of the country where the institute is located plus a number (e.g. PER001).\ - \ The current set of institute codes is available from http://www.fao.org/wiews.\ - \ For those institutes not yet having an FAO Code, or for those with \"\ - obsolete\" codes, see \"Common formatting rules (v)\"." - required: false - schema: - type: string - name: binomialName in: query description: List of the full binomial name (scientific name) to identify @@ -842,13 +717,13 @@ paths: required: false schema: type: string - - name: genu + - name: genus in: query description: List of Genus names to identify germplasm required: false schema: type: string - - name: specy + - name: species in: query description: List of Species names to identify germplasm required: false @@ -860,14 +735,14 @@ paths: required: false schema: type: string - - name: includeParent + - name: includeParents in: query description: "If this parameter is true, include the array of parents in the\ \ response" required: false schema: type: boolean - - name: includeSibling + - name: includeSiblings in: query description: "If this parameter is true, include the array of siblings in\ \ the response" @@ -904,7 +779,6 @@ paths: schema: type: integer format: int32 - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -930,7 +804,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/PedigreeNode" + type: array + items: + $ref: "#/components/schemas/PedigreeNode" responses: "200": $ref: "#/components/responses/PedigreeNodeListResponse" @@ -969,15 +845,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: crossingProjectDbId in: query description: Search for Crossing Projects with this unique id @@ -1014,7 +881,6 @@ paths: - TODO - DONE - SKIPPED - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -1040,7 +906,15 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/PlannedCross" + type: object + additionalProperties: + $ref: "#/components/schemas/PlannedCross" + example: "{_1={additionalInfo={}, crossType={}, crossingProject={},\ + \ externalReferences=[{}], parent1={}, parent2={}, plannedCrossDbId=47edd16c,\ + \ plannedCrossName=487acf5a, status={}, crosses=[{}]}, _2={additionalInfo={},\ + \ crossType={}, crossingProject={}, externalReferences=[{}], parent1={},\ + \ parent2={}, plannedCrossDbId=47edd16d, plannedCrossName=487acf5b,\ + \ status={}, crosses=[{}]}}" responses: "200": $ref: "#/components/responses/PlannedCrossListResponse" @@ -1061,7 +935,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/PlannedCross" + type: array + items: + $ref: "#/components/schemas/PlannedCross" responses: "200": $ref: "#/components/responses/PlannedCrossListResponse" @@ -1113,15 +989,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: seedLotDbId in: query description: Unique id for a seed lot on this server @@ -1140,7 +1007,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -1166,7 +1032,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/SeedLotNewRequest" + type: array + items: + $ref: "#/components/schemas/SeedLotNewRequest" responses: "200": $ref: "#/components/responses/SeedLotListResponse" @@ -1176,12 +1044,39 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + /attributes/categories: + get: + tags: + - GermplasmAttributes + summary: Get the attributeCategories of GermplasmAttribute + description: List all available GermplasmAttribute attributeCategories + parameters: + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/GermplasmAttributeAttributeCategoryListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" /breedingmethods/{breedingMethodDbId}: get: tags: - Germplasm summary: Get the details of a specific BreedingMethod description: Get details for a BreedingMethod + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: breedingMethodDbId + in: path + description: the unique identifier for this breeding method + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/BreedingMethodSingleResponse" @@ -1191,12 +1086,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /crossingprojects/{crossingProjectDbId}: get: tags: - CrossingProjects summary: Get the details of a specific CrossingProject description: Get details for a CrossingProject + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: crossingProjectDbId + in: path + description: The unique identifier for a crossing project + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/CrossingProjectSingleResponse" @@ -1206,6 +1111,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - CrossingProjects @@ -1213,6 +1120,12 @@ paths: description: Update the details for an existing CrossingProject parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: crossingProjectDbId + in: path + description: The unique identifier for a crossing project + required: true + schema: + type: string requestBody: content: application/json: @@ -1227,12 +1140,27 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /germplasm/{germplasmDbId}: get: tags: - Germplasm summary: Get the details of a specific Germplasm description: Get details for a Germplasm + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: germplasmDbId + in: path + description: "The ID which uniquely identifies a germplasm within the given\ + \ database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code\ + \ used to identify the biological material in the data file. Should be unique\ + \ within the Investigation. Can correspond to experimental plant ID, inventory\ + \ lot ID, etc. This material identification is different from a BiosampleID\ + \ which corresponds to Observation Unit or Samples sections below." + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/GermplasmSingleResponse" @@ -1242,6 +1170,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Germplasm @@ -1249,6 +1179,17 @@ paths: description: Update the details for an existing Germplasm parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: germplasmDbId + in: path + description: "The ID which uniquely identifies a germplasm within the given\ + \ database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code\ + \ used to identify the biological material in the data file. Should be unique\ + \ within the Investigation. Can correspond to experimental plant ID, inventory\ + \ lot ID, etc. This material identification is different from a BiosampleID\ + \ which corresponds to Observation Unit or Samples sections below." + required: true + schema: + type: string requestBody: content: application/json: @@ -1263,12 +1204,53 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /germplasm/{germplasmDbId}/mcpd: + get: + tags: + - Germplasm + summary: Get the details of a specific GermplasmMCPD + description: Get details for a GermplasmMCPD + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: germplasmDbId + in: path + description: "The ID which uniquely identifies a germplasm within the given\ + \ database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code\ + \ used to identify the biological material in the data file. Should be unique\ + \ within the Investigation. Can correspond to experimental plant ID, inventory\ + \ lot ID, etc. This material identification is different from a BiosampleID\ + \ which corresponds to Observation Unit or Samples sections below." + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/GermplasmMCPDSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /attributes/{attributeDbId}: get: tags: - GermplasmAttributes summary: Get the details of a specific GermplasmAttribute description: Get details for a GermplasmAttribute + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: attributeDbId + in: path + description: The ID which uniquely identifies this attribute within the given + database server + required: false + schema: + type: string responses: "200": $ref: "#/components/responses/GermplasmAttributeSingleResponse" @@ -1278,6 +1260,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - GermplasmAttributes @@ -1285,6 +1269,13 @@ paths: description: Update the details for an existing GermplasmAttribute parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: attributeDbId + in: path + description: The ID which uniquely identifies this attribute within the given + database server + required: false + schema: + type: string requestBody: content: application/json: @@ -1299,12 +1290,23 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /attributevalues/{attributeValueDbId}: get: tags: - GermplasmAttributeValues summary: Get the details of a specific GermplasmAttributeValue description: Get details for a GermplasmAttributeValue + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: attributeValueDbId + in: path + description: The ID which uniquely identifies this attribute value within + the given database server + required: false + schema: + type: string responses: "200": $ref: "#/components/responses/GermplasmAttributeValueSingleResponse" @@ -1314,6 +1316,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - GermplasmAttributeValues @@ -1321,6 +1325,13 @@ paths: description: Update the details for an existing GermplasmAttributeValue parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: attributeValueDbId + in: path + description: The ID which uniquely identifies this attribute value within + the given database server + required: false + schema: + type: string requestBody: content: application/json: @@ -1335,12 +1346,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /seedlots/{seedLotDbId}: get: tags: - SeedLots summary: Get the details of a specific SeedLot description: Get details for a SeedLot + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: seedLotDbId + in: path + description: Unique DbId for the Seed Lot + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/SeedLotSingleResponse" @@ -1350,6 +1371,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - SeedLots @@ -1357,6 +1380,12 @@ paths: description: Update the details for an existing SeedLot parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: seedLotDbId + in: path + description: Unique DbId for the Seed Lot + required: true + schema: + type: string requestBody: content: application/json: @@ -1371,6 +1400,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/germplasm: post: tags: @@ -1384,6 +1415,13 @@ paths: \ the results of the search.
\nReview the Search\ \ Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/GermplasmSearchRequest" responses: "200": $ref: "#/components/responses/GermplasmListResponse" @@ -1408,6 +1446,13 @@ paths: \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/GermplasmAttributeSearchRequest" responses: "200": $ref: "#/components/responses/GermplasmAttributeListResponse" @@ -1432,6 +1477,13 @@ paths: \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/GermplasmAttributeValueSearchRequest" responses: "200": $ref: "#/components/responses/GermplasmAttributeValueListResponse" @@ -1456,6 +1508,13 @@ paths: \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PedigreeNodeSearchRequest" responses: "200": $ref: "#/components/responses/PedigreeNodeListResponse" @@ -1486,6 +1545,16 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/GermplasmListResponse" @@ -1515,6 +1584,16 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/GermplasmAttributeListResponse" @@ -1545,6 +1624,16 @@ paths: \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/GermplasmAttributeValueListResponse" @@ -1573,10 +1662,20 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." - responses: - "200": - $ref: "#/components/responses/PedigreeNodeListResponse" - "400": + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/PedigreeNodeListResponse" + "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" @@ -1584,103 +1683,678 @@ paths: $ref: "#/components/responses/403Forbidden" components: schemas: + AcquisitionSourceCode: + type: string + description: "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used\ + \ at 2 different levels of detail: either by using the general codes (in bold-face)\ + \ such as 10, 20, 30, 40, etc., or by using the more specific codes, such\ + \ as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland\ + \ \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm\ + \ or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen\ + \ or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture\ + \ \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n\ + 40) Institute, Experimental station, Research organization, Genebank \n50)\ + \ Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n\ + 62) Field margin \n99) Other (Elaborate in REMARKS field)" + enum: + - "10" + - "11" + - "12" + - "13" + - "14" + - "15" + - "20" + - "21" + - "22" + - "23" + - "24" + - "25" + - "26" + - "27" + - "28" + - "30" + - "40" + - "50" + - "60" + - "61" + - "62" + - "99" AdditionalInfo: - type: object - properties: - additionalProperties: - type: string + type: string + additionalProperties: + description: A free space containing any additional information related to + a particular object. description: "A free space containing any additional information related to\ \ a particular object. A data source may provide any JSON object, unrestricted\ \ by the BrAPI specification." + nullable: true + AlleleMatrixPagination: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension of + the matrix + format: int32 + example: 500 + AlleleMatrixRequest: + type: object + properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + dataMatrixAbbreviations: + type: array + description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ + \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ + \ in the response." + items: + type: string + dataMatrixNames: + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + germplasmDbIds: + type: array + description: A list of IDs which uniquely identify `Germplasm` within the + given database server + items: + type: string + germplasmNames: + type: array + description: A list of human readable `Germplasm` names + items: + type: string + germplasmPUIs: + type: array + description: A list of permanent unique identifiers associated with `Germplasm` + items: + type: string + pagination: + type: array + description: Pagination for the matrix + items: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension + of the matrix + format: int32 + example: 500 + positionRanges: + type: array + description: "The postion range to search\n
\nUses the format \":-\"\ + \ where is the chromosome name, is \nthe starting position\ + \ of the range, and is the ending position of the range" + items: + type: string + preview: + type: boolean + description: "Default Value = false\n
\nIf 'preview' is set to true,\ + \ then the server should only return the lists of 'callSetDbIds', \n'variantDbIds',\ + \ and 'variantSetDbIds'. The server should not return any matrix data.\ + \ This\nis intended to be a preview and give the client a sense of how\ + \ large the matrix returned will be\n
\nIf 'preview' is set to false\ + \ or not set (default), then the server should return all the matrix\n\ + data as requested." + example: true + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + items: + type: string + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + example: "." + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string Attribute: required: - attributeName - - method - - scale - - trait + - methodDbId + - methodName + - scaleDbId + - scaleName + - traitName type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" attributeCategory: type: string + description: General category for the attribute. very similar to Trait class. + example: Morphological attributeDbId: type: string + description: The ID which uniquely identifies this attribute within the + given database server attributeDescription: type: string + description: A human readable description of this attribute + example: Height of the plant measured in meters by a tape attributeName: type: string + description: A human readable name for this attribute + example: Plant Height 1 attributePUI: type: string + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + example: http://my-traits.com/trait/CO_123:0008012 commonCropName: type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true contextOfUse: type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true items: type: string defaultValue: type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" growthStage: type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true institution: type: string + description: Name of institution submitting the variable + nullable: true language: type: string - method: - $ref: "#/components/schemas/Method" + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string ontologyReference: $ref: "#/components/schemas/OntologyReference" - scale: - $ref: "#/components/schemas/Scale" + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string scientist: type: string + description: Name of scientist submitting the variable. + nullable: true status: type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true submissionTimestamp: type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true synonyms: type: array + description: Other variable names + nullable: true items: type: string - trait: - $ref: "#/components/schemas/Trait" + traitDbId: + type: string + traitName: + type: string + traitPUI: + type: string + BiologicalStatusOfAccessionCode: + type: string + description: "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used\ + \ at 3 different levels of detail: either by using the general codes such\ + \ as 100, 200, 300, 400, or by using the more specific codes such as 110,\ + \ 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown\ + \ \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research\ + \ material \n410) Breeders line \n411) Synthetic population \n412) Hybrid\ + \ \n413) Founder stock/base population \n414) Inbred line (parent of hybrid\ + \ cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic\ + \ stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations)\ + \ \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids,\ + \ amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n\ + 500) Advanced or improved cultivar (conventional breeding methods) \n600)\ + \ GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)" + enum: + - "100" + - "110" + - "120" + - "130" + - "200" + - "300" + - "400" + - "410" + - "411" + - "412" + - "413" + - "414" + - "415" + - "416" + - "420" + - "421" + - "422" + - "423" + - "500" + - "600" + - "999" BreedingMethod: required: - - abbreviation - breedingMethodDbId - - breedingMethodName - - description type: object properties: abbreviation: type: string + description: A shortened version of the human readable name for a Breeding + Method + nullable: true breedingMethodDbId: type: string + description: the unique identifier for this breeding method breedingMethodName: type: string + description: the human readable identifier for this breeding method + nullable: true description: type: string + description: human readable description of the breeding method + nullable: true description: The techniques and protocol used to produce a Cross or Germplasm - Contact: - required: - - contactDbId + CallRequest: type: object properties: - contactDbId: - type: string - email: - type: string - instituteName: - type: string - name: - type: string - orcid: - type: string - type: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + example: "." + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variant` within the + given database server + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string + CallSetRequest: + type: object + properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + callSetNames: + type: array + description: A list of human readable names associated with `CallSets` + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + items: + type: string + sampleNames: + type: array + description: A list of human readable names associated with `Samples` + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string + CollectingInfo: + type: object + properties: + collectingDate: + type: string + description: "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD]\ + \ where YYYY is the year, MM is the month and DD is the day. Missing data\ + \ (MM or DD) should be indicated with hyphens or \"00\" [double zero]." + format: date + nullable: true + collectingInstitutes: + type: array + description: Institutes which collected the sample + nullable: true + items: + $ref: "#/components/schemas/Institute" + collectingMissionIdentifier: + type: string + description: "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting\ + \ mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\"\ + , \"CN_426\")." + nullable: true + example: CIATFOR_052 + collectingNumber: + type: string + description: "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by\ + \ the collector(s) of the sample, normally composed of the name or initials\ + \ of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier\ + \ is essential for identifying duplicates held in different collections." + nullable: true + example: ab109909 + collectingSite: + type: object + properties: + coordinateUncertainty: + type: string + description: MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with + the coordinates in metres. Leave the value empty if the uncertainty + is unknown. + nullable: true + example: "20" + elevation: + type: string + description: MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site + expressed in metres above sea level. Negative values are allowed. + nullable: true + example: "35" + georeferencingMethod: + type: string + description: "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method\ + \ used (GPS, determined from map, gazetteer, or estimated using software).\ + \ Leave the value empty if georeferencing method is not known." + nullable: true + example: WGS84 + latitudeDecimal: + type: string + description: MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal + degrees. Positive values are North of the Equator; negative values + are South of the Equator (e.g. -44.6975). + nullable: true + example: "+42.445295" + latitudeDegrees: + type: string + description: "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes\ + \ (2 digits), and seconds (2 digits) followed by N (North) or S (South)\ + \ (e.g. 103020S). Every missing digit (minutes or seconds) should\ + \ be indicated with a hyphen. Leading zeros are required (e.g. 10" + nullable: true + example: 42 26 43.1 N + locationDescription: + type: string + description: "MCPD (v2.1) (COLLSITE) 14. Location information below\ + \ the country level that describes where the accession was collected,\ + \ preferable in English. This might include the distance in kilometres\ + \ and direction from the nearest town, village or map grid reference\ + \ point, (e.g. 7 km south of Townsville)." + nullable: true + example: South east hill near institute buildings + longitudeDecimal: + type: string + description: MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in + decimal degrees. Positive values are East of the Greenwich Meridian; + negative values are West of the Greenwich Meridian (e.g. +120.9123). + nullable: true + example: "-076.471934" + longitudeDegrees: + type: string + description: "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes\ + \ (2 digits), and seconds (2 digits) followed by E (East) or W (West)\ + \ (e.g. 0762510W). Every missing digit (minutes or seconds) should\ + \ be indicated with a hyphen. Leading zeros are required (e.g. 076" + nullable: true + example: 76 28 19.0 W + spatialReferenceSystem: + type: string + description: MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial + reference system upon which the coordinates given in decimal latitude + and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 + datum. + nullable: true + example: WGS84 + description: Information about the location where the sample was collected + nullable: true + description: Information about the collection of a germplasm + CollectingSite: + type: object + properties: + coordinateUncertainty: type: string - description: A persons contact information + description: MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with + the coordinates in metres. Leave the value empty if the uncertainty is + unknown. + nullable: true + example: "20" + elevation: + type: string + description: MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed + in metres above sea level. Negative values are allowed. + nullable: true + example: "35" + georeferencingMethod: + type: string + description: "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used\ + \ (GPS, determined from map, gazetteer, or estimated using software).\ + \ Leave the value empty if georeferencing method is not known." + nullable: true + example: WGS84 + latitudeDecimal: + type: string + description: MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal + degrees. Positive values are North of the Equator; negative values are + South of the Equator (e.g. -44.6975). + nullable: true + example: "+42.445295" + latitudeDegrees: + type: string + description: "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2\ + \ digits), and seconds (2 digits) followed by N (North) or S (South) (e.g.\ + \ 103020S). Every missing digit (minutes or seconds) should be indicated\ + \ with a hyphen. Leading zeros are required (e.g. 10" + nullable: true + example: 42 26 43.1 N + locationDescription: + type: string + description: "MCPD (v2.1) (COLLSITE) 14. Location information below the\ + \ country level that describes where the accession was collected, preferable\ + \ in English. This might include the distance in kilometres and direction\ + \ from the nearest town, village or map grid reference point, (e.g. 7\ + \ km south of Townsville)." + nullable: true + example: South east hill near institute buildings + longitudeDecimal: + type: string + description: MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal + degrees. Positive values are East of the Greenwich Meridian; negative + values are West of the Greenwich Meridian (e.g. +120.9123). + nullable: true + example: "-076.471934" + longitudeDegrees: + type: string + description: "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2\ + \ digits), and seconds (2 digits) followed by E (East) or W (West) (e.g.\ + \ 0762510W). Every missing digit (minutes or seconds) should be indicated\ + \ with a hyphen. Leading zeros are required (e.g. 076" + nullable: true + example: 76 28 19.0 W + spatialReferenceSystem: + type: string + description: MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial + reference system upon which the coordinates given in decimal latitude + and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum. + nullable: true + example: WGS84 + description: Information about the location where the sample was collected + CommonCropNamesParameters: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string ContentMixture: type: object properties: @@ -1696,7 +2370,9 @@ components: type: string mixturePercentage: type: integer + description: The percentage of the given germplasm in the seed lot mixture. format: int32 + nullable: true seedLotDbId: type: string seedLotName: @@ -1728,38 +2404,30 @@ components: type: string format: uri Cross: - required: - - crossDbId - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - crossName: - type: string - crossType: - $ref: "#/components/schemas/CrossType" - crossingProjectDbId: - type: string - crossingProjectName: - type: string - parent1: - $ref: "#/components/schemas/CrossParent" - parent2: - $ref: "#/components/schemas/CrossParent" - plannedCrossDbId: - type: string - plannedCrossName: - type: string - description: The identifiers and metadata represent that specific organisms - have mated to produce offspring with particular traits or genes. The offspring - of a Cross might be developed into a Germplasm if the desired traits are present. + allOf: + - $ref: "#/components/schemas/CrossNewRequest" + - required: + - crossDbId + type: object + properties: + crossDbId: + type: string + description: the unique identifier for a cross + description: The identifiers and metadata represent that specific organisms + have mated to produce offspring with particular traits or genes. The offspring + of a Cross might be developed into a Germplasm if the desired traits are + present. CrossAttribute: type: object properties: crossAttributeName: type: string + description: the human readable name of a cross attribute + nullable: true crossAttributeValue: type: string + description: the value of a cross attribute + nullable: true crossDbId: type: string crossName: @@ -1768,23 +2436,34 @@ components: \ crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative\ \ Humidity', 'crossAttributeValue':'80%'" CrossNewRequest: - required: - - crossDbId - - crossDbId type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" - crossDbId: - type: string + crossAttributes: + type: array + description: Set of custom attributes associated with a cross + nullable: true + items: + $ref: "#/components/schemas/CrossAttribute" crossName: type: string + description: the human readable name for a cross + nullable: true crossType: $ref: "#/components/schemas/CrossType" crossingProjectDbId: type: string crossingProjectName: type: string + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" parent1: $ref: "#/components/schemas/CrossParent" parent2: @@ -1793,14 +2472,24 @@ components: type: string plannedCrossName: type: string + pollinationEvents: + type: array + description: The list of pollination events that occurred for this cross. + nullable: true + items: + $ref: "#/components/schemas/PollinationEvent" description: The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present. CrossParent: type: object properties: - germplasm: - $ref: "#/components/schemas/Germplasm" + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string observationUnitDbId: type: string observationUnitName: @@ -1810,6 +2499,64 @@ components: parentType: $ref: "#/components/schemas/ParentType" description: The identifying information gor the parent material of a cross. + CrossRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + CrossStatus: + type: string + enum: + - TODO + - DONE + - SKIPPED CrossType: type: string description: "The type of cross make. Accepted values for this field are 'BIPARENTAL',\ @@ -1824,8 +2571,20 @@ components: - BULK_OPEN_POLLINATED - DOUBLE_HAPLOID CrossingProject: + allOf: + - $ref: "#/components/schemas/CrossingProjectNewRequest" + - required: + - crossingProjectDbId + type: object + properties: + crossingProjectDbId: + type: string + description: The unique identifier for a crossing project + description: "A project structure where a list of PlannedCrosses is generated,\ + \ the crossing events occur in the field, and the resulting actual Crosses\ + \ can documented." + CrossingProjectNewRequest: required: - - crossingProjectDbId - crossingProjectName type: object properties: @@ -1833,10 +2592,31 @@ components: $ref: "#/components/schemas/AdditionalInfo" commonCropName: type: string + description: the common name of a crop (for multi-crop systems) + nullable: true crossingProjectDescription: type: string + description: the description for a crossing project + nullable: true crossingProjectName: type: string + description: The human readable name for a crossing project + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + potentialParents: + type: array + description: |- + A list of all the potential parents in the crossing block, available in the crossing project +
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object. + nullable: true + items: + $ref: "#/components/schemas/CrossParent" programDbId: type: string programName: @@ -1844,37 +2624,69 @@ components: description: "A project structure where a list of PlannedCrosses is generated,\ \ the crossing events occur in the field, and the resulting actual Crosses\ \ can documented." - CrossingProjectNewRequest: - required: - - crossingProjectDbId - - crossingProjectDbId - - crossingProjectName + CrossingProjectRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - crossingProjectDbId: - type: string - crossingProjectDescription: - type: string - crossingProjectName: - type: string - programDbId: - type: string - programName: - type: string - description: "A project structure where a list of PlannedCrosses is generated,\ - \ the crossing events occur in the field, and the resulting actual Crosses\ - \ can documented." + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + includePotentialParents: + type: boolean + description: "If the parameter 'includePotentialParents' is false, the array\ + \ 'potentialParents' should be empty, null, or excluded from the response\ + \ object." + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string Donor: type: object properties: donorAccessionNumber: type: string + description: |- + The accession number assigned by the donor + + MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard. + nullable: true donorInstituteCode: type: string + description: |- + The institute code for the donor institute +
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard. + nullable: true germplasmDbId: type: string germplasmName: @@ -1882,28 +2694,143 @@ components: germplasmPUI: type: string description: Identifier assigned to an accession by the material donor. - ExperimentalDesign: + DonorInfo: type: object properties: - PUI: - type: string - description: - type: string - studyDbId: + donorAccessionNumber: type: string - studyName: + description: MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession + by the donor. Follows ACCENUMB standard. + nullable: true + example: A0090204 + donorAccessionPui: + type: string + description: PUI (DOI mostly) of the accession in the donor system. + nullable: true + example: http://pui.per/accession/A0010025 + donorInstitute: + $ref: "#/components/schemas/Institute" + description: Information about an accession donor + EventRequest: + type: object + properties: + dateRangeEnd: type: string - studyPUI: + description: Filter based on an Event start date. + format: date-time + dateRangeStart: type: string - description: The experimental and statistical design full description plus a - category PUI taken from crop research ontology or agronomy ontology + description: Filter based on an Event start date. + format: date-time + eventDbIds: + type: array + description: Filter based on an Event DbId. + items: + type: string + eventTypes: + type: array + description: Filter based on an Event Type + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string ExternalReference: type: object properties: referenceId: type: string + description: The external reference ID. Could be a simple string or a URI. + nullable: true referenceSource: type: string + description: An identifier for the source system or database of this reference + nullable: true + GenomeMapRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + mapDbIds: + type: array + description: The ID which uniquely identifies a `GenomeMap` + items: + type: string + mapPUIs: + type: array + description: The DOI or other permanent identifier for a `GenomeMap` + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scientificName: + type: array + description: "Full scientific binomial format name. This includes Genus,\ + \ Species, and Sub-species" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + types: + type: array + description: "The type of map, usually \"Genetic\" or \"Physical\"" + items: + type: string GeoJSON: type: object properties: @@ -1911,6 +2838,8 @@ components: $ref: "#/components/schemas/GeoJSONGeometry" type: type: string + description: The literal string "Feature" + example: Feature description: |- One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. @@ -1927,10 +2856,12 @@ components: properties: coordinates: type: array + description: A single position items: type: number type: type: string + description: The literal string "Point" description: |- Copied from RFC 7946 Section 3.1.1 @@ -1943,6 +2874,7 @@ components: properties: coordinates: type: array + description: An array of linear rings items: type: array items: @@ -1951,11 +2883,54 @@ components: type: number type: type: string + description: The literal string "Polygon" description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ \ precisely in that order and using decimal numbers. Altitude or elevation\ \ MAY be included as an optional third element." + GeoJSONPoint: + required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + description: A single position + items: + type: number + type: + type: string + description: The literal string "Point" + description: |- + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + GeoJSONPolygon: + required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + description: An array of linear rings + items: + type: array + items: + type: array + items: + type: number + type: + type: string + description: The literal string "Polygon" + description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ + \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ + \ The first two elements are longitude and latitude, or\neasting and northing,\ + \ precisely in that order and using decimal numbers. Altitude or elevation\ + \ MAY be included as an optional third element." GeoJSONSearchArea: type: object properties: @@ -1973,115 +2948,46 @@ components: $ref: "#/components/schemas/ObservationUnitPosition" type: type: string + description: The literal string "Feature" + example: Feature Germplasm: - required: - - commonCropName - - germplasmDbId - - germplasmName - - germplasmPUI - type: object - properties: - accessionNumber: - type: string - acquisitionDate: - type: string - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - biologicalStatusOfAccessionCode: - type: string - description: "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can\ - \ be used at 3 different levels of detail: either by using the general\ - \ codes such as 100, 200, 300, 400, or by using the more specific codes\ - \ such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild\ - \ \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace\ - \ \n400) Breeding/research material \n410) Breeders line \n411) Synthetic\ - \ population \n412) Hybrid \n413) Founder stock/base population \n414)\ - \ Inbred line (parent of hybrid cultivar) \n415) Segregating population\ - \ \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion\ - \ mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome\ - \ addition/substitution, aneuploids, amphiploids) \n423) Other genetic\ - \ stocks (e.g. mapping populations) \n500) Advanced or improved cultivar\ - \ (conventional breeding methods) \n600) GMO (by genetic engineering)\ - \ \n999) Other (Elaborate in REMARKS field)" - enum: - - "100" - - "110" - - "120" - - "130" - - "200" - - "300" - - "400" - - "410" - - "411" - - "412" - - "413" - - "414" - - "415" - - "416" - - "420" - - "421" - - "422" - - "423" - - "500" - - "600" - - "999" - biologicalStatusOfAccessionDescription: - type: string - breedingMethodDbId: - type: string - breedingMethodName: - type: string - collection: - type: string - commonCropName: - type: string - countryOfOriginCode: - type: string - defaultDisplayName: - type: string - documentationURL: - type: string - genus: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - germplasmPreprocessing: - type: string - instituteCode: - type: string - instituteName: - type: string - pedigree: - type: string - sampleDbIds: - type: array - items: + allOf: + - $ref: "#/components/schemas/GermplasmNewRequest" + - required: + - germplasmDbId + type: object + properties: + germplasmDbId: type: string - seedSource: - type: string - seedSourceDescription: - type: string - species: - type: string - speciesAuthority: - type: string - subtaxa: - type: string - subtaxaAuthority: - type: string - description: "The conceptual identifiers and metadata describing a genetically\ - \ unique organism that is noteworthy in some way. Depending on context, a\ - \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ - \ Germplasm is conceptual data, not necessarily associated to a real physical\ - \ object, so Seed/Inventory Lots and Observation Units become physical instantiations\ - \ of a particular Germplasm. Note a Germplasm is unique and noteworthy, so\ - \ a Cross may or may not create a new Germplasm, since not every Cross is\ - \ unique or noteworthy." + description: "The ID which uniquely identifies a germplasm within the\ + \ given database server \n
MIAPPE V1.1 (DM-41) Biological material\ + \ ID - Code used to identify the biological material in the data file.\ + \ Should be unique within the Investigation. Can correspond to experimental\ + \ plant ID, inventory lot ID, etc. This material identification is different\ + \ from a BiosampleID which corresponds to Observation Unit or Samples\ + \ sections below." + description: "The conceptual identifiers and metadata describing a genetically\ + \ unique organism that is noteworthy in some way. Depending on context,\ + \ a Germplasm might be synonymous with Accession, Line, or Genotype. Note\ + \ that Germplasm is conceptual data, not necessarily associated to a real\ + \ physical object, so Seed/Inventory Lots and Observation Units become physical\ + \ instantiations of a particular Germplasm. Note a Germplasm is unique and\ + \ noteworthy, so a Cross may or may not create a new Germplasm, since not\ + \ every Cross is unique or noteworthy." GermplasmAttribute: + allOf: + - $ref: "#/components/schemas/GermplasmAttributeNewRequest" + - type: object + properties: + attributeDbId: + type: string + description: The ID which uniquely identifies this attribute within the + given database server + description: "The Trait-Method-Scale definition for a variable, specifically\ + \ variables related to Germplasm. Similar to an ObservationVariable, but\ + \ related to a Germplasm instead of an ObservationUnit" + GermplasmAttributeNewRequest: required: - - attributeDbId - attributeName - methodDbId - methodName @@ -2094,36 +3000,77 @@ components: $ref: "#/components/schemas/AdditionalInfo" attributeCategory: type: string + description: General category for the attribute. very similar to Trait class. + example: Morphological attributeDescription: type: string + description: A human readable description of this attribute + example: Height of the plant measured in meters by a tape attributeName: type: string + description: A human readable name for this attribute + example: Plant Height 1 attributePUI: type: string + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + example: http://my-traits.com/trait/CO_123:0008012 attributeValueDbIds: type: array + description: attributeValues + nullable: true items: type: string commonCropName: type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true + contextOfUse: + type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true + items: + type: string defaultValue: type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" growthStage: type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true institution: type: string + description: Name of institution submitting the variable + nullable: true language: type: string + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true methodDbId: type: string methodName: type: string methodPUI: type: string - ontologyReferenceDbId: - type: string + ontologyReference: + $ref: "#/components/schemas/OntologyReference" scaleDbId: type: string scaleName: @@ -2132,10 +3079,24 @@ components: type: string scientist: type: string + description: Name of scientist submitting the variable. + nullable: true status: type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true submissionTimestamp: type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true + synonyms: + type: array + description: Other variable names + nullable: true + items: + type: string traitDbId: type: string traitName: @@ -2145,84 +3106,402 @@ components: description: "The Trait-Method-Scale definition for a variable, specifically\ \ variables related to Germplasm. Similar to an ObservationVariable, but related\ \ to a Germplasm instead of an ObservationUnit" - GermplasmAttributeNewRequest: - required: - - attributeDbId - - attributeName - - methodDbId - - methodName - - scaleDbId - - scaleName - - traitName + GermplasmAttributeRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - attributeCategory: - type: string - attributeDbId: - type: string - attributeDescription: - type: string - attributeName: - type: string - attributePUI: - type: string - attributeValueDbIds: + attributeCategories: type: array + description: General category for the attribute. very similar to Trait class. + items: + type: string + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + items: + type: string + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + items: + type: string + attributePUIs: + type: array + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for items: type: string - commonCropName: - type: string - defaultValue: - type: string - documentationURL: - type: string - growthStage: - type: string - institution: - type: string - language: - type: string - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string - ontologyReferenceDbId: - type: string - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string - scientist: - type: string - status: - type: string - submissionTimestamp: - type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string - description: "The Trait-Method-Scale definition for a variable, specifically\ - \ variables related to Germplasm. Similar to an ObservationVariable, but related\ - \ to a Germplasm instead of an ObservationUnit" GermplasmAttributeSearchRequest: type: object - properties: {} + properties: + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + attributeCategories: + type: array + description: General category for the attribute. very similar to Trait class. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + attributePUIs: + type: array + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string description: "The Trait-Method-Scale definition for a variable, specifically\ \ variables related to Germplasm. Similar to an ObservationVariable, but related\ \ to a Germplasm instead of an ObservationUnit" GermplasmAttributeValue: + allOf: + - $ref: "#/components/schemas/GermplasmAttributeValueNewRequest" + - type: object + properties: + attributeValueDbId: + type: string + description: The ID which uniquely identifies this attribute value within + the given database server + description: "The value recorded for a particular Trait/Attribute and a particular\ + \ Germplasm. Similar to an Observation value, but more concrete, applying\ + \ to the whole Germplasm instead of a single ObservationUnit." + GermplasmAttributeValueNewRequest: required: - attributeName - - attributeValueDbId type: object properties: additionalInfo: @@ -2235,6 +3514,18 @@ components: type: string determinedDate: type: string + description: The date the value of this attribute was determined for a given + germplasm + format: date-time + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" germplasmDbId: type: string germplasmName: @@ -2243,41 +3534,189 @@ components: type: string value: type: string + description: The value of this attribute for a given germplasm + nullable: true description: "The value recorded for a particular Trait/Attribute and a particular\ \ Germplasm. Similar to an Observation value, but more concrete, applying\ \ to the whole Germplasm instead of a single ObservationUnit." - GermplasmAttributeValueNewRequest: - required: - - attributeName - - attributeValueDbId + GermplasmAttributeValueRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - attributeDbId: - type: string - attributeName: - type: string - attributePUI: - type: string - attributeValueDbId: - type: string - determinedDate: - type: string - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - value: - type: string - description: "The value recorded for a particular Trait/Attribute and a particular\ - \ Germplasm. Similar to an Observation value, but more concrete, applying\ - \ to the whole Germplasm instead of a single ObservationUnit." + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + items: + type: string + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + items: + type: string + attributeValueDbIds: + type: array + description: List of Germplasm Attribute Value IDs to search for + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: List of scales to filter search results + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: List of trait unique ID to filter search results + items: + type: string GermplasmAttributeValueSearchRequest: type: object - properties: {} + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + attributeValueDbIds: + type: array + description: List of Germplasm Attribute Value IDs to search for + items: + type: string + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + items: + type: string + traitDbIds: + type: array + description: List of trait unique ID to filter search results + items: + type: string + scaleDbIds: + type: array + description: List of scales to filter search results + items: + type: string description: "The value recorded for a particular Trait/Attribute and a particular\ \ Germplasm. Similar to an Observation value, but more concrete, applying\ \ to the whole Germplasm instead of a single ObservationUnit." @@ -2301,19 +3740,425 @@ components: type: string description: "A germplasm reference that is a direct child of this germplasm.\ \ These represent edges in the tree, connecting to other nodes." - GermplasmNewRequest: + GermplasmMCPD: required: - commonCropName - germplasmDbId - - germplasmDbId + - germplasmName + - germplasmPUI + type: object + properties: + accessionNames: + type: array + description: "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered\ + \ names or other designations given to the material received, other than\ + \ the donors accession number (23) or collecting number (3). First letter\ + \ uppercase." + nullable: true + items: + type: string + accessionNumber: + type: string + description: |- + The unique identifier for a material or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true + example: A0000003 + acquisitionDate: + type: string + description: "The date a material or germplasm was acquired by the genebank\ + \ \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the\ + \ collection [YYYYMMDD] where YYYY is the year, MM is the month and DD\ + \ is the day. Missing data (MM or DD) should be indicated with hyphens\ + \ or \"00\" [double zero]." + format: date + nullable: true + acquisitionSourceCode: + type: string + description: "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be\ + \ used at 2 different levels of detail: either by using the general codes\ + \ (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific\ + \ codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland\ + \ \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic\ + \ habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n\ + 23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24)\ + \ Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n\ + 28) Park \n30) Market or shop \n40) Institute, Experimental station, Research\ + \ organization, Genebank \n50) Seed company \n60) Weedy, disturbed or\ + \ ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate\ + \ in REMARKS field)" + nullable: true + example: "26" + enum: + - "10" + - "11" + - "12" + - "13" + - "14" + - "15" + - "20" + - "21" + - "22" + - "23" + - "24" + - "25" + - "26" + - "27" + - "28" + - "30" + - "40" + - "50" + - "60" + - "61" + - "62" + - "99" + alternateIDs: + type: array + description: "MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to\ + \ exist in other collections for this accession. Use the following format:\ + \ INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated\ + \ by a colon without space. Pairs of INSTCODE and identifier are separated\ + \ by a semicolon without space. When the institute is not known, the identifier\ + \ should be preceded by a colon. " + nullable: true + items: + type: string + ancestralData: + type: string + description: "MCPD (v2.1) (ANCEST) 20. Information about either pedigree\ + \ or other description of ancestral information (e.g. parent variety in\ + \ case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas'\ + \ or a description 'mutation found in Hanna', 'selection from Irene' or\ + \ 'cross involving amongst others Hanna and Irene'." + nullable: true + example: A0000001/A0000002 + biologicalStatusOfAccessionCode: + type: string + description: "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can\ + \ be used at 3 different levels of detail: either by using the general\ + \ codes such as 100, 200, 300, 400, or by using the more specific codes\ + \ such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild\ + \ \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace\ + \ \n400) Breeding/research material \n410) Breeders line \n411) Synthetic\ + \ population \n412) Hybrid \n413) Founder stock/base population \n414)\ + \ Inbred line (parent of hybrid cultivar) \n415) Segregating population\ + \ \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion\ + \ mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome\ + \ addition/substitution, aneuploids, amphiploids) \n423) Other genetic\ + \ stocks (e.g. mapping populations) \n500) Advanced or improved cultivar\ + \ (conventional breeding methods) \n600) GMO (by genetic engineering)\ + \ \n999) Other (Elaborate in REMARKS field)" + nullable: true + example: "421" + enum: + - "100" + - "110" + - "120" + - "130" + - "200" + - "300" + - "400" + - "410" + - "411" + - "412" + - "413" + - "414" + - "415" + - "416" + - "420" + - "421" + - "422" + - "423" + - "500" + - "600" + - "999" + breedingInstitutes: + type: array + description: |- + A list of institutes that were involved with breeding a material/germplasm +
MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. +
MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available. + nullable: true + items: + $ref: "#/components/schemas/Institute" + collectingInfo: + type: object + properties: + collectingDate: + type: string + description: "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample\ + \ [YYYYMMDD] where YYYY is the year, MM is the month and DD is the\ + \ day. Missing data (MM or DD) should be indicated with hyphens or\ + \ \"00\" [double zero]." + format: date + nullable: true + collectingInstitutes: + type: array + description: Institutes which collected the sample + nullable: true + items: + $ref: "#/components/schemas/Institute" + collectingMissionIdentifier: + type: string + description: "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting\ + \ mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\"\ + , \"CN_426\")." + nullable: true + example: CIATFOR_052 + collectingNumber: + type: string + description: "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned\ + \ by the collector(s) of the sample, normally composed of the name\ + \ or initials of the collector(s) followed by a number (e.g. \"ab109909\"\ + ). This identifier is essential for identifying duplicates held in\ + \ different collections." + nullable: true + example: ab109909 + collectingSite: + type: object + properties: + coordinateUncertainty: + type: string + description: MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated + with the coordinates in metres. Leave the value empty if the uncertainty + is unknown. + nullable: true + example: "20" + elevation: + type: string + description: MCPD (v2.1) (ELEVATION) 16. Elevation of collecting + site expressed in metres above sea level. Negative values are + allowed. + nullable: true + example: "35" + georeferencingMethod: + type: string + description: "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing\ + \ method used (GPS, determined from map, gazetteer, or estimated\ + \ using software). Leave the value empty if georeferencing method\ + \ is not known." + nullable: true + example: WGS84 + latitudeDecimal: + type: string + description: MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in + decimal degrees. Positive values are North of the Equator; negative + values are South of the Equator (e.g. -44.6975). + nullable: true + example: "+42.445295" + latitudeDegrees: + type: string + description: "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes\ + \ (2 digits), and seconds (2 digits) followed by N (North) or\ + \ S (South) (e.g. 103020S). Every missing digit (minutes or seconds)\ + \ should be indicated with a hyphen. Leading zeros are required\ + \ (e.g. 10" + nullable: true + example: 42 26 43.1 N + locationDescription: + type: string + description: "MCPD (v2.1) (COLLSITE) 14. Location information below\ + \ the country level that describes where the accession was collected,\ + \ preferable in English. This might include the distance in kilometres\ + \ and direction from the nearest town, village or map grid reference\ + \ point, (e.g. 7 km south of Townsville)." + nullable: true + example: South east hill near institute buildings + longitudeDecimal: + type: string + description: MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed + in decimal degrees. Positive values are East of the Greenwich + Meridian; negative values are West of the Greenwich Meridian (e.g. + +120.9123). + nullable: true + example: "-076.471934" + longitudeDegrees: + type: string + description: "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes\ + \ (2 digits), and seconds (2 digits) followed by E (East) or W\ + \ (West) (e.g. 0762510W). Every missing digit (minutes or seconds)\ + \ should be indicated with a hyphen. Leading zeros are required\ + \ (e.g. 076" + nullable: true + example: 76 28 19.0 W + spatialReferenceSystem: + type: string + description: MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or + spatial reference system upon which the coordinates given in decimal + latitude and decimal longitude are based (e.g. WGS84). The GPS + uses the WGS84 datum. + nullable: true + example: WGS84 + description: Information about the location where the sample was collected + nullable: true + description: Information about the collection of a germplasm + commonCropName: + type: string + description: "MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example:\ + \ \"malting barley\", \"mas\". " + nullable: true + example: malting barley + countryOfOrigin: + type: string + description: "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the\ + \ country in which the sample was originally collected (e.g. landrace,\ + \ crop wild relative, farmers\" variety), bred or selected (breeding lines,\ + \ GMOs, segregating populations, hybrids, modern cultivars, etc.). Note:\ + \ Descriptors 14 to 16 below should be completed accordingly only if it\ + \ was \"collected\"." + nullable: true + example: Peru + donorInfo: + type: object + properties: + donorAccessionNumber: + type: string + description: MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession + by the donor. Follows ACCENUMB standard. + nullable: true + example: A0090204 + donorAccessionPui: + type: string + description: PUI (DOI mostly) of the accession in the donor system. + nullable: true + example: http://pui.per/accession/A0010025 + donorInstitute: + $ref: "#/components/schemas/Institute" + description: Information about an accession donor + genus: + type: string + description: MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase + letter required. + nullable: true + example: Aspergillus + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + instituteCode: + type: string + description: "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute\ + \ where the accession is maintained. The codes consist of the 3-letter\ + \ ISO 3166 country code of the country where the institute is located\ + \ plus a number (e.g. PER001). The current set of institute codes is available\ + \ from http://www.fao.org/wiews. For those institutes not yet having an\ + \ FAO Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + nullable: true + example: PER001 + mlsStatus: + type: string + description: "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with\ + \ regards to the Multilateral System (MLS) of the International Treaty\ + \ on Plant Genetic Resources for Food and Agriculture. Leave the value\ + \ empty if the status is not known 0 No (not included) 1 Yes (included)\ + \ 99 Other (elaborate in REMARKS field, e.g. \"under development\")" + nullable: true + example: "0" + enum: + - "" + - "0" + - "1" + - "99" + remarks: + type: string + description: MCPD (v2.1) (REMARKS) 28. The remarks field is used to add + notes or to elaborate on descriptors with value 99 or 999 (= Other). Prefix + remarks with the field name they refer to and a colon (:) without space + (e.g. COLLSRC:riverside). Distinct remarks referring to different fields + are separated by semi-colons without space. + nullable: true + example: This is an example remark to demonstrate that any notable information + can be put here + safetyDuplicateInstitutes: + type: array + description: "safetyDuplicateInstitutes: SafetyDuplicateInstitutes" + nullable: true + items: + $ref: "#/components/schemas/Institute" + species: + type: string + description: "MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific\ + \ name in lowercase letters. Only the following abbreviation is allowed:\ + \ \"sp.\" " + nullable: true + example: fructus + speciesAuthority: + type: string + description: MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species + name. + nullable: true + example: "Smith, 1822" + storageTypeCodes: + type: array + description: "MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under\ + \ different types of storage, multiple choices are allowed, separated\ + \ by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards\ + \ 1994 for details on storage type.) 10) Seed collection 11) Short term\ + \ 12) Medium term 13) Long term 20) Field collection 30) In vitro collection\ + \ 40) Cryo-preserved collection 50) DNA collection 99) Other (elaborate\ + \ in REMARKS field)" + nullable: true + items: + type: string + enum: + - "10" + - "11" + - "12" + - "13" + - "20" + - "30" + - "40" + - "50" + - "99" + subtaxon: + type: string + description: "MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any\ + \ additional taxonomic identifier. The following abbreviations are allowed:\ + \ \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\"\ + \ (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\"\ + )." + nullable: true + example: Aspergillus fructus A + subtaxonAuthority: + type: string + description: MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority + at the most detailed taxonomic level. + nullable: true + example: "Smith, 1822" + description: "The conceptual identifiers and metadata describing a genetically\ + \ unique organism that is noteworthy in some way. Depending on context, a\ + \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ + \ Germplasm is conceptual data, not necessarily associated to a real physical\ + \ object, so Seed/Inventory Lots and Observation Units become physical instantiations\ + \ of a particular Germplasm. Note a Germplasm is unique and noteworthy, so\ + \ a Cross may or may not create a new Germplasm, since not every Cross is\ + \ unique or noteworthy." + GermplasmNewRequest: + required: + - commonCropName - germplasmName - germplasmPUI type: object properties: accessionNumber: type: string + description: |- + The unique identifier for a material or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true acquisitionDate: type: string + description: "The date a material or germplasm was acquired by the genebank\ + \ \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the\ + \ collection [YYYYMMDD] where YYYY is the year, MM is the month and DD\ + \ is the day. Missing data (MM or DD) should be indicated with hyphens\ + \ or \"00\" [double zero]." + nullable: true additionalInfo: $ref: "#/components/schemas/AdditionalInfo" biologicalStatusOfAccessionCode: @@ -2332,6 +4177,7 @@ components: \ stocks (e.g. mapping populations) \n500) Advanced or improved cultivar\ \ (conventional breeding methods) \n600) GMO (by genetic engineering)\ \ \n999) Other (Elaborate in REMARKS field)" + nullable: true enum: - "100" - "110" @@ -2356,52 +4202,189 @@ components: - "999" biologicalStatusOfAccessionDescription: type: string + description: Supplemental text description for 'biologicalStatusOfAccessionCode' + nullable: true breedingMethodDbId: type: string breedingMethodName: type: string collection: type: string + description: A specific panel/collection/population name this germplasm + belongs to. + nullable: true commonCropName: type: string + description: "Common name for the crop \n\nMCPD (v2.1) (CROPNAME) 10. Common\ + \ name of the crop. Example: \"malting barley\", \"mas\"." countryOfOriginCode: type: string + description: "3-letter ISO 3166-1 code of the country in which the sample\ + \ was originally collected \n\nMCPD (v2.1) (ORIGCTY) 13. 3-letter ISO\ + \ 3166-1 code of the country in which the sample was originally collected\ + \ (e.g. landrace, crop wild relative, farmers variety), bred or selected\ + \ (breeding lines, GMOs, segregating populations, hybrids, modern cultivars,\ + \ etc.). Note- Descriptors 14 to 16 below should be completed accordingly\ + \ only if it was \"collected\"." + nullable: true defaultDisplayName: type: string + description: Human readable name used for display purposes + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + donors: + type: array + description: List of donor institutes + nullable: true + items: + $ref: "#/components/schemas/Donor" + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" genus: type: string - germplasmDbId: - type: string + description: |- + Genus name for taxon. Initial uppercase letter required. + + MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required. + + MIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature. + nullable: true germplasmName: type: string + description: |- + Name of the germplasm. It can be the preferred name and does not have to be unique. + + MCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space. + germplasmOrigin: + type: array + description: "Information for material (orchard, natural sites, ...). Geographic\ + \ identification of the plants from which seeds or cutting have been taken\ + \ to produce that germplasm." + nullable: true + items: + $ref: "#/components/schemas/GermplasmOrigin" germplasmPUI: type: string + description: |- + The Permanent Unique Identifier which represents a germplasm + + MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. + + MIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source + + MCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties. germplasmPreprocessing: type: string + description: "Description of any process or treatment applied uniformly\ + \ to the germplasm, prior to the study itself. Can be provided as free\ + \ text or as an accession number from a suitable controlled vocabulary." + nullable: true instituteCode: type: string + description: "The code for the institute that maintains the material. \n\ + \nMCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the\ + \ accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + nullable: true instituteName: type: string + description: The name of the institute that maintains the material + nullable: true pedigree: type: string + description: |- + The cross name and optional selection history. + + MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'. + nullable: true sampleDbIds: type: array + description: samples + nullable: true items: type: string seedSource: type: string + description: |- + An identifier for the source of the biological material +
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: "mother_accession X father_accession", or, if father is unknown, as "mother_accession X UNKNOWN". For in situ material, the region of provenance may be used when an accession is not available. + nullable: true seedSourceDescription: type: string + description: |- + Description of the material source + + MIAPPE V1.1 (DM-56) Material source description - Description of the material source + nullable: true species: type: string + description: "Specific epithet portion of the scientific name in lowercase\ + \ letters.\n\nMCPD (v2.1) (SPECIES) 6. Specific epithet portion of the\ + \ scientific name in lowercase letters. Only the following abbreviation\ + \ is allowed: \"sp.\" \n\nMIAPPE V1.1 (DM-44) Species - Species name (formally:\ + \ specific epithet) for the organism under study, according to standard\ + \ scientific nomenclature." + nullable: true speciesAuthority: type: string + description: "The authority organization responsible for tracking and maintaining\ + \ the species name \n\nMCPD (v2.1) (SPAUTHOR) 7. Provide the authority\ + \ for the species name." + nullable: true + storageTypes: + type: array + description: The type of storage this germplasm is kept in at a genebank. + nullable: true + items: + $ref: "#/components/schemas/StorageType" subtaxa: type: string + description: |- + Subtaxon can be used to store any additional taxonomic identifier. + + MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: "subsp." (for subspecies); "convar." (for convariety); "var." (for variety); "f." (for form); "Group" (for "cultivar group"). + + MIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group). + nullable: true subtaxaAuthority: type: string + description: |- + The authority organization responsible for tracking and maintaining the subtaxon information + + MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level. + nullable: true + synonyms: + type: array + description: |- + List of alternative names or IDs used to reference this germplasm + + MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. + nullable: true + items: + $ref: "#/components/schemas/Synonym" + taxonIds: + type: array + description: |- + The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. + + MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. + nullable: true + items: + $ref: "#/components/schemas/TaxonId" description: "The conceptual identifiers and metadata describing a genetically\ \ unique organism that is noteworthy in some way. Depending on context, a\ \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ @@ -2415,6 +4398,21 @@ components: properties: coordinateUncertainty: type: string + description: Uncertainty associated with the coordinates in meters. Leave + the value empty if the uncertainty is unknown. + nullable: true + coordinates: + type: array + description: |- + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + nullable: true + items: + $ref: "#/components/schemas/GeoJSON" germplasmDbId: type: string germplasmName: @@ -2424,6 +4422,20 @@ components: description: "Information for material (orchard, natural sites, ...). Geographic\ \ identification of the plants from which seeds or cutting have been taken\ \ to produce that germplasm." + GermplasmParameters: + type: object + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string GermplasmParent: required: - germplasmDbId @@ -2444,9 +4456,268 @@ components: type: string description: "A germplasm reference that is a direct parent of this germplasm.\ \ These represent edges in the tree, connecting to other nodes." + GermplasmRequest: + type: object + properties: + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + items: + type: string + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + items: + type: string + parentDbIds: + type: array + description: Search for Germplasm with these parents + items: + type: string + progenyDbIds: + type: array + description: Search for Germplasm with these children + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string GermplasmSearchRequest: type: object - properties: {} + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + items: + type: string + parentDbIds: + type: array + description: Search for Germplasm with these parents + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + items: + type: string + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + items: + type: string + progenyDbIds: + type: array + description: Search for Germplasm with these children + items: + type: string description: "The conceptual identifiers and metadata describing a genetically\ \ unique organism that is noteworthy in some way. Depending on context, a\ \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ @@ -2455,745 +4726,4175 @@ components: \ of a particular Germplasm. Note a Germplasm is unique and noteworthy, so\ \ a Cross may or may not create a new Germplasm, since not every Cross is\ \ unique or noteworthy." - GrowthFacility: - type: object - properties: - PUI: - type: string - description: - type: string - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - description: Short description of the facility in which the study was carried - out. - ListType: - type: string - description: The type of objects that are referenced in a List - enum: - - germplasm - - markers - - variants - - programs - - trials - - studies - - observationUnits - - observations - - observationVariables - - samples - Method: - required: - - methodDbId - - methodName - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - bibliographicalReference: - type: string - description: - type: string - formula: - type: string - methodClass: - type: string - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string - ontologyReferenceDbId: - type: string - description: "A description of the way an Observation should be collected. \n\ -
For example, an ObservationVariable might be defined with a Trait of \"\ - plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This\ - \ variable would be distinct from a variable with the Method \"estimation\"\ - \ or \"drone image processing\". " - ObservationUnitHierarchyLevel: + ImageRequest: type: object properties: - levelName: - type: string - levelOrder: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + descriptiveOntologyTerms: + type: array + description: "A list of terms to formally describe the image to search for.\ + \ Each item could be a simple Tag, an Ontology reference Id, or a full\ + \ ontology URL." + items: + type: string + imageDbIds: + type: array + description: A list of image Ids to search for + items: + type: string + imageFileNames: + type: array + description: Image file names to search for. + items: + type: string + imageFileSizeMax: type: integer + description: A maximum image file size to search for. format: int32 - description: "The exact level and level code of an observation unit. \n\nFor\ - \ more information on Observation Levels, please review the Observation\ - \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ - Type of observation unit in textual form, usually one of the following: study,\ - \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ - \ types is possible but not recommended. \nThe observation unit type can not\ - \ be used to indicate sub-plant levels. However, observations can still be\ - \ made on the sub-plant level, as long as the details are indicated in the\ - \ associated observed variable (see observed variables). \nAlternatively,\ - \ it is possible to use samples for more detailed tracing of sub-plant units,\ - \ attaching the observations to them instead.\" " - ObservationUnitPosition: - type: object - properties: - entryType: - type: string - description: "The type of entry for this observation unit. ex. \"CHECK\"\ - , \"TEST\", \"FILLER\"" - enum: - - CHECK - - TEST - - FILLER - observationLevel: - $ref: "#/components/schemas/ObservationUnitLevel" - observationUnitDbId: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string - positionCoordinateX: + example: 20000000 + imageFileSizeMin: + type: integer + description: A minimum image file size to search for. + format: int32 + example: 1000 + imageHeightMax: + type: integer + description: A maximum image height to search for. + format: int32 + example: 1080 + imageHeightMin: + type: integer + description: A minimum image height to search for. + format: int32 + example: 720 + imageLocation: + $ref: "#/components/schemas/GeoJSONSearchArea" + imageNames: + type: array + description: Human readable names to search for. + items: + type: string + imageTimeStampRangeEnd: type: string - positionCoordinateXType: - $ref: "#/components/schemas/PositionCoordinateType" - positionCoordinateY: + description: The latest timestamp to search for. + format: date-time + imageTimeStampRangeStart: type: string - positionCoordinateYType: - $ref: "#/components/schemas/PositionCoordinateType" - description: All positional and layout information related to this Observation - Unit - OntologyReference: - required: - - ontology + description: The earliest timestamp to search for. + format: date-time + imageWidthMax: + type: integer + description: A maximum image width to search for. + format: int32 + example: 1920 + imageWidthMin: + type: integer + description: A minimum image width to search for. + format: int32 + example: 1280 + mimeTypes: + type: array + description: A set of image file types to search for. + items: + type: string + observationDbIds: + type: array + description: A list of observation Ids this image is associated with to + search for + items: + type: string + observationUnitDbIds: + type: array + description: A set of observation unit identifiers to search for. + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + Institute: type: object properties: - ontology: - $ref: "#/components/schemas/Ontology" - ontologyReferenceDbId: + instituteAddress: + type: string + description: MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute + collecting the sample. This descriptor should be used only if COLLCODE + can not be filled since the FAO WIEWS code for this institute is not available. + Multiple values are separated by a semicolon without space. + nullable: true + example: "123 Main Street, Lima, Peru, 5555" + instituteCode: type: string - version: + description: "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute\ + \ collecting the sample. If the holding institute has collected the material,\ + \ the collecting institute code (COLLCODE) should be the same as the holding\ + \ institute code (INSTCODE). Follows INSTCODE standard. Multiple values\ + \ are separated by a semicolon without space." + nullable: true + example: PER001 + instituteName: type: string - description: "MIAPPE V1.1 (DM-85) Variable accession number - Accession number\ - \ of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession\ - \ number - Accession number of the trait in a suitable controlled vocabulary\ - \ (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number\ - \ - Accession number of the method in a suitable controlled vocabulary (Crop\ - \ Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number -\ - \ Accession number of the scale in a suitable controlled vocabulary (Crop\ - \ Ontology)." - OntologyTerm: + description: MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting + the sample. This descriptor should be used only if COLLCODE can not be + filled because the FAO WIEWS code for this institute is not available. + Multiple values are separated by a semicolon without space. + nullable: true + example: The BrAPI Institute + description: The details of an Institute or other simular entity. + ListRequest: type: object properties: - term: - type: string - termURI: - type: string - description: A pointer to an ontology used by a genomic reference - ParentType: - type: string - description: "The type of parent used during crossing. Accepted values for this\ - \ field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn\ - \ a pedigree record, the 'parentType' describes each parent of a particular\ - \ germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe\ - \ how this germplasm was crossed to generate a particular progeny. \\nFor\ - \ example, given a record for germplasm A, having a progeny B and C. The 'parentType'\ - \ field for progeny B item refers \\nto the 'parentType' of A toward B. The\ - \ 'parentType' field for progeny C item refers to the 'parentType' of A toward\ - \ C.\\nIn this way, A could be a male parent to B, but a female parent to\ - \ C. " - enum: - - MALE - - FEMALE - - SELF - - POPULATION - - CLONAL - PedigreeNode: - required: - - germplasmDbId - - germplasmName - - germplasmPUI + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dateCreatedRangeEnd: + type: string + description: Define the end for an interval of time and only include Lists + that are created within this interval. + format: date-time + dateCreatedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are created within this interval. + format: date-time + dateModifiedRangeEnd: + type: string + description: Define the end for an interval of time and only include Lists + that are modified within this interval. + format: date-time + dateModifiedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are modified within this interval. + format: date-time + listDbIds: + type: array + description: An array of primary database identifiers to identify a set + of Lists + items: + type: string + listNames: + type: array + description: An array of human readable names to identify a set of Lists + items: + type: string + listOwnerNames: + type: array + description: An array of names for the people or entities who are responsible + for a set of Lists + items: + type: string + listOwnerPersonDbIds: + type: array + description: An array of primary database identifiers to identify people + or entities who are responsible for a set of Lists + items: + type: string + listSources: + type: array + description: "An array of terms identifying lists from different sources\ + \ (ie 'USER', 'SYSTEM', etc)" + items: + type: string + listType: + $ref: "#/components/schemas/ListType" + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + LocationParameters: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - breedingMethodDbId: - type: string - breedingMethodName: - type: string - crossingProjectDbId: - type: string - crossingProjectName: - type: string - crossingYear: - type: integer - format: int32 - defaultDisplayName: - type: string - familyCode: - type: string - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - pedigreeNodeDbId: - type: string - pedigreeString: - type: string - siblingDbIds: + locationDbIds: type: array + description: The location ids to search for items: type: string - description: "A representation of a particular Germplasm within a pedigree tree,\ - \ and all the links to its parents, siblings, and children. From a list of\ - \ PedigreeNode objects, a client application should have all the information\ - \ it needs to draw a pedigree tree visualization, or calculate genetic distances." - PedigreeNodeSearchRequest: + locationNames: + type: array + description: A human readable names to search for + items: + type: string + LocationRequest: type: object properties: - includeFullTree: - type: boolean - includeParents: - type: boolean - includeProgeny: - type: boolean - includeSiblings: - type: boolean - pedigreeDepth: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Locations + items: + type: string + altitudeMax: + type: number + description: The maximum altitude to search for + example: 200 + altitudeMin: + type: number + description: The minimum altitude to search for + example: 20 + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + coordinates: + $ref: "#/components/schemas/GeoJSONSearchArea" + countryCodes: + type: array + description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ + \ spec" + items: + type: string + countryNames: + type: array + description: The full name of the country to search for + items: + type: string + instituteAddresses: + type: array + description: The street address of the institute to search for + items: + type: string + instituteNames: + type: array + description: The name of the institute to search for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + locationTypes: + type: array + description: "The type of location this represents (ex. Breeding Location,\ + \ Storage Location, etc)" + items: + type: string + parentLocationDbIds: + type: array + description: "The unique identifier for a Location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + items: + type: string + parentLocationNames: + type: array + description: "A human readable name for a location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + MarkerPositionRequest: + type: object + properties: + linkageGroupNames: + type: array + description: A list of Uniquely Identifiable linkage group names + items: + type: string + mapDbIds: + type: array + description: A list of IDs which uniquely identify `GenomeMaps` within the + given database server + items: + type: string + maxPosition: type: integer + description: The maximum position of markers in a given map format: int32 - progenyDepth: + example: 4000 + minPosition: type: integer + description: The minimum position of markers in a given map format: int32 - description: "A representation of a particular Germplasm within a pedigree tree,\ - \ and all the links to its parents, siblings, and children. From a list of\ - \ PedigreeNode objects, a client application should have all the information\ - \ it needs to draw a pedigree tree visualization, or calculate genetic distances." - PlannedCross: - required: - - plannedCrossDbId - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - crossType: - $ref: "#/components/schemas/CrossType" - crossingProjectDbId: - type: string - crossingProjectName: - type: string - parent1: - $ref: "#/components/schemas/CrossParent" - parent2: - $ref: "#/components/schemas/CrossParent" - plannedCrossDbId: - type: string - plannedCrossName: - type: string - status: - type: string - description: "The status of this planned cross. Is it waiting to be performed\ - \ ('TODO'), has it been completed successfully ('DONE'), or has it not\ - \ been done on purpose ('SKIPPED')." - enum: - - TODO - - DONE - - SKIPPED - description: Information regarding the intention to mate specific organisms - together to produce offspring with desired traits. A PlannedCross becomes - an actual Cross when the desired mating event actually occurs in the field. - PollinationEvent: + example: 250 + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server + items: + type: string + MethodRequest: type: object properties: - crossDbId: - type: string - crossName: - type: string - pollinationNumber: - type: string - pollinationSuccessful: - type: boolean - pollinationTimeStamp: - type: string - description: A Pollination Event that was used or attempted for a Cross. - Scale: - required: - - scaleDbId - - scaleName + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + methodDbIds: + type: array + description: The unique identifier for a method. + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + MlsStatus: + type: string + description: "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards\ + \ to the Multilateral System (MLS) of the International Treaty on Plant Genetic\ + \ Resources for Food and Agriculture. Leave the value empty if the status\ + \ is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in\ + \ REMARKS field, e.g. \"under development\")" + enum: + - "" + - "0" + - "1" + - "99" + ObservationRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - dataType: - type: string - description: |- -

Class of the scale, entries can be

-

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

-

"Date" - The date class is for events expressed in a time format, See ISO 8601

-

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

-

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

-

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

-

"Ordinal" - Ordinal scales are scales composed of ordered categories

-

"Text" - A free text is used to express the trait.

- enum: - - Code - - Date - - Duration - - Nominal - - Numerical - - Ordinal - - Text - decimalPlaces: - type: integer - format: int32 - ontologyReferenceDbId: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationDbIds: + type: array + description: The unique id of an Observation + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationTimeStampRangeEnd: type: string - scaleDbId: + description: Timestamp range end + format: date-time + observationTimeStampRangeStart: type: string - scaleName: - type: string - scalePUI: - type: string - units: - type: string - validValues: - $ref: "#/components/schemas/ValidValues" - description: "A Scale describes the units and acceptable values for an ObservationVariable.\ - \ \n
For example, an ObservationVariable might be defined with a Trait\ - \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ - . This variable would be distinct from a variable with the Scale \"inches\"\ - \ or \"pixels\"." - SeedLot: - required: - - seedLotDbId - - seedLotName + description: Timestamp range start + format: date-time + observationUnitDbIds: + type: array + description: The unique id of an Observation Unit + items: + type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ObservationUnitHierarchyLevel: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - amount: - type: number - createdDate: - type: string - lastUpdated: - type: string - locationDbId: - type: string - locationName: - type: string - programDbId: - type: string - programName: - type: string - seedLotDescription: - type: string - seedLotName: - type: string - sourceCollection: - type: string - storageLocation: - type: string - units: + levelName: type: string - description: "A SeedLot, also known as an InventoryLot, is a collection of starting\ - \ material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The\ - \ amount of material available for each Germplasm can be increased by seed\ - \ production and decreased by planting or trading with another breeding Program." - SeedLotNewRequest: - required: - - seedLotDbId - - seedLotDbId - - seedLotName + description: "A name for this level \n\n**Standard Level Names: study, field,\ + \ entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\ + \nFor more information on Observation Levels, please review the Observation Levels documentation. " + nullable: true + levelOrder: + type: integer + description: "`levelOrder` defines where that level exists in the hierarchy\ + \ of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy\ + \ (ie field -> 1) and higher numbers are at the bottom of the hierarchy\ + \ (ie plant -> 9). \n\nFor more information on Observation Levels, please\ + \ review the Observation Levels documentation. " + format: int32 + nullable: true + description: "The exact level and level code of an observation unit. \n\nFor\ + \ more information on Observation Levels, please review the Observation\ + \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ + Type of observation unit in textual form, usually one of the following: study,\ + \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ + \ types is possible but not recommended. \nThe observation unit type can not\ + \ be used to indicate sub-plant levels. However, observations can still be\ + \ made on the sub-plant level, as long as the details are indicated in the\ + \ associated observed variable (see observed variables). \nAlternatively,\ + \ it is possible to use samples for more detailed tracing of sub-plant units,\ + \ attaching the observations to them instead.\" " + ObservationUnitRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - amount: - type: number - createdDate: - type: string - lastUpdated: - type: string - locationDbId: - type: string - locationName: - type: string - programDbId: - type: string - programName: - type: string - seedLotDbId: - type: string - seedLotDescription: - type: string - seedLotName: - type: string - sourceCollection: - type: string - storageLocation: - type: string - units: - type: string - description: "A SeedLot, also known as an InventoryLot, is a collection of starting\ - \ material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The\ - \ amount of material available for each Germplasm can be increased by seed\ - \ production and decreased by planting or trading with another breeding Program." - SeedLotTransaction: - required: - - transactionDbId + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + includeObservations: + type: boolean + description: "Use this parameter to include a list of observations embedded\ + \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ + \ your own risk. It may return large, unpaginated lists of observation\ + \ data. Only set this value to True if you are sure you need to." + example: false + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationUnitDbIds: + type: array + description: The unique id of an observation unit + items: + type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitNames: + type: array + description: The human readable identifier for an Observation Unit + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ObservationVariableParameters: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - amount: - type: number - seedLotDbId: - type: string - seedLotName: - type: string - transactionDbId: - type: string - transactionDescription: - type: string - transactionTimestamp: - type: string - units: - type: string - description: The record of an event where material was moved in or out of a - particular SeedLot - StorageType: + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + ObservationVariableRequest: type: object properties: - code: - type: string - description: "The 2 digit code representing the type of storage this germplasm\ - \ is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm\ - \ is maintained under different types of storage, multiple choices are\ - \ allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI\ - \ Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection\ - \ \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection\ - \ \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA\ - \ collection \n99) Other (elaborate in REMARKS field)" - enum: - - "10" - - "11" - - "12" - - "13" - - "20" - - "30" - - "40" - - "50" - - "99" - description: - type: string - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - description: The type of storage this germplasm is kept in at a genebank. - Synonym: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + OntologyParameters: type: object properties: - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - synonym: - type: string - type: - type: string - description: Alternative names or IDs used to reference this germplasm - TaxonId: - required: - - sourceName - - taxonId + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + OntologyRequest: type: object properties: - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - sourceName: - type: string - taxonId: - type: string - description: "The list of IDs for this SPECIES from different sources. If present,\ - \ NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl.\ - \ The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism\ - \ - An identifier for the organism at the species level. Use of the NCBI taxon\ - \ ID is recommended." - Trait: - required: - - traitName + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + ontologyNames: + type: array + description: The human readable identifier for an ontology definition. + items: + type: string + OntologyTerm: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - attribute: - type: string - attributePUI: - type: string - entity: - type: string - entityPUI: - type: string - mainAbbreviation: - type: string - ontologyReferenceDbId: - type: string - status: - type: string - traitClass: - type: string - traitDbId: - type: string - traitDescription: - type: string - traitName: + term: type: string - traitPUI: + description: Ontology term - the label of the ontology term the termId is + pointing to. + nullable: true + termURI: type: string - description: "A Trait describes what property is being observed. \n
For example,\ - \ an ObservationVariable might be defined with a Trait of \"plant height\"\ - , a Scale of \"meters\", and a Method of \"tape measure\". This variable would\ - \ be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\"\ - . " - TraitDataType: + description: Ontology term identifier - the CURIE for an ontology term. + It differs from the standard GA4GH schema's :ref:`id ` in that it is a + CURIE pointing to an information resource outside of the scope of the + schema or its resource implementation. + nullable: true + description: A pointer to an ontology used by a genomic reference + ParentType: type: string - description: |- -

Class of the scale, entries can be

-

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

-

"Date" - The date class is for events expressed in a time format, See ISO 8601

-

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

-

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

-

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

-

"Ordinal" - Ordinal scales are scales composed of ordered categories

-

"Text" - A free text is used to express the trait.

+ description: "The type of parent used during crossing. Accepted values for this\ + \ field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn\ + \ a pedigree record, the 'parentType' describes each parent of a particular\ + \ germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe\ + \ how this germplasm was crossed to generate a particular progeny. \\nFor\ + \ example, given a record for germplasm A, having a progeny B and C. The 'parentType'\ + \ field for progeny B item refers \\nto the 'parentType' of A toward B. The\ + \ 'parentType' field for progeny C item refers to the 'parentType' of A toward\ + \ C.\\nIn this way, A could be a male parent to B, but a female parent to\ + \ C. " enum: - - Code - - Date - - Duration - - Nominal - - Numerical - - Ordinal - - Text - Variable: + - MALE + - FEMALE + - SELF + - POPULATION + - CLONAL + PedigreeNode: required: - - method - - scale - - trait + - germplasmDbId + - germplasmName + - germplasmPUI + - pedigreeNodeDbId type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" - commonCropName: + breedingMethodDbId: type: string - contextOfUse: - type: array - items: - type: string - defaultValue: + breedingMethodName: type: string - documentationURL: + crossingProjectDbId: type: string - growthStage: + crossingProjectName: type: string - institution: + crossingYear: + type: integer + description: The year the parents were originally crossed + format: int32 + nullable: true + defaultDisplayName: type: string - language: + description: Human readable name used for display purposes + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + familyCode: type: string - method: - $ref: "#/components/schemas/Method" - ontologyReference: - $ref: "#/components/schemas/OntologyReference" - scale: - $ref: "#/components/schemas/Scale" - scientist: + description: The code representing the family of this germplasm + nullable: true + germplasmDbId: type: string - status: + germplasmName: type: string - submissionTimestamp: + germplasmPUI: type: string - synonyms: + parents: + type: array + description: "A list of parent germplasm references in the pedigree tree\ + \ for this germplasm. These represent edges in the tree, connecting to\ + \ other nodes.\n
Typically, this array should only have one parent\ + \ (clonal or self) or two parents (cross). In some special cases, there\ + \ may be more parents, usually when the exact parent is not known. \n\ +
If the parameter 'includeParents' is set to false, then this array\ + \ should be empty, null, or not present in the response." + nullable: true + items: + $ref: "#/components/schemas/GermplasmParent" + pedigreeNodeDbId: + type: string + description: The ID which uniquely identifies a pedigree node + nullable: true + pedigreeString: + type: string + description: The string representation of the pedigree for this germplasm + in PURDY notation + nullable: true + progeny: type: array + description: "A list of germplasm references that are direct children of\ + \ this germplasm. These represent edges in the tree, connecting to other\ + \ nodes.\n
The given germplasm could have a large number of progeny,\ + \ across a number of different breeding methods. The 'parentType' shows\ + \ \n the type of parent this germplasm is to each of the child germplasm\ + \ references.\n
If the parameter 'includeProgeny' is set to false,\ + \ then this array should be empty, null, or not present in the response." + nullable: true + items: + $ref: "#/components/schemas/GermplasmChild" + siblingDbIds: + type: array + description: "A list of sibling germplasm references in the pedigree tree\ + \ for this germplasm. These represent edges in the tree, connecting to\ + \ other nodes.\n
Siblings share at least one parent with the given\ + \ germplasm. \n
If the parameter 'includeSiblings' is set to false,\ + \ then this array should be empty, null, or not present in the response." + nullable: true items: type: string - trait: - $ref: "#/components/schemas/Trait" - description: "A unique combination of Trait, Method, and Scale to define a clear\ - \ context for an Observation." - basePagination: - required: - - currentPage - - pageSize + description: "A representation of a particular Germplasm within a pedigree tree,\ + \ and all the links to its parents, siblings, and children. From a list of\ + \ PedigreeNode objects, a client application should have all the information\ + \ it needs to draw a pedigree tree visualization, or calculate genetic distances." + PedigreeNodeRequest: type: object properties: - currentPage: - type: integer - description: The index number for the returned page of data. This should - always match the requested page number or the default page (0). - example: 0 - default: 0 - pageSize: - type: integer - description: "The number of data elements returned, aka the size of the\ - \ current page. If the requested page does not have enough elements to\ - \ fill a page at the requested page size, this field should indicate the\ - \ actual number of elements returned." - example: 1000 - default: 1000 - totalCount: - type: integer - description: The total number of elements that are available on the server - and match the requested query parameters. - example: 10 - totalPages: + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + items: + type: string + includeFullTree: + type: boolean + description: "If this parameter is true, recursively include ALL of the\ + \ nodes available in this pedigree tree" + example: true + includeParents: + type: boolean + description: "If this parameter is true, include the array of parents in\ + \ the response" + example: true + includeProgeny: + type: boolean + description: "If this parameter is true, include the array of progeny in\ + \ the response" + example: true + includeSiblings: + type: boolean + description: "If this parameter is true, include the array of siblings in\ + \ the response" + example: true + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + items: + type: string + pedigreeDepth: type: integer - description: "The total number of pages of elements available on the server.\ - \ This should be calculated with the following formula. \n
totalPages\ - \ = CEILING( totalCount / requested_page_size)" - example: 1 - description: "The pagination object is applicable only when the payload contains\ - \ a \"data\" key. It describes the pagination of the data contained in the\ - \ \"data\" array, as a way to identify which subset of data is being returned.\ - \ \n
Pages are zero indexed, so the first page will be page 0 (zero)." - dataFile: - required: - - fileURL - type: object - properties: - fileURL: - type: string - description: The absolute URL where the file is located - format: uri - example: https://wiki.brapi.org/examples/datafile.xlsx - fileName: - type: string - description: The name of the file - example: datafile.xlsx - fileSize: + description: "Recursively include this number of levels up the tree in the\ + \ response (parents, grand-parents, great-grand-parents, etc)" + format: int32 + example: 3 + progenyDepth: type: integer - description: The size of the file in bytes - example: 4398 - fileDescription: - type: string - description: A human readable description of the file contents - example: This is an Excel data file - fileType: - type: string - description: The type or format of the file. Preferably MIME Type. - example: application/vnd.ms-excel - fileMD5Hash: - type: string - description: The MD5 Hash of the file contents to be used as a check sum - example: c2365e900c81a89cf74d83dab60df146 - description: A dataFile contains a URL and the relevant file metadata to represent - a file - metadata: - allOf: - - $ref: "#/components/schemas/metadataBase" - - type: object - properties: - pagination: - $ref: "#/components/schemas/basePagination" - metadataBase: - type: object - properties: - datafiles: + description: "Recursively include this number of levels down the tree in\ + \ the response (children, grand-children, great-grand-children, etc)" + format: int32 + example: 3 + programDbIds: type: array - description: "The datafiles contains a list of file URLs and metadata. \n\ - These files contain additional information related to the returned object\ - \ and can be retrieved by a subsequent call. \nThis could be a supplementary\ - \ data file, an informational file, the uploaded file where the data originated\ - \ from, a generated file representing the whole dataset in a particular\ - \ format, or any other related file. " - example: [] + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." items: - $ref: "#/components/schemas/dataFile" - status: + type: string + programNames: type: array - description: "The status field contains a list of informational status messages\ - \ from the server. \nIf no status is reported, an empty list should be\ - \ returned. See Error Reporting for more information." + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: - $ref: "#/components/schemas/status" - description: "An object in the BrAPI standard response model that describes\ - \ some information about the service call being performed. This includes supplementary\ - \ data, status log messages, and pagination information." - metadataTokenPagination: - allOf: - - $ref: "#/components/schemas/metadataBase" - - type: object - properties: - pagination: - $ref: "#/components/schemas/tokenPagination" - status: - required: - - message - - messageType + type: string + species: + type: array + description: List of Species names to identify germplasm + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + PedigreeNodeSearchRequest: type: object properties: - message: - type: string - description: A short message concerning the status of this request/response - example: "Request accepted, response successful" - messageType: - type: string - description: The logging level for the attached message - example: INFO - enum: - - DEBUG - - ERROR - - WARNING - - INFO - description: An array of status messages to convey technical logging information - from the server to the client. - tokenPagination: - allOf: - - $ref: "#/components/schemas/basePagination" - - required: - - nextPageToken - type: object - properties: - nextPageToken: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: type: string - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The string token used to query the next page of data." - example: cb668f63 - deprecated: true - currentPageToken: + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + items: type: string - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The string token used to query the current page of data." - example: 48bc6ac1 - deprecated: true - prevPageToken: + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: type: string - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The string token used to query the previous page of data." - example: 9659857e - deprecated: true - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The pagination object is applicable only when the payload contains\ - \ a \"data\" key. It describes the pagination of the data contained in the\ - \ \"data\" array, as a way to identify which subset of data is being returned.\ - \ \n
Tokenized pages are for large data sets which can not be efficiently\ - \ broken into indexed pages. Use the nextPageToken and prevPageToken to\ - \ construct an additional query and move to the next or previous page respectively.\ - \ " - example: - currentPage: 0 - pageSize: 1000 - totalCount: 10 - totalPages: 1 - responses: + includeParents: + type: boolean + description: "If this parameter is true, include the array of parents in\ + \ the response" + example: true + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + progenyDepth: + type: integer + description: "Recursively include this number of levels down the tree in\ + \ the response (children, grand-children, great-grand-children, etc)" + format: int32 + example: 3 + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + items: + type: string + includeProgeny: + type: boolean + description: "If this parameter is true, include the array of progeny in\ + \ the response" + example: true + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + items: + type: string + includeSiblings: + type: boolean + description: "If this parameter is true, include the array of siblings in\ + \ the response" + example: true + species: + type: array + description: List of Species names to identify germplasm + items: + type: string + pedigreeDepth: + type: integer + description: "Recursively include this number of levels up the tree in the\ + \ response (parents, grand-parents, great-grand-parents, etc)" + format: int32 + example: 3 + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + items: + type: string + includeFullTree: + type: boolean + description: "If this parameter is true, recursively include ALL of the\ + \ nodes available in this pedigree tree" + example: true + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + items: + type: string + description: "A representation of a particular Germplasm within a pedigree tree,\ + \ and all the links to its parents, siblings, and children. From a list of\ + \ PedigreeNode objects, a client application should have all the information\ + \ it needs to draw a pedigree tree visualization, or calculate genetic distances." + PersonRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + emailAddresses: + type: array + description: email address for this person + items: + type: string + firstNames: + type: array + description: Persons first name + items: + type: string + lastNames: + type: array + description: Persons last name + items: + type: string + mailingAddresses: + type: array + description: physical address of this person + items: + type: string + middleNames: + type: array + description: Persons middle name + items: + type: string + personDbIds: + type: array + description: Unique ID for this person + items: + type: string + phoneNumbers: + type: array + description: phone number of this person + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + userIDs: + type: array + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + items: + type: string + PlannedCross: + required: + - plannedCrossDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + crossType: + $ref: "#/components/schemas/CrossType" + crossingProjectDbId: + type: string + crossingProjectName: + type: string + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + parent1: + $ref: "#/components/schemas/CrossParent" + parent2: + $ref: "#/components/schemas/CrossParent" + plannedCrossDbId: + type: string + description: the unique identifier for a planned cross + plannedCrossName: + type: string + description: the human readable name for a planned cross + nullable: true + status: + type: string + description: "The status of this planned cross. Is it waiting to be performed\ + \ ('TODO'), has it been completed successfully ('DONE'), or has it not\ + \ been done on purpose ('SKIPPED')." + nullable: true + enum: + - TODO + - DONE + - SKIPPED + description: Information regarding the intention to mate specific organisms + together to produce offspring with desired traits. A PlannedCross becomes + an actual Cross when the desired mating event actually occurs in the field. + PlannedCrossRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + plannedCrossDbIds: + type: array + description: Search for Planned Cross with this unique id + items: + type: string + plannedCrossNames: + type: array + description: Search for Planned Cross with this human readable name + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + statuses: + type: array + description: "The status of this planned cross. Is it waiting to be performed\ + \ ('TODO'), has it been completed successfully ('DONE'), or has it not\ + \ been done on purpose ('SKIPPED')." + items: + type: string + enum: + - TODO + - DONE + - SKIPPED + PlannedCrossStatus: + type: string + description: "The status of this planned cross. Is it waiting to be performed\ + \ ('TODO'), has it been completed successfully ('DONE'), or has it not been\ + \ done on purpose ('SKIPPED')." + enum: + - TODO + - DONE + - SKIPPED + PlateRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit + items: + type: string + plateBarcodes: + type: array + description: A unique identifier physically attached to the plate + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a plate of samples + items: + type: string + plateNames: + type: array + description: The human readable name of a plate of samples + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a sample + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related Samples + items: + type: string + sampleNames: + type: array + description: The human readable name of the sample + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + PollinationEvent: + type: object + properties: + crossDbId: + type: string + crossName: + type: string + pollinationNumber: + type: string + description: The unique identifier for this pollination event + nullable: true + pollinationSuccessful: + type: boolean + description: True if the pollination was successful + nullable: true + pollinationTimeStamp: + type: string + description: The timestamp when the pollination took place + format: date-time + nullable: true + description: A Pollination Event that was used or attempted for a Cross. + ProgramParameters: + type: object + properties: + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + ProgramRequest: + type: object + properties: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Programs + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + leadPersonDbIds: + type: array + description: The person DbIds of the program leader to search for + items: + type: string + leadPersonNames: + type: array + description: The names of the program leader to search for + items: + type: string + objectives: + type: array + description: A program objective to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + programTypes: + type: array + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding " + items: + type: string + description: |- + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding. + enum: + - STANDARD + - PROJECT + ReferenceBasesRequest: + type: object + properties: + end: + type: integer + description: "The end position (0-based, exclusive) of this query. Defaults\ + \ to the length of this `Reference`." + format: int32 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + start: + type: integer + description: |- + The start position (0-based) of this query. Defaults to 0. + Genomic positions are non-negative integers less than reference length. + Requests spanning the join of circular genomes are represented as + two requests one on each side of the join (position 0). + format: int32 + ReferenceRequest: + type: object + properties: + accessions: + type: array + description: "If specified, return the references for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + isDerived: + type: boolean + description: "A sequence X is said to be derived from source sequence Y,\ + \ if X and Y are of the same length and the per-base sequence divergence\ + \ at A/C/G/T bases is sufficiently small. Two sequences derived from the\ + \ same official sequence share the same coordinates and annotations, and\ + \ can be replaced with the official sequence for certain use cases." + format: boolean + maxLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 90000 + md5checksums: + type: array + description: "If specified, return the references for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + minLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 4000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: A list of IDs which uniquely identify `References` within the + given database server + items: + type: string + referenceSetDbIds: + type: array + description: A list of IDs which uniquely identify `ReferenceSets` within + the given database server + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ReferenceSetRequest: + type: object + properties: + accessions: + type: array + description: "If set, return the reference sets for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + assemblyPUIs: + type: array + description: "If set, return the reference sets for which the `assemblyId`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + md5checksums: + type: array + description: "If set, return the reference sets for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceSetDbIds: + type: array + description: The `ReferenceSets` to search. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + SampleRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an `ObservationUnit` + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a `Plate` of `Samples` + items: + type: string + plateNames: + type: array + description: The human readable name of a `Plate` of `Samples` + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a `Sample` + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related `Samples` + items: + type: string + sampleNames: + type: array + description: The human readable name of the `Sample` + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ScaleRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a scale. + items: + type: string + SeasonRequest: + type: object + properties: + seasonDbIds: + type: array + description: "The unique identifier for a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'." + items: + type: string + seasonNames: + type: array + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + items: + type: string + seasons: + type: array + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + items: + type: string + years: + type: array + description: The 4 digit year of a season. Example "2017" + items: + type: string + SeedLot: + allOf: + - $ref: "#/components/schemas/SeedLotNewRequest" + - required: + - seedLotDbId + type: object + properties: + seedLotDbId: + type: string + description: Unique DbId for the Seed Lot + description: "A SeedLot, also known as an InventoryLot, is a collection of\ + \ starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm.\ + \ The amount of material available for each Germplasm can be increased by\ + \ seed production and decreased by planting or trading with another breeding\ + \ Program." + SeedLotNewRequest: + required: + - seedLotName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + amount: + type: number + description: "The current balance of the amount of material in a SeedLot.\ + \ Could be a count (seeds, bulbs, etc) or a weight (kg of seed)." + nullable: true + contentMixture: + type: array + description: "The mixture of germplasm present in the seed lot.\n
\n\ + If this seed lot only contains a single germplasm, the response should\ + \ contain the name \nand DbId of that germplasm with a mixturePercentage\ + \ value of 100\n
\nIf the seed lot contains a mixture of different\ + \ germplasm, the response should contain \nthe name and DbId every germplasm\ + \ present. The mixturePercentage field should contain \nthe ratio of each\ + \ germplasm in the total mixture. All of the mixturePercentage values\ + \ \nin this array should sum to equal 100." + nullable: true + items: + $ref: "#/components/schemas/ContentMixture" + createdDate: + type: string + description: The time stamp for when this seed lot was created + format: date-time + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + lastUpdated: + type: string + description: The timestamp for the last update to this Seed Lot (including + transactions) + format: date-time + nullable: true + locationDbId: + type: string + locationName: + type: string + programDbId: + type: string + programName: + type: string + seedLotDescription: + type: string + description: A general description of this Seed Lot + nullable: true + seedLotName: + type: string + description: A human readable name for this Seed Lot + sourceCollection: + type: string + description: "The description of the source where this material was originally\ + \ collected (wild, nursery, etc)" + nullable: true + storageLocation: + type: string + description: Description the storage location + nullable: true + transactions: + type: array + description: "The complete history of transactions for this seed lot. This\ + \ includes seed increases, seed usage (planting), and trading with other\ + \ breeding programs." + nullable: true + items: + $ref: "#/components/schemas/SeedLotTransaction" + units: + type: string + description: "A description of the things being counted in a SeedLot (seeds,\ + \ bulbs, kg, tree, etc)" + nullable: true + description: "A SeedLot, also known as an InventoryLot, is a collection of starting\ + \ material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The\ + \ amount of material available for each Germplasm can be increased by seed\ + \ production and decreased by planting or trading with another breeding Program." + SeedLotRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seedLotDbIds: + type: array + description: Unique id for a seed lot on this server + items: + type: string + SeedLotTransaction: + required: + - transactionDbId + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + amount: + type: number + description: "The number of units being transferred between SeedLots. Could\ + \ be a count (seeds, bulbs, etc) or a weight (kg of seed)." + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + seedLotDbId: + type: string + seedLotName: + type: string + transactionDbId: + type: string + description: Unique DbId for the Seed Lot Transaction + transactionDescription: + type: string + description: A general description of this Seed Lot Transaction + nullable: true + transactionTimestamp: + type: string + description: The time stamp for when the transaction occurred + format: date-time + nullable: true + units: + type: string + description: "A description of the things being transferred between SeedLots\ + \ in a transaction (seeds, bulbs, kg, etc)" + nullable: true + description: The record of an event where material was moved in or out of a + particular SeedLot + SortBy: + type: string + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + SortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + StorageType: + type: object + properties: + code: + type: string + description: "The 2 digit code representing the type of storage this germplasm\ + \ is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm\ + \ is maintained under different types of storage, multiple choices are\ + \ allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI\ + \ Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection\ + \ \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection\ + \ \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA\ + \ collection \n99) Other (elaborate in REMARKS field)" + nullable: true + enum: + - "10" + - "11" + - "12" + - "13" + - "20" + - "30" + - "40" + - "50" + - "99" + description: + type: string + description: A supplemental text description of the storage type + nullable: true + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + description: The type of storage this germplasm is kept in at a genebank. + StorageTypeCode: + type: string + description: "The 2 digit code representing the type of storage this germplasm\ + \ is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is\ + \ maintained under different types of storage, multiple choices are allowed,\ + \ separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards\ + \ 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term\ + \ \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro\ + \ collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other\ + \ (elaborate in REMARKS field)" + enum: + - "10" + - "11" + - "12" + - "13" + - "20" + - "30" + - "40" + - "50" + - "99" + StudyParameters: + type: object + properties: + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + StudyRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Study is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: The ID which uniquely identifies a season + items: + type: string + sortBy: + type: string + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + studyCodes: + type: array + description: A short human readable code for a study + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + studyPUIs: + type: array + description: "Permanent unique identifier associated with study data. For\ + \ example, a URI or DOI" + items: + type: string + studyTypes: + type: array + description: "The type of study being performed. ex. \"Yield Trial\", etc" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + Synonym: + type: object + properties: + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + synonym: + type: string + description: Alternative name or ID used to reference this germplasm + nullable: true + type: + type: string + description: A descriptive classification for this synonym + nullable: true + description: Alternative names or IDs used to reference this germplasm + TaxonId: + required: + - sourceName + - taxonId + type: object + properties: + germplasmDbId: + type: string + germplasmName: + type: string + germplasmPUI: + type: string + sourceName: + type: string + description: The human readable name of the taxonomy provider + taxonId: + type: string + description: "The identifier (name, ID, URI) of a particular taxonomy within\ + \ the source provider" + description: "The list of IDs for this SPECIES from different sources. If present,\ + \ NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl.\ + \ The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism\ + \ - An identifier for the organism at the species level. Use of the NCBI taxon\ + \ ID is recommended." + TraitDataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + TraitRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a trait. + items: + type: string + TrialParameters: + type: object + properties: + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + TrialRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Trial is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + contactDbIds: + type: array + description: List of contact entities associated with this trial + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + searchDateRangeEnd: + type: string + description: "The end of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + searchDateRangeStart: + type: string + description: "The start of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + sortBy: + type: string + description: Name of the field to sort by. + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + trialPUIs: + type: array + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + items: + type: string + Variable: + required: + - methodDbId + - methodName + - scaleDbId + - scaleName + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true + contextOfUse: + type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true + items: + type: string + defaultValue: + type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true + documentationURL: + type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + growthStage: + type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true + institution: + type: string + description: Name of institution submitting the variable + nullable: true + language: + type: string + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + scientist: + type: string + description: Name of scientist submitting the variable. + nullable: true + status: + type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true + submissionTimestamp: + type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true + synonyms: + type: array + description: Other variable names + nullable: true + items: + type: string + traitDbId: + type: string + traitName: + type: string + traitPUI: + type: string + description: "A unique combination of Trait, Method, and Scale to define a clear\ + \ context for an Observation." + VariableBaseClassParameters: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + VariantRequest: + type: object + properties: + callSetDbIds: + type: array + description: "**Deprecated in v2.1** Parameter unnecessary. Github issue\ + \ number #474 \n
Only return variant calls which belong to call sets\ + \ with these IDs. If unspecified, return all variants and no variant call\ + \ objects." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + end: + type: integer + description: "The end of the window (0-based, exclusive) for which overlapping\ + \ variants should be returned." + format: int32 + example: 1500 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbId: + type: string + description: |- + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + example: 120a2d5c + referenceDbIds: + type: array + description: The unique identifier representing a genotype `Reference` + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype `ReferenceSet` + items: + type: string + start: + type: integer + description: "The beginning of the window (0-based, inclusive) for which\ + \ overlapping variants should be returned. Genomic positions are non-negative\ + \ integers less than reference length. Requests spanning the join of circular\ + \ genomes are represented as two requests one on each side of the join\ + \ (position 0)." + format: int32 + example: 100 + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` + items: + type: string + VariantSetRequest: + type: object + properties: + callSetDbIds: + type: array + description: The unique identifier representing a CallSet + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: The unique identifier representing a genotype Reference + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype ReferenceSet + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantDbIds: + type: array + description: The unique identifier representing a Variant + items: + type: string + variantSetDbIds: + type: array + description: The unique identifier representing a VariantSet + items: + type: string + basePagination: + required: + - currentPage + - pageSize + type: object + properties: + currentPage: + type: integer + description: The index number for the returned page of data. This should + always match the requested page number or the default page (0). + example: 0 + default: 0 + pageSize: + type: integer + description: "The number of data elements returned, aka the size of the\ + \ current page. If the requested page does not have enough elements to\ + \ fill a page at the requested page size, this field should indicate the\ + \ actual number of elements returned." + example: 1000 + default: 1000 + totalCount: + type: integer + description: The total number of elements that are available on the server + and match the requested query parameters. + example: 10 + totalPages: + type: integer + description: "The total number of pages of elements available on the server.\ + \ This should be calculated with the following formula. \n
totalPages\ + \ = CEILING( totalCount / requested_page_size)" + example: 1 + description: "The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Pages are zero indexed, so the first page will be page 0 (zero)." + dataFile: + required: + - fileURL + type: object + properties: + fileURL: + type: string + description: The absolute URL where the file is located + format: uri + example: https://wiki.brapi.org/examples/datafile.xlsx + fileName: + type: string + description: The name of the file + example: datafile.xlsx + fileSize: + type: integer + description: The size of the file in bytes + example: 4398 + fileDescription: + type: string + description: A human readable description of the file contents + example: This is an Excel data file + fileType: + type: string + description: The type or format of the file. Preferably MIME Type. + example: application/vnd.ms-excel + fileMD5Hash: + type: string + description: The MD5 Hash of the file contents to be used as a check sum + example: c2365e900c81a89cf74d83dab60df146 + description: A dataFile contains a URL and the relevant file metadata to represent + a file + metadata: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/basePagination" + metadataBase: + type: object + properties: + datafiles: + type: array + description: "The datafiles contains a list of file URLs and metadata. \n\ + These files contain additional information related to the returned object\ + \ and can be retrieved by a subsequent call. \nThis could be a supplementary\ + \ data file, an informational file, the uploaded file where the data originated\ + \ from, a generated file representing the whole dataset in a particular\ + \ format, or any other related file. " + example: [] + items: + $ref: "#/components/schemas/dataFile" + status: + type: array + description: "The status field contains a list of informational status messages\ + \ from the server. \nIf no status is reported, an empty list should be\ + \ returned. See Error Reporting for more information." + items: + $ref: "#/components/schemas/status" + description: "An object in the BrAPI standard response model that describes\ + \ some information about the service call being performed. This includes supplementary\ + \ data, status log messages, and pagination information." + metadataTokenPagination: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/tokenPagination" + status: + required: + - message + - messageType + type: object + properties: + message: + type: string + description: A short message concerning the status of this request/response + example: "Request accepted, response successful" + messageType: + type: string + description: The logging level for the attached message + example: INFO + enum: + - DEBUG + - ERROR + - WARNING + - INFO + description: An array of status messages to convey technical logging information + from the server to the client. + tokenPagination: + allOf: + - $ref: "#/components/schemas/basePagination" + - required: + - nextPageToken + type: object + properties: + nextPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the next page of data." + example: cb668f63 + deprecated: true + currentPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the current page of data." + example: 48bc6ac1 + deprecated: true + prevPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the previous page of data." + example: 9659857e + deprecated: true + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken to\ + \ construct an additional query and move to the next or previous page respectively.\ + \ " + example: + currentPage: 0 + pageSize: 1000 + totalCount: 10 + totalPages: 1 + responses: + VariantSingleResponse: + description: OK + content: + application/json: + schema: + title: VariantSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Variant" + SeedLotSingleResponse: + description: OK + content: + application/json: + schema: + title: SeedLotSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/SeedLot" + "202AcceptedSearchResponse": + description: Accepted + content: + application/json: + schema: + title: 202AcceptedSearchResponse + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + type: object + properties: + searchResultsDbId: + type: string + example: 551ae08c + StudyStudyTypeListResponse: + description: OK + content: + application/json: + schema: + title: StudyStudyTypeListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: string + StudySingleResponse: + description: OK + content: + application/json: + schema: + title: StudySingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Study" + MarkerPositionListResponse: + description: OK + content: + application/json: + schema: + title: MarkerPositionListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/MarkerPosition" + TrialListResponse: + description: OK + content: + application/json: + schema: + title: TrialListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Trial" + SeedLotListResponse: + description: OK + content: + application/json: + schema: + title: SeedLotListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/SeedLot" + VariantSetListResponse: + description: OK + content: + application/json: + schema: + title: VariantSetListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/VariantSet" + SampleSingleResponse: + description: OK + content: + application/json: + schema: + title: SampleSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Sample" + CallSetListResponse: + description: OK + content: + application/json: + schema: + title: CallSetListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/CallSet" + CallSetSingleResponse: + description: OK + content: + application/json: + schema: + title: CallSetSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/CallSet" + VariantSetSingleResponse: + description: OK + content: + application/json: + schema: + title: VariantSetSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/VariantSet" + ReferenceSetSingleResponse: + description: OK + content: + application/json: + schema: + title: ReferenceSetSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ReferenceSet" + CrossListResponse: + description: OK + content: + application/json: + schema: + title: CrossListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Cross" + PlateListResponse: + description: OK + content: + application/json: + schema: + title: PlateListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Plate" + SeasonListResponse: + description: OK + content: + application/json: + schema: + title: SeasonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Season" + ReferenceBasesSingleResponse: + description: OK + content: + application/json: + schema: + title: ReferenceBasesSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ReferenceBases" + ReferenceListResponse: + description: OK + content: + application/json: + schema: + title: ReferenceListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Reference" + AlleleMatrixListResponse: + description: OK + content: + application/json: + schema: + title: AlleleMatrixListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/AlleleMatrix" + GenomeMapSingleResponse: + description: OK + content: + application/json: + schema: + title: GenomeMapSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GenomeMap" + PersonListResponse: + description: OK + content: + application/json: + schema: + title: PersonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Person" + PlannedCrossListResponse: + description: OK + content: + application/json: + schema: + title: PlannedCrossListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/PlannedCross" + LocationListResponse: + description: OK + content: + application/json: + schema: + title: LocationListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Location" + "403Forbidden": + description: Forbidden + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to + perform this action + ProgramListResponse: + description: OK + content: + application/json: + schema: + title: ProgramListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Program" + ListListResponse: + description: OK + content: + application/json: + schema: + title: ListListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/List" + "400BadRequest": + description: Bad Request + content: + application/json: + schema: + type: string + example: |- + ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object + + ERROR - 2018-10-08T18:15:11Z - Invalid query parameter + + ERROR - 2018-10-08T18:15:11Z - Required parameter is missing + CrossingProjectListResponse: + description: OK + content: + application/json: + schema: + title: CrossingProjectListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/CrossingProject" + GermplasmAttributeSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GermplasmAttribute" "401Unauthorized": description: Unauthorized content: @@ -3250,12 +8951,12 @@ components: type: array items: $ref: "#/components/schemas/Germplasm" - SeedLotSingleResponse: + CrossingProjectSingleResponse: description: OK content: application/json: schema: - title: SeedLotSingleResponse + title: CrossingProjectSingleResponse required: - metadata - result @@ -3266,31 +8967,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/SeedLot" - "202AcceptedSearchResponse": - description: Accepted - content: - application/json: - schema: - title: 202AcceptedSearchResponse - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - type: object - properties: - searchResultsDbId: - type: string - example: 551ae08c - StudySingleResponse: + $ref: "#/components/schemas/CrossingProject" + SampleListResponse: description: OK content: application/json: schema: - title: StudySingleResponse + title: SampleListResponse required: - metadata - result @@ -3301,13 +8984,20 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Study" - CrossingProjectSingleResponse: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Sample" + GermplasmMCPDSingleResponse: description: OK content: application/json: schema: - title: CrossingProjectSingleResponse + title: GermplasmMCPDSingleResponse required: - metadata - result @@ -3318,13 +9008,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/CrossingProject" - TrialListResponse: + $ref: "#/components/schemas/GermplasmMCPD" + ReferenceSetListResponse: description: OK content: application/json: schema: - title: TrialListResponse + title: ReferenceSetListResponse required: - metadata - result @@ -3342,13 +9032,13 @@ components: data: type: array items: - $ref: "#/components/schemas/Trial" - SeedLotListResponse: + $ref: "#/components/schemas/ReferenceSet" + TrialSingleResponse: description: OK content: application/json: schema: - title: SeedLotListResponse + title: TrialSingleResponse required: - metadata - result @@ -3359,20 +9049,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/SeedLot" - TrialSingleResponse: + $ref: "#/components/schemas/Trial" + GermplasmSingleResponse: description: OK content: application/json: schema: - title: TrialSingleResponse + title: GermplasmSingleResponse required: - metadata - result @@ -3383,13 +9066,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Trial" - GermplasmSingleResponse: + $ref: "#/components/schemas/Germplasm" + SeasonSingleResponse: description: OK content: application/json: schema: - title: GermplasmSingleResponse + title: SeasonSingleResponse required: - metadata - result @@ -3400,13 +9083,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Germplasm" - SeasonSingleResponse: + $ref: "#/components/schemas/Season" + ReferenceSingleResponse: description: OK content: application/json: schema: - title: SeasonSingleResponse + title: ReferenceSingleResponse required: - metadata - result @@ -3417,7 +9100,7 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Season" + $ref: "#/components/schemas/Reference" "404NotFound": description: Not Found content: @@ -3450,12 +9133,12 @@ components: type: array items: $ref: "#/components/schemas/Study" - CrossListResponse: + LinkageGroupListResponse: description: OK content: application/json: schema: - title: CrossListResponse + title: LinkageGroupListResponse required: - metadata - result @@ -3473,13 +9156,13 @@ components: data: type: array items: - $ref: "#/components/schemas/Cross" - BreedingMethodSingleResponse: + $ref: "#/components/schemas/LinkageGroup" + CallListResponse: description: OK content: application/json: schema: - title: BreedingMethodSingleResponse + title: CallListResponse required: - metadata - result @@ -3490,13 +9173,20 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/BreedingMethod" - LocationSingleResponse: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Call" + BreedingMethodSingleResponse: description: OK content: application/json: schema: - title: LocationSingleResponse + title: BreedingMethodSingleResponse required: - metadata - result @@ -3507,13 +9197,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Location" - SeasonListResponse: + $ref: "#/components/schemas/BreedingMethod" + LocationSingleResponse: description: OK content: application/json: schema: - title: SeasonListResponse + title: LocationSingleResponse required: - metadata - result @@ -3524,14 +9214,7 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Season" + $ref: "#/components/schemas/Location" PersonSingleResponse: description: OK content: @@ -3549,36 +9232,12 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/Person" - PersonListResponse: - description: OK - content: - application/json: - schema: - title: PersonListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Person" - PlannedCrossListResponse: + VariantListResponse: description: OK content: application/json: schema: - title: PlannedCrossListResponse + title: VariantListResponse required: - metadata - result @@ -3596,13 +9255,13 @@ components: data: type: array items: - $ref: "#/components/schemas/PlannedCross" - LocationListResponse: + $ref: "#/components/schemas/Variant" + PlateSingleResponse: description: OK content: application/json: schema: - title: LocationListResponse + title: PlateSingleResponse required: - metadata - result @@ -3613,14 +9272,7 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Location" + $ref: "#/components/schemas/Plate" GermplasmAttributeValueListResponse: description: OK content: @@ -3645,14 +9297,6 @@ components: type: array items: $ref: "#/components/schemas/GermplasmAttributeValue" - "403Forbidden": - description: Forbidden - content: - application/json: - schema: - type: string - example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to - perform this action BreedingMethodListResponse: description: OK content: @@ -3677,29 +9321,12 @@ components: type: array items: $ref: "#/components/schemas/BreedingMethod" - GermplasmAttributeValueSingleResponse: - description: OK - content: - application/json: - schema: - title: GermplasmAttributeValueSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/GermplasmAttributeValue" - ProgramListResponse: + GermplasmAttributeAttributeCategoryListResponse: description: OK content: application/json: schema: - title: ProgramListResponse + title: GermplasmAttributeAttributeCategoryListResponse required: - metadata - result @@ -3717,13 +9344,13 @@ components: data: type: array items: - $ref: "#/components/schemas/Program" - ListListResponse: + type: string + GermplasmAttributeValueSingleResponse: description: OK content: application/json: schema: - title: ListListResponse + title: GermplasmAttributeValueSingleResponse required: - metadata - result @@ -3734,32 +9361,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/List" - "400BadRequest": - description: Bad Request - content: - application/json: - schema: - type: string - example: |- - ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object - - ERROR - 2018-10-08T18:15:11Z - Invalid query parameter - - ERROR - 2018-10-08T18:15:11Z - Required parameter is missing - CrossingProjectListResponse: + $ref: "#/components/schemas/GermplasmAttributeValue" + GenomeMapListResponse: description: OK content: application/json: schema: - title: CrossingProjectListResponse + title: GenomeMapListResponse required: - metadata - result @@ -3777,7 +9385,7 @@ components: data: type: array items: - $ref: "#/components/schemas/CrossingProject" + $ref: "#/components/schemas/GenomeMap" PedigreeNodeListResponse: description: OK content: @@ -3836,23 +9444,6 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/Program" - GermplasmAttributeSingleResponse: - description: OK - content: - application/json: - schema: - title: GermplasmAttributeSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/GermplasmAttribute" parameters: externalReferenceID: name: externalReferenceID @@ -3917,6 +9508,18 @@ components: schema: type: integer example: 1000 + authorizationHeader: + name: Authorization + in: header + description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ + \ {token_string} " + required: false + style: simple + explode: false + schema: + pattern: ^Bearer .*$ + type: string + example: Bearer XXXX page: name: page in: query @@ -3945,18 +9548,6 @@ components: schema: type: string example: 33c27874 - authorizationHeader: - name: Authorization - in: header - description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ - \ {token_string} " - required: false - style: simple - explode: false - schema: - pattern: ^Bearer .*$ - type: string - example: Bearer XXXX securitySchemes: AuthorizationToken: type: http diff --git a/Specification/Generated/BrAPI-Phenotyping.yaml b/Specification/Generated/BrAPI-Phenotyping.yaml index d7a04c78..b5a49dee 100644 --- a/Specification/Generated/BrAPI-Phenotyping.yaml +++ b/Specification/Generated/BrAPI-Phenotyping.yaml @@ -16,12 +16,6 @@ paths: required: false schema: type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - name: observationUnitDbId in: query description: The ID which uniquely identifies an observation unit. @@ -46,12 +40,14 @@ paths: required: false schema: type: string + format: date-time - name: dateRangeEnd in: query description: Filter based on an Event start date. required: false schema: type: string + format: date-time - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" - $ref: "#/components/parameters/authorizationHeader" @@ -93,15 +89,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: descriptiveOntologyTerm in: query description: "A list of terms to formally describe the image to search for.\ @@ -110,83 +97,12 @@ paths: required: false schema: type: string - - name: imageFileName - in: query - description: Image file names to search for. - required: false - schema: - type: string - - name: imageFileSizeMax - in: query - description: A maximum image file size to search for. - required: false - schema: - type: integer - format: int32 - - name: imageFileSizeMin - in: query - description: A minimum image file size to search for. - required: false - schema: - type: integer - format: int32 - - name: imageHeightMax - in: query - description: A maximum image height to search for. - required: false - schema: - type: integer - format: int32 - - name: imageHeightMin - in: query - description: A minimum image height to search for. - required: false - schema: - type: integer - format: int32 - - name: imageLocation - in: query - required: false - schema: - $ref: "#/components/schemas/GeoJSONSearchArea" - name: imageName in: query description: Human readable names to search for. required: false schema: type: string - - name: imageTimeStampRangeEnd - in: query - description: The latest timestamp to search for. - required: false - schema: - type: string - - name: imageTimeStampRangeStart - in: query - description: The earliest timestamp to search for. - required: false - schema: - type: string - - name: imageWidthMax - in: query - description: A maximum image width to search for. - required: false - schema: - type: integer - format: int32 - - name: imageWidthMin - in: query - description: A minimum image width to search for. - required: false - schema: - type: integer - format: int32 - - name: mimeType - in: query - description: A set of image file types to search for. - required: false - schema: - type: string - name: observationDbId in: query description: A list of observation Ids this image is associated with to search @@ -206,7 +122,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -232,7 +147,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ImageNewRequest" + type: array + items: + $ref: "#/components/schemas/ImageNewRequest" responses: "200": $ref: "#/components/responses/ImageListResponse" @@ -279,16 +196,7 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - - name: scaleDbId + - name: methodDbId in: query description: The unique identifier for a method. required: false @@ -300,7 +208,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -326,7 +233,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/MethodNewRequest" + type: array + items: + $ref: "#/components/schemas/MethodNewRequest" responses: "200": $ref: "#/components/responses/MethodListResponse" @@ -361,123 +270,145 @@ paths: required: false schema: type: string - - name: germplasmName - in: query - description: List of human readable names to identify germplasm to search - for - required: false - schema: - type: string - name: locationDbId in: query description: The location ids to search for required: false schema: type: string - - name: locationName - in: query - description: A human readable names to search for - required: false - schema: - type: string - name: observationVariableDbId in: query description: The DbIds of Variables to search for required: false schema: type: string - - name: observationVariableName + - name: programDbId in: query - description: The names of Variables to search for + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." required: false schema: type: string - - name: observationVariablePUI + - name: studyDbId in: query - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" + description: List of study identifiers to search for required: false schema: type: string - - name: programDbId + - name: trialDbId in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." + description: The ID which uniquely identifies a trial to search for required: false schema: type: string - - name: programName + - name: observationDbId in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: The unique id of an Observation required: false schema: type: string - - name: studyDbId + - name: observationUnitDbId in: query - description: List of study identifiers to search for + description: The unique id of an Observation Unit required: false schema: type: string - - name: studyName + - name: observationUnitLevelName in: query - description: List of study names to filter search results + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on Observation\ + \ Levels, please review the Observation Levels documentation. " required: false schema: type: string - - name: trialDbId + - name: observationUnitLevelOrder in: query - description: The ID which uniquely identifies a trial to search for + description: "The Observation Unit Level Order Number. Returns only the observation\ + \ unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " required: false schema: type: string - - name: trialName + - name: observationUnitLevelCode in: query - description: The human readable name of a trial to search for + description: "The Observation Unit Level Code. This parameter should be used\ + \ together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " required: false schema: type: string - - name: observationDbId + - name: observationUnitLevelRelationshipName in: query - description: The unique id of an Observation + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a relationship\ + \ level. \n
**Standard Level Names: study, field, entry, rep, block,\ + \ sub-block, plot, sub-plot, plant, pot, sample** \n
For more information\ + \ on Observation Levels, please review the Observation Levels\ + \ documentation. " required: false schema: type: string - - name: observationUnitDbId + - name: observationUnitLevelRelationshipOrder in: query - description: The unique id of an Observation Unit + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " required: false schema: type: string - - name: observationLevel + - name: observationUnitLevelRelationshipCode in: query - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " required: false schema: - $ref: "#/components/schemas/ObservationUnitLevel" - - name: observationLevelRelationship + type: string + - name: observationUnitLevelRelationshipDbId in: query - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + description: "The observationUnitDbId associated with a particular level and\ + \ code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " required: false schema: - $ref: "#/components/schemas/ObservationUnitLevelRelationship" + type: string - name: observationTimeStampRangeEnd in: query description: Timestamp range end required: false schema: type: string + format: date-time - name: observationTimeStampRangeStart in: query description: Timestamp range start required: false schema: type: string + format: date-time - name: seasonDbId in: query description: "The year or Phenotyping campaign of a multi-annual study (trees,\ @@ -485,7 +416,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -511,7 +441,18 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ObservationNewRequest" + type: object + additionalProperties: + $ref: "#/components/schemas/ObservationNewRequest" + example: "{_1={additionalInfo={}, collector=1835c514,\ + \ externalReferences=[{}], geoCoordinates={}, germplasm={}, observationDbId=5cbd4c1c,\ + \ observationTimeStamp=2020-08-12T18:10:40.413Z, observationUnit={},\ + \ observationVariable={}, season={}, study={}, uploadedBy=3fc74c0a,\ + \ value=4ee59cb0, images=[{}]}, _2={additionalInfo={},\ + \ collector=1835c515, externalReferences=[{}], geoCoordinates={},\ + \ germplasm={}, observationDbId=5cbd4c1d, observationTimeStamp=2020-08-12T18:10:40.413Z,\ + \ observationUnit={}, observationVariable={}, season={}, study={},\ + \ uploadedBy=3fc74c0b, value=4ee59cb1, images=[{}]}}" responses: "200": $ref: "#/components/responses/ObservationListResponse" @@ -532,7 +473,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ObservationNewRequest" + type: array + items: + $ref: "#/components/schemas/ObservationNewRequest" responses: "200": $ref: "#/components/responses/ObservationListResponse" @@ -567,112 +510,126 @@ paths: required: false schema: type: string - - name: germplasmName - in: query - description: List of human readable names to identify germplasm to search - for - required: false - schema: - type: string - name: locationDbId in: query description: The location ids to search for required: false schema: type: string - - name: locationName - in: query - description: A human readable names to search for - required: false - schema: - type: string - name: studyDbId in: query description: List of study identifiers to search for required: false schema: type: string - - name: studyName + - name: programDbId in: query - description: List of study names to filter search results + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." required: false schema: type: string - - name: observationVariableDbId + - name: trialDbId in: query - description: The DbIds of Variables to search for + description: The ID which uniquely identifies a trial to search for required: false schema: type: string - - name: observationVariableName + - name: observationUnitDbId in: query - description: The names of Variables to search for + description: The unique id of an observation unit required: false schema: type: string - - name: observationVariablePUI + - name: observationUnitName in: query - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" + description: The human readable identifier for an Observation Unit required: false schema: type: string - - name: programDbId + - name: observationUnitLevelName in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on Observation\ + \ Levels, please review the Observation Levels documentation. " required: false schema: type: string - - name: programName + - name: observationUnitLevelOrder in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: "The Observation Unit Level Order Number. Returns only the observation\ + \ unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " required: false schema: type: string - - name: trialDbId + - name: observationUnitLevelCode in: query - description: The ID which uniquely identifies a trial to search for + description: "The Observation Unit Level Code. This parameter should be used\ + \ together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " required: false schema: type: string - - name: trialName + - name: observationUnitLevelRelationshipName in: query - description: The human readable name of a trial to search for + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a relationship\ + \ level. \n
**Standard Level Names: study, field, entry, rep, block,\ + \ sub-block, plot, sub-plot, plant, pot, sample** \n
For more information\ + \ on Observation Levels, please review the Observation Levels\ + \ documentation. " required: false schema: type: string - - name: observationUnitDbId + - name: observationUnitLevelRelationshipOrder in: query - description: The unique id of an observation unit + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " required: false schema: type: string - - name: observationUnitName + - name: observationUnitLevelRelationshipCode in: query - description: The human readable identifier for an Observation Unit + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " required: false schema: type: string - - name: observationLevel - in: query - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel - required: false - schema: - $ref: "#/components/schemas/ObservationUnitLevel" - - name: observationLevelRelationship + - name: observationUnitLevelRelationshipDbId in: query - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + description: "The observationUnitDbId associated with a particular level and\ + \ code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " required: false schema: - $ref: "#/components/schemas/ObservationUnitLevelRelationship" - - name: includeObservation + type: string + - name: includeObservations in: query description: "Use this parameter to include a list of observations embedded\ \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at your\ @@ -688,7 +645,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -714,7 +670,18 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ObservationUnitNewRequest" + type: object + additionalProperties: + $ref: "#/components/schemas/ObservationUnitNewRequest" + example: "{_1={additionalInfo={}, cross={}, externalReferences=[{}],\ + \ germplasm={}, location={}, observationUnitDbId=59ce1af8, observationUnitName=5a5b18e6,\ + \ observationUnitPUI=491c6d6d, observationUnitPosition=[{}], program={},\ + \ seedLot={}, study={}, treatments=[{}], trial={}, samples=[{}], events=[{}],\ + \ images=[{}], observations=[{}]}, _2={additionalInfo={},\ + \ cross={}, externalReferences=[{}], germplasm={}, location={}, observationUnitDbId=59ce1af9,\ + \ observationUnitName=5a5b18e7, observationUnitPUI=491c6d6e, observationUnitPosition=[{}],\ + \ program={}, seedLot={}, study={}, treatments=[{}], trial={}, samples=[{}],\ + \ events=[{}], images=[{}], observations=[{}]}}" responses: "200": $ref: "#/components/responses/ObservationUnitListResponse" @@ -735,7 +702,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ObservationUnitNewRequest" + type: array + items: + $ref: "#/components/schemas/ObservationUnitNewRequest" responses: "200": $ref: "#/components/responses/ObservationUnitListResponse" @@ -793,39 +762,12 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - - name: studyDbId - in: query - description: List of study identifiers to search for - required: false - schema: - type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - name: trialDbId in: query description: The ID which uniquely identifies a trial to search for required: false schema: type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - name: studyDbId in: query description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ @@ -881,12 +823,6 @@ paths: required: false schema: type: string - - name: dataType - in: query - description: List of scale data types to filter search results - required: false - schema: - $ref: "#/components/schemas/TraitDataType" - name: traitClass in: query description: List of trait classes to filter search results @@ -914,40 +850,6 @@ paths: required: false schema: type: string - - name: traitAttribute - in: query - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the attribute is the observed feature (or characteristic) of the entity\ - \ e.g., for \"grain colour\", attribute = \"colour\"" - required: false - schema: - type: string - - name: traitAttributePUI - in: query - description: |- - The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI -
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" - required: false - schema: - type: string - - name: traitEntity - in: query - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the entity is the part of the plant that the trait refers to e.g., for\ - \ \"grain colour\", entity = \"grain\"" - required: false - schema: - type: string - - name: traitEntityPUI - in: query - description: "The Permanent Unique Identifier of a Trait Entity, usually in\ - \ the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\"\ - \ + \"Attribute\", the entity is the part of the plant that the trait refers\ - \ to e.g., for \"grain colour\", entity = \"grain\" " - required: false - schema: - type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -973,7 +875,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ObservationVariableNewRequest" + type: array + items: + $ref: "#/components/schemas/ObservationVariableNewRequest" responses: "200": $ref: "#/components/responses/ObservationVariableListResponse" @@ -1027,7 +931,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/OntologyNewRequest" + type: array + items: + $ref: "#/components/schemas/OntologyNewRequest" responses: "200": $ref: "#/components/responses/OntologyListResponse" @@ -1074,15 +980,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: scaleDbId in: query description: The unique identifier for a scale. @@ -1095,7 +992,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -1121,7 +1017,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ScaleNewRequest" + type: array + items: + $ref: "#/components/schemas/ScaleNewRequest" responses: "200": $ref: "#/components/responses/ScaleListResponse" @@ -1168,15 +1066,6 @@ paths: required: false schema: type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - name: traitDbId in: query description: The unique identifier for a trait. @@ -1189,7 +1078,6 @@ paths: required: false schema: type: string - - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" @@ -1215,7 +1103,9 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/TraitNewRequest" + type: array + items: + $ref: "#/components/schemas/TraitNewRequest" responses: "200": $ref: "#/components/responses/TraitListResponse" @@ -1231,6 +1121,14 @@ paths: - Images summary: Get the details of a specific Image description: Get details for a Image + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: imageDbId + in: path + description: The unique identifier of an image + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/ImageSingleResponse" @@ -1240,6 +1138,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Images @@ -1247,6 +1147,12 @@ paths: description: Update the details for an existing Image parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: imageDbId + in: path + description: The unique identifier of an image + required: true + schema: + type: string requestBody: content: application/json: @@ -1261,21 +1167,64 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - /methods/{methodDbId}: - get: + "404": + $ref: "#/components/responses/404NotFound" + /images/{imageDbId}/imagecontent: + put: tags: - - Methods - summary: Get the details of a specific Method - description: Get details for a Method - responses: - "200": - $ref: "#/components/responses/MethodSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": + - Images + summary: Update the details for an existing string + description: Update the details for an existing string + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: imageDbId + in: path + description: The unique identifier of an image + required: true + schema: + type: string + requestBody: + content: + image/*: + schema: + type: string + format: binary + responses: + "200": + $ref: "#/components/responses/ImageSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /methods/{methodDbId}: + get: + tags: + - Methods + summary: Get the details of a specific Method + description: Get details for a Method + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: methodDbId + in: path + description: Method unique identifier + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/MethodSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Methods @@ -1283,6 +1232,12 @@ paths: description: Update the details for an existing Method parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: methodDbId + in: path + description: Method unique identifier + required: true + schema: + type: string requestBody: content: application/json: @@ -1297,12 +1252,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /observations/{observationDbId}: get: tags: - Observations summary: Get the details of a specific Observation description: Get details for a Observation + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: observationDbId + in: path + description: The ID which uniquely identifies an observation + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/ObservationSingleResponse" @@ -1312,12 +1277,25 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /observationunits/{observationUnitDbId}: get: tags: - ObservationUnits summary: Get the details of a specific ObservationUnit description: Get details for a ObservationUnit + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: observationUnitDbId + in: path + description: "The ID which uniquely identifies an observation unit\n\nMIAPPE\ + \ V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation\ + \ unit in data files containing the values observed or measured on that\ + \ unit. Must be locally unique. " + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/ObservationUnitSingleResponse" @@ -1327,12 +1305,25 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /variables/{observationVariableDbId}: get: tags: - ObservationVariables summary: Get the details of a specific ObservationVariable description: Get details for a ObservationVariable + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: observationVariableDbId + in: path + description: |- + Variable unique identifier + + MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/ObservationVariableSingleResponse" @@ -1342,6 +1333,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - ObservationVariables @@ -1349,6 +1342,15 @@ paths: description: Update the details for an existing ObservationVariable parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: observationVariableDbId + in: path + description: |- + Variable unique identifier + + MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. + required: true + schema: + type: string requestBody: content: application/json: @@ -1363,12 +1365,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /ontologies/{ontologyDbId}: get: tags: - Ontologies summary: Get the details of a specific Ontology description: Get details for a Ontology + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: ontologyDbId + in: path + description: Ontology database unique identifier + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/OntologySingleResponse" @@ -1378,6 +1390,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Ontologies @@ -1385,6 +1399,12 @@ paths: description: Update the details for an existing Ontology parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: ontologyDbId + in: path + description: Ontology database unique identifier + required: true + schema: + type: string requestBody: content: application/json: @@ -1399,12 +1419,23 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /scales/{scaleDbId}: get: tags: - Scales summary: Get the details of a specific Scale description: Get details for a Scale + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: scaleDbId + in: path + description: "Unique identifier of the scale. If left blank, the upload system\ + \ will automatically generate a scale ID." + required: true + schema: + type: string responses: "200": $ref: "#/components/responses/ScaleSingleResponse" @@ -1414,6 +1445,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Scales @@ -1421,6 +1454,13 @@ paths: description: Update the details for an existing Scale parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: scaleDbId + in: path + description: "Unique identifier of the scale. If left blank, the upload system\ + \ will automatically generate a scale ID." + required: true + schema: + type: string requestBody: content: application/json: @@ -1435,12 +1475,22 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /traits/{traitDbId}: get: tags: - Traits summary: Get the details of a specific Trait description: Get details for a Trait + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: traitDbId + in: path + description: The ID which uniquely identifies a trait + required: false + schema: + type: string responses: "200": $ref: "#/components/responses/TraitSingleResponse" @@ -1450,6 +1500,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" put: tags: - Traits @@ -1457,6 +1509,12 @@ paths: description: Update the details for an existing Trait parameters: - $ref: "#/components/parameters/authorizationHeader" + - name: traitDbId + in: path + description: The ID which uniquely identifies a trait + required: false + schema: + type: string requestBody: content: application/json: @@ -1471,6 +1529,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/images: post: tags: @@ -1483,6 +1543,13 @@ paths: \ `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.\ \
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ImageSearchRequest" responses: "200": $ref: "#/components/responses/ImageListResponse" @@ -1507,6 +1574,13 @@ paths: \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationSearchRequest" responses: "200": $ref: "#/components/responses/ObservationListResponse" @@ -1531,6 +1605,13 @@ paths: \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationUnitSearchRequest" responses: "200": $ref: "#/components/responses/ObservationUnitListResponse" @@ -1555,6 +1636,13 @@ paths: \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationVariableSearchRequest" responses: "200": $ref: "#/components/responses/ObservationVariableListResponse" @@ -1585,6 +1673,16 @@ paths: \ \nUse this endpoint to retrieve the results of the search.
\nReview\ \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/ImageListResponse" @@ -1613,6 +1711,16 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/ObservationListResponse" @@ -1642,6 +1750,16 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/ObservationUnitListResponse" @@ -1671,6 +1789,16 @@ paths: \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" responses: "200": $ref: "#/components/responses/ObservationVariableListResponse" @@ -1683,205 +1811,566 @@ paths: components: schemas: AdditionalInfo: - type: object - properties: - additionalProperties: - type: string + type: string + additionalProperties: + description: A free space containing any additional information related to + a particular object. description: "A free space containing any additional information related to\ \ a particular object. A data source may provide any JSON object, unrestricted\ \ by the BrAPI specification." - AlleleMatrix: - required: - - callSetDbIds - - variantSetDbIds + nullable: true + AlleleMatrixPagination: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension of + the matrix + format: int32 + example: 500 + AlleleMatrixRequest: type: object properties: callSetDbIds: type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + dataMatrixAbbreviations: + type: array + description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ + \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ + \ in the response." + items: + type: string + dataMatrixNames: + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." items: type: string expandHomozygotes: type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + germplasmDbIds: + type: array + description: A list of IDs which uniquely identify `Germplasm` within the + given database server + items: + type: string + germplasmNames: + type: array + description: A list of human readable `Germplasm` names + items: + type: string + germplasmPUIs: + type: array + description: A list of permanent unique identifiers associated with `Germplasm` + items: + type: string + pagination: + type: array + description: Pagination for the matrix + items: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension + of the matrix + format: int32 + example: 500 + positionRanges: + type: array + description: "The postion range to search\n
\nUses the format \":-\"\ + \ where is the chromosome name, is \nthe starting position\ + \ of the range, and is the ending position of the range" + items: + type: string + preview: + type: boolean + description: "Default Value = false\n
\nIf 'preview' is set to true,\ + \ then the server should only return the lists of 'callSetDbIds', \n'variantDbIds',\ + \ and 'variantSetDbIds'. The server should not return any matrix data.\ + \ This\nis intended to be a preview and give the client a sense of how\ + \ large the matrix returned will be\n
\nIf 'preview' is set to false\ + \ or not set (default), then the server should return all the matrix\n\ + data as requested." + example: true + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + items: + type: string sepPhased: type: string + description: The string used as a separator for phased allele calls. + example: '|' sepUnphased: type: string + description: The string used as a separator for unphased allele calls. + example: / unknownString: type: string + description: The string used as a representation for missing data. + example: "." variantDbIds: type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server items: type: string variantSetDbIds: type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server items: type: string - description: "The AlleleMatrix object is used to describe a matrix of genotyping\ - \ results. This 2d array of data reduces the overall size of the response\ - \ for larger datasets, when compared to the Calls endpoints. This makes genotype\ - \ data retrieval faster and easier." Attribute: required: - attributeName - - method - - scale - - trait + - methodDbId + - methodName + - scaleDbId + - scaleName + - traitName type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" attributeCategory: type: string + description: General category for the attribute. very similar to Trait class. + example: Morphological attributeDbId: type: string + description: The ID which uniquely identifies this attribute within the + given database server attributeDescription: type: string + description: A human readable description of this attribute + example: Height of the plant measured in meters by a tape attributeName: type: string + description: A human readable name for this attribute + example: Plant Height 1 attributePUI: type: string + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + example: http://my-traits.com/trait/CO_123:0008012 commonCropName: type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true contextOfUse: type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true items: type: string defaultValue: type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" growthStage: type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true institution: type: string + description: Name of institution submitting the variable + nullable: true language: type: string - method: - $ref: "#/components/schemas/Method" + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string ontologyReference: $ref: "#/components/schemas/OntologyReference" - scale: - $ref: "#/components/schemas/Scale" + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string scientist: type: string + description: Name of scientist submitting the variable. + nullable: true status: type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true submissionTimestamp: type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true synonyms: type: array + description: Other variable names + nullable: true items: type: string - trait: - $ref: "#/components/schemas/Trait" - Call: - required: - - callSetDbId - - variantDbId - - variantSetDbId - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - callSetDbId: - type: string - callSetName: - type: string - genotypeValue: - type: string - phaseSet: - type: string - variantDbId: + traitDbId: type: string - variantSetDbId: + traitName: type: string - variantSetName: + traitPUI: type: string - description: "A `Call` represents the determination of genotype with respect\ - \ to a particular `Variant`. \n\nIt may include associated information such\ - \ as quality and phasing. For example, a call might assign a probability of\ - \ 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name\ - \ NA_12345." - Contact: - required: - - contactDbId + CallRequest: type: object properties: - contactDbId: - type: string - email: - type: string - instituteName: - type: string - name: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + sepPhased: type: string - orcid: + description: The string used as a separator for phased allele calls. + example: '|' + sepUnphased: type: string - type: + description: The string used as a separator for unphased allele calls. + example: / + unknownString: type: string - description: A persons contact information - ContentTypes: - type: string - enum: - - application/json - - text/csv - - text/tsv - - application/flapjack - Context: - title: context - type: array - description: "The JSON-LD Context is used to provide JSON-LD definitions to\ - \ each field in a JSON object. By providing an array of context file urls,\ - \ a BrAPI response object becomes JSON-LD compatible. \n\nFor more information,\ - \ see https://w3c.github.io/json-ld-syntax/#the-context" - example: - - https://brapi.org/jsonld/context/metadata.jsonld - items: - type: string - format: uri - CrossParent: + description: The string used as a representation for missing data. + example: "." + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variant` within the + given database server + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string + CallSetRequest: type: object properties: - germplasm: - $ref: "#/components/schemas/Germplasm" - observationUnitDbId: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string - parentType: - $ref: "#/components/schemas/ParentType" - description: The identifying information gor the parent material of a cross. - CrossType: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + callSetNames: + type: array + description: A list of human readable names associated with `CallSets` + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + items: + type: string + sampleNames: + type: array + description: A list of human readable names associated with `Samples` + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + items: + type: string + CommonCropNamesParameters: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + ContentTypes: + type: string + enum: + - application/json + - text/csv + - text/tsv + - application/flapjack + Context: + title: context + type: array + description: "The JSON-LD Context is used to provide JSON-LD definitions to\ + \ each field in a JSON object. By providing an array of context file urls,\ + \ a BrAPI response object becomes JSON-LD compatible. \n\nFor more information,\ + \ see https://w3c.github.io/json-ld-syntax/#the-context" + example: + - https://brapi.org/jsonld/context/metadata.jsonld + items: + type: string + format: uri + CrossRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + CrossStatus: type: string - description: "The type of cross make. Accepted values for this field are 'BIPARENTAL',\ - \ 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED'\ - \ and 'DOUBLE_HAPLOID'." enum: - - BIPARENTAL - - SELF - - OPEN_POLLINATED - - BULK - - BULK_SELFED - - BULK_OPEN_POLLINATED - - DOUBLE_HAPLOID + - TODO + - DONE + - SKIPPED + CrossingProjectRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + includePotentialParents: + type: boolean + description: "If the parameter 'includePotentialParents' is false, the array\ + \ 'potentialParents' should be empty, null, or excluded from the response\ + \ object." + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string DocumentationLink: type: object properties: URL: type: string - ontologyReferenceDbId: - type: string + description: The URL or URI to the documentation + format: uri + nullable: true type: type: string description: "The type of documentation, which can be OBO Foundry, an RDF\ \ term or a webpage." + nullable: true enum: - OBO - RDF - WEBPAGE description: Links to various ontology documentation + DocumentationLinkType: + type: string + description: "The type of documentation, which can be OBO Foundry, an RDF term\ + \ or a webpage." + enum: + - OBO + - RDF + - WEBPAGE + EntryType: + type: string + description: "The type of entry for this observation unit. ex. \"CHECK\", \"\ + TEST\", \"FILLER\"" + enum: + - CHECK + - TEST + - FILLER Event: required: - eventDbId @@ -1890,18 +2379,45 @@ components: properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" + eventDateRange: + type: array + description: "An object describing when a particular Event has taken place.\ + \ An Event can occur at one or more discrete time points (`discreteDates`)\ + \ or an event can happen continuously over a longer period of time (`startDate`,\ + \ `endDate`)" + nullable: true + items: + $ref: "#/components/schemas/EventDateRange" eventDbId: type: string + description: Internal database identifier eventDescription: type: string + description: "A detailed, human-readable description of this event\n
MIAPPE\ + \ V1.1 (DM-67) Event description - Description of the event, including\ + \ details such as amount applied and possibly duration of the event. " + nullable: true + eventParameters: + type: array + description: A list of objects describing additional event parameters. Each + of the following accepts a human-readable value or URI + nullable: true + items: + $ref: "#/components/schemas/EventParameter" eventType: type: string + description: |- + An identifier for this event type, in the form of an ontology class reference +
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other +
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology). + nullable: true eventTypeDbId: type: string - observationUnitDbIds: - type: array - items: - type: string + description: |- + An identifier for this event type, in the form of an ontology class reference +
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other +
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology). + nullable: true studyDbId: type: string studyName: @@ -1919,14 +2435,29 @@ components: properties: discreteDates: type: array + description: |- + A list of dates when the event occurred +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + nullable: true items: type: string + format: date-time endDate: type: string + description: |- + The end of a continuous or regularly repetitive event +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + format: date-time + nullable: true eventDbId: type: string startDate: type: string + description: |- + The beginning of a continuous or regularly repetitive event +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + format: date-time + nullable: true description: "An object describing when a particular Event has taken place.\ \ An Event can occur at one or more discrete time points (`discreteDates`)\ \ or an event can happen continuously over a longer period of time (`startDate`,\ @@ -1936,48 +2467,177 @@ components: properties: code: type: string + description: |- + The shortened code name of an event parameter +
ICASA "Code_Display" + nullable: true description: type: string + description: A human readable description of this event parameter. This + description is usually associated with the 'name' and 'code' of an event + parameter. + nullable: true eventDbId: type: string name: type: string + description: |- + The full name of an event parameter +
ICASA "Variable_Name" + nullable: true units: type: string + description: "The units or data type of the 'value'. \n
If the 'value'\ + \ comes from a standardized vocabulary or an encoded list of values, then\ + \ 'unit' should be 'code'. \n
If the 'value' IS NOT a number, then\ + \ 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc.\ + \ \n
If the value IS a number, then 'unit' should specify the units\ + \ used eg. 'ml', 'cm', etc\n
ICASA \"Unit_or_type\"" + nullable: true value: type: string + description: The single value of this event parameter. This single value + is accurate for all the dates in the date range. If 'value' is populated + then 'valuesByDate' should NOT be populated. + nullable: true valueDescription: type: string + description: "If the event parameter 'unit' field is 'code', then use 'valueDescription'\ + \ to add a human readable description to the value." + nullable: true valuesByDate: type: array + description: An array of values corresponding to each timestamp in the 'discreteDates' + array of this event. The 'valuesByDate' array should exactly match the + size of the 'discreteDates' array. If 'valuesByDate' is populated then + 'value' should NOT be populated. + nullable: true items: type: string description: "Additional metadata to describe an event, based on the ICASA standard\ \ model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep),\ \ and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters\ \ for a Tillage event." - ExperimentalDesign: + EventRequest: type: object properties: - PUI: - type: string - description: - type: string - studyDbId: - type: string - studyName: + dateRangeEnd: type: string - studyPUI: + description: Filter based on an Event start date. + format: date-time + dateRangeStart: type: string - description: The experimental and statistical design full description plus a - category PUI taken from crop research ontology or agronomy ontology + description: Filter based on an Event start date. + format: date-time + eventDbIds: + type: array + description: Filter based on an Event DbId. + items: + type: string + eventTypes: + type: array + description: Filter based on an Event Type + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string ExternalReference: type: object properties: referenceId: type: string + description: The external reference ID. Could be a simple string or a URI. + nullable: true referenceSource: type: string + description: An identifier for the source system or database of this reference + nullable: true + GenomeMapRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + mapDbIds: + type: array + description: The ID which uniquely identifies a `GenomeMap` + items: + type: string + mapPUIs: + type: array + description: The DOI or other permanent identifier for a `GenomeMap` + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scientificName: + type: array + description: "Full scientific binomial format name. This includes Genus,\ + \ Species, and Sub-species" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + types: + type: array + description: "The type of map, usually \"Genetic\" or \"Physical\"" + items: + type: string GeoJSON: type: object properties: @@ -1985,6 +2645,8 @@ components: $ref: "#/components/schemas/GeoJSONGeometry" type: type: string + description: The literal string "Feature" + example: Feature description: |- One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. @@ -2001,10 +2663,12 @@ components: properties: coordinates: type: array + description: A single position items: type: number type: type: string + description: The literal string "Point" description: |- Copied from RFC 7946 Section 3.1.1 @@ -2017,6 +2681,7 @@ components: properties: coordinates: type: array + description: An array of linear rings items: type: array items: @@ -2025,11 +2690,54 @@ components: type: number type: type: string + description: The literal string "Polygon" description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ \ precisely in that order and using decimal numbers. Altitude or elevation\ \ MAY be included as an optional third element." + GeoJSONPoint: + required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + description: A single position + items: + type: number + type: + type: string + description: The literal string "Point" + description: |- + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + GeoJSONPolygon: + required: + - coordinateDbIds + - type + type: object + properties: + coordinates: + type: array + description: An array of linear rings + items: + type: array + items: + type: array + items: + type: number + type: + type: string + description: The literal string "Polygon" + description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ + \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ + \ The first two elements are longitude and latitude, or\neasting and northing,\ + \ precisely in that order and using decimal numbers. Altitude or elevation\ + \ MAY be included as an optional third element." GeoJSONSearchArea: type: object properties: @@ -2047,179 +2755,519 @@ components: $ref: "#/components/schemas/ObservationUnitPosition" type: type: string - Germplasm: - required: - - commonCropName - - germplasmDbId - - germplasmName - - germplasmPUI + description: The literal string "Feature" + example: Feature + GermplasmAttributeRequest: type: object properties: - accessionNumber: - type: string - acquisitionDate: - type: string - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - biologicalStatusOfAccessionCode: - type: string - description: "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can\ - \ be used at 3 different levels of detail: either by using the general\ - \ codes such as 100, 200, 300, 400, or by using the more specific codes\ - \ such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild\ - \ \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace\ - \ \n400) Breeding/research material \n410) Breeders line \n411) Synthetic\ - \ population \n412) Hybrid \n413) Founder stock/base population \n414)\ - \ Inbred line (parent of hybrid cultivar) \n415) Segregating population\ - \ \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion\ - \ mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome\ - \ addition/substitution, aneuploids, amphiploids) \n423) Other genetic\ - \ stocks (e.g. mapping populations) \n500) Advanced or improved cultivar\ - \ (conventional breeding methods) \n600) GMO (by genetic engineering)\ - \ \n999) Other (Elaborate in REMARKS field)" - enum: - - "100" - - "110" - - "120" - - "130" - - "200" - - "300" - - "400" - - "410" - - "411" - - "412" - - "413" - - "414" - - "415" - - "416" - - "420" - - "421" - - "422" - - "423" - - "500" - - "600" - - "999" - biologicalStatusOfAccessionDescription: - type: string - breedingMethodDbId: - type: string - breedingMethodName: - type: string - collection: - type: string - commonCropName: - type: string - countryOfOriginCode: - type: string - defaultDisplayName: - type: string - documentationURL: - type: string - genus: - type: string - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - germplasmPreprocessing: - type: string - instituteCode: - type: string - instituteName: - type: string - pedigree: - type: string - sampleDbIds: + attributeCategories: type: array + description: General category for the attribute. very similar to Trait class. items: type: string - seedSource: - type: string - seedSourceDescription: - type: string - species: - type: string - speciesAuthority: - type: string - subtaxa: - type: string - subtaxaAuthority: - type: string - description: "The conceptual identifiers and metadata describing a genetically\ - \ unique organism that is noteworthy in some way. Depending on context, a\ - \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ - \ Germplasm is conceptual data, not necessarily associated to a real physical\ - \ object, so Seed/Inventory Lots and Observation Units become physical instantiations\ - \ of a particular Germplasm. Note a Germplasm is unique and noteworthy, so\ - \ a Cross may or may not create a new Germplasm, since not every Cross is\ - \ unique or noteworthy." - GermplasmOrigin: - type: object - properties: - coordinateUncertainty: - type: string - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - description: "Information for material (orchard, natural sites, ...). Geographic\ - \ identification of the plants from which seeds or cutting have been taken\ - \ to produce that germplasm." - GrowthFacility: + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + items: + type: string + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + items: + type: string + attributePUIs: + type: array + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + GermplasmAttributeValueRequest: type: object properties: - PUI: - type: string - description: - type: string - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - description: Short description of the facility in which the study was carried - out. + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + items: + type: string + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + items: + type: string + attributeValueDbIds: + type: array + description: List of Germplasm Attribute Value IDs to search for + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: List of scales to filter search results + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: List of trait unique ID to filter search results + items: + type: string + GermplasmParameters: + type: object + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + GermplasmRequest: + type: object + properties: + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + items: + type: string + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + items: + type: string + parentDbIds: + type: array + description: Search for Germplasm with these parents + items: + type: string + progenyDbIds: + type: array + description: Search for Germplasm with these children + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string Image: - required: - - imageDbId + allOf: + - $ref: "#/components/schemas/ImageNewRequest" + - required: + - imageDbId + type: object + properties: + imageDbId: + type: string + description: The unique identifier of an image + description: The metadata for an image file that is connected to some phenotypic + observation data. + ImageNewRequest: type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" copyright: type: string + description: The copyright information of this image. Example 'Copyright + 2018 Bob Robertson' + nullable: true description: type: string + description: The human readable description of an image. + nullable: true + descriptiveOntologyTerms: + type: array + description: "A list of terms to formally describe the image. Each item\ + \ could be a simple Tag, an Ontology reference Id, or a full ontology\ + \ URL." + nullable: true + items: + type: string + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + imageContent: + type: string + description: The content of the image + format: binary imageFileName: type: string + description: "The name of the image file. Might be the same as 'imageName',\ + \ but could be different." + nullable: true imageFileSize: type: integer + description: The size of the image in Bytes. format: int32 + nullable: true imageHeight: type: integer + description: The height of the image in Pixels. format: int32 + nullable: true imageLocation: $ref: "#/components/schemas/GeoJSON" imageName: type: string + description: "The human readable name of an image. Might be the same as\ + \ 'imageFileName', but could be different." + nullable: true imageTimeStamp: type: string + description: The date and time the image was taken + format: date-time + nullable: true imageURL: type: string + description: "The complete, absolute URI path to the image file. Images\ + \ might be stored on a different host or path than the BrAPI web server." + nullable: true imageWidth: type: integer + description: The width of the image in Pixels. format: int32 + nullable: true mimeType: type: string - observationDbIds: - type: array - items: - type: string + description: "The file type of the image. Examples 'image/jpeg', 'image/png',\ + \ 'image/svg', etc" + nullable: true observationUnitDbId: type: string observationUnitName: @@ -2228,99 +3276,472 @@ components: type: string description: The metadata for an image file that is connected to some phenotypic observation data. - ImageNewRequest: - required: - - imageDbId - - imageDbId + ImageRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - copyright: - type: string - description: - type: string - imageDbId: - type: string - imageFileName: - type: string - imageFileSize: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + descriptiveOntologyTerms: + type: array + description: "A list of terms to formally describe the image to search for.\ + \ Each item could be a simple Tag, an Ontology reference Id, or a full\ + \ ontology URL." + items: + type: string + imageDbIds: + type: array + description: A list of image Ids to search for + items: + type: string + imageFileNames: + type: array + description: Image file names to search for. + items: + type: string + imageFileSizeMax: type: integer + description: A maximum image file size to search for. format: int32 - imageHeight: + example: 20000000 + imageFileSizeMin: + type: integer + description: A minimum image file size to search for. + format: int32 + example: 1000 + imageHeightMax: + type: integer + description: A maximum image height to search for. + format: int32 + example: 1080 + imageHeightMin: type: integer + description: A minimum image height to search for. format: int32 + example: 720 imageLocation: - $ref: "#/components/schemas/GeoJSON" - imageName: - type: string - imageTimeStamp: + $ref: "#/components/schemas/GeoJSONSearchArea" + imageNames: + type: array + description: Human readable names to search for. + items: + type: string + imageTimeStampRangeEnd: type: string - imageURL: + description: The latest timestamp to search for. + format: date-time + imageTimeStampRangeStart: type: string - imageWidth: + description: The earliest timestamp to search for. + format: date-time + imageWidthMax: type: integer + description: A maximum image width to search for. format: int32 - mimeType: - type: string + example: 1920 + imageWidthMin: + type: integer + description: A minimum image width to search for. + format: int32 + example: 1280 + mimeTypes: + type: array + description: A set of image file types to search for. + items: + type: string observationDbIds: type: array + description: A list of observation Ids this image is associated with to + search for + items: + type: string + observationUnitDbIds: + type: array + description: A set of observation unit identifiers to search for. + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string - observationUnitDbId: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string - description: The metadata for an image file that is connected to some phenotypic - observation data. ImageSearchRequest: type: object properties: imageFileSizeMax: type: integer + description: A maximum image file size to search for. format: int32 - imageFileSizeMin: + example: 20000000 + imageFileNames: + type: array + description: Image file names to search for. + items: + type: string + imageTimeStampRangeStart: + type: string + description: The earliest timestamp to search for. + format: date-time + imageDbIds: + type: array + description: A list of image Ids to search for + items: + type: string + observationUnitDbIds: + type: array + description: A set of observation unit identifiers to search for. + items: + type: string + imageNames: + type: array + description: Human readable names to search for. + items: + type: string + imageWidthMin: type: integer + description: A minimum image width to search for. format: int32 + example: 1280 imageHeightMax: type: integer + description: A maximum image height to search for. format: int32 - imageHeightMin: - type: integer - format: int32 + example: 1080 + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + descriptiveOntologyTerms: + type: array + description: "A list of terms to formally describe the image to search for.\ + \ Each item could be a simple Tag, an Ontology reference Id, or a full\ + \ ontology URL." + items: + type: string imageLocation: $ref: "#/components/schemas/GeoJSONSearchArea" imageTimeStampRangeEnd: type: string - imageTimeStampRangeStart: - type: string - imageWidthMax: + description: The latest timestamp to search for. + format: date-time + mimeTypes: + type: array + description: A set of image file types to search for. + items: + type: string + observationDbIds: + type: array + description: A list of observation Ids this image is associated with to + search for + items: + type: string + imageHeightMin: type: integer + description: A minimum image height to search for. format: int32 - imageWidthMin: + example: 720 + imageFileSizeMin: + type: integer + description: A minimum image file size to search for. + format: int32 + example: 1000 + imageWidthMax: type: integer + description: A maximum image width to search for. format: int32 + example: 1920 description: The metadata for an image file that is connected to some phenotypic observation data. - ListType: - type: string - description: The type of objects that are referenced in a List - enum: - - germplasm - - markers - - variants - - programs - - trials - - studies - - observationUnits - - observations - - observationVariables - - samples + ListRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dateCreatedRangeEnd: + type: string + description: Define the end for an interval of time and only include Lists + that are created within this interval. + format: date-time + dateCreatedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are created within this interval. + format: date-time + dateModifiedRangeEnd: + type: string + description: Define the end for an interval of time and only include Lists + that are modified within this interval. + format: date-time + dateModifiedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are modified within this interval. + format: date-time + listDbIds: + type: array + description: An array of primary database identifiers to identify a set + of Lists + items: + type: string + listNames: + type: array + description: An array of human readable names to identify a set of Lists + items: + type: string + listOwnerNames: + type: array + description: An array of names for the people or entities who are responsible + for a set of Lists + items: + type: string + listOwnerPersonDbIds: + type: array + description: An array of primary database identifiers to identify people + or entities who are responsible for a set of Lists + items: + type: string + listSources: + type: array + description: "An array of terms identifying lists from different sources\ + \ (ie 'USER', 'SYSTEM', etc)" + items: + type: string + listType: + $ref: "#/components/schemas/ListType" + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + LocationParameters: + type: object + properties: + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + LocationRequest: + type: object + properties: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Locations + items: + type: string + altitudeMax: + type: number + description: The maximum altitude to search for + example: 200 + altitudeMin: + type: number + description: The minimum altitude to search for + example: 20 + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + coordinates: + $ref: "#/components/schemas/GeoJSONSearchArea" + countryCodes: + type: array + description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ + \ spec" + items: + type: string + countryNames: + type: array + description: The full name of the country to search for + items: + type: string + instituteAddresses: + type: array + description: The street address of the institute to search for + items: + type: string + instituteNames: + type: array + description: The name of the institute to search for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + locationTypes: + type: array + description: "The type of location this represents (ex. Breeding Location,\ + \ Storage Location, etc)" + items: + type: string + parentLocationDbIds: + type: array + description: "The unique identifier for a Location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + items: + type: string + parentLocationNames: + type: array + description: "A human readable name for a location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + MarkerPositionRequest: + type: object + properties: + linkageGroupNames: + type: array + description: A list of Uniquely Identifiable linkage group names + items: + type: string + mapDbIds: + type: array + description: A list of IDs which uniquely identify `GenomeMaps` within the + given database server + items: + type: string + maxPosition: + type: integer + description: The maximum position of markers in a given map + format: int32 + example: 4000 + minPosition: + type: integer + description: The minimum position of markers in a given map + format: int32 + example: 250 + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server + items: + type: string Method: + allOf: + - $ref: "#/components/schemas/MethodNewRequest" + - required: + - methodDbId + type: object + properties: + methodDbId: + type: string + description: Method unique identifier + nullable: true + description: "A description of the way an Observation should be collected.\ + \ \n
For example, an ObservationVariable might be defined with a Trait\ + \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ + . This variable would be distinct from a variable with the Method \"estimation\"\ + \ or \"drone image processing\". " + MethodNewRequest: required: - - methodDbId - methodName type: object properties: @@ -2328,62 +3749,130 @@ components: $ref: "#/components/schemas/AdditionalInfo" bibliographicalReference: type: string + description: |- + Bibliographical reference describing the method. +
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method. + nullable: true description: type: string + description: |- + Method description +
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number) + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" formula: type: string + description: "For computational methods i.e., when the method consists in\ + \ assessing the trait by computing measurements, write the generic formula\ + \ used for the calculation" + nullable: true methodClass: type: string + description: "Method class (examples: \"Measurement\", \"Counting\", \"\ + Estimation\", \"Computation\", etc.)" + nullable: true methodName: type: string + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation methodPUI: type: string - ontologyReferenceDbId: - type: string + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + nullable: true + ontologyReference: + $ref: "#/components/schemas/OntologyReference" description: "A description of the way an Observation should be collected. \n\
For example, an ObservationVariable might be defined with a Trait of \"\ plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This\ \ variable would be distinct from a variable with the Method \"estimation\"\ \ or \"drone image processing\". " - MethodNewRequest: - required: - - methodDbId - - methodDbId - - methodName + MethodRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - bibliographicalReference: - type: string - description: - type: string - formula: - type: string - methodClass: - type: string - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string - ontologyReferenceDbId: - type: string - description: "A description of the way an Observation should be collected. \n\ -
For example, an ObservationVariable might be defined with a Trait of \"\ - plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This\ - \ variable would be distinct from a variable with the Method \"estimation\"\ - \ or \"drone image processing\". " + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + methodDbIds: + type: array + description: The unique identifier for a method. + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string Observation: - required: - - observationDbId + allOf: + - $ref: "#/components/schemas/ObservationNewRequest" + - required: + - observationDbId + type: object + properties: + observationDbId: + type: string + description: The ID which uniquely identifies an observation + description: A value assigned for a specific ObservationVariable when observing + a specific ObservationUnit. + ObservationNewRequest: type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" collector: type: string + description: The name or identifier of the entity which collected the observation + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" geoCoordinates: $ref: "#/components/schemas/GeoJSON" germplasmDbId: @@ -2394,6 +3883,9 @@ components: type: string observationTimeStamp: type: string + description: The date and time when this observation was made + format: date-time + nullable: true observationUnitDbId: type: string observationUnitName: @@ -2418,67 +3910,333 @@ components: type: string uploadedBy: type: string + description: The name or id of the user who uploaded the observation to + the database system + nullable: true value: type: string + description: The value of the data collected as an observation + nullable: true description: A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. - ObservationNewRequest: - required: - - observationDbId - - observationDbId + ObservationRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - collector: - type: string - geoCoordinates: - $ref: "#/components/schemas/GeoJSON" - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - observationDbId: - type: string - observationTimeStamp: - type: string - observationUnitDbId: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string - observationVariableDbId: - type: string - observationVariableName: - type: string - observationVariablePUI: - type: string - seasonDbId: - type: string - seasonName: - type: string - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - uploadedBy: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationDbIds: + type: array + description: The unique id of an Observation + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationTimeStampRangeEnd: type: string - value: + description: Timestamp range end + format: date-time + observationTimeStampRangeStart: type: string - description: A value assigned for a specific ObservationVariable when observing - a specific ObservationUnit. + description: Timestamp range start + format: date-time + observationUnitDbIds: + type: array + description: The unique id of an Observation Unit + items: + type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string ObservationSearchRequest: type: object properties: - observationTimeStampRangeEnd: - type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The unique id of an Observation Unit + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationDbIds: + type: array + description: The unique id of an Observation + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string observationTimeStampRangeStart: type: string + description: Timestamp range start + format: date-time + observationTimeStampRangeEnd: + type: string + description: Timestamp range end + format: date-time description: A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. ObservationTreatment: @@ -2486,8 +4244,21 @@ components: properties: factor: type: string + description: |- + The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc + + MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor. + nullable: true + example: test-factor:dia2020-2-nv.fertilizer modality: type: string + description: "The treatment/factor description. ex. 'low fertilizer', 'yellow\ + \ rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental\ + \ Factor description - Free text description of the experimental factor.\ + \ This includes all relevant treatments planned and protocol planned for\ + \ all the plants targeted by a given experimental factor. " + nullable: true + example: test-factor:dia2020-2-nv.lf observationUnitDbId: type: string observationUnitName: @@ -2497,61 +4268,85 @@ components: description: A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor. ObservationUnit: - required: - - observationUnitDbId + allOf: + - $ref: "#/components/schemas/ObservationUnitNewRequest" + - required: + - observationUnitDbId + type: object + properties: + observationUnitDbId: + type: string + description: "The ID which uniquely identifies an observation unit\n\n\ + MIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify\ + \ the observation unit in data files containing the values observed\ + \ or measured on that unit. Must be locally unique. " + description: "A representation of the physical entity being observed during\ + \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ + \ but it could include things like Fields, Blocks, or Samples." + ObservationUnitHierarchyLevel: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - crossDbId: + levelName: type: string - crossName: + description: "A name for this level \n\n**Standard Level Names: study, field,\ + \ entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\ + \nFor more information on Observation Levels, please review the Observation Levels documentation. " + nullable: true + levelOrder: + type: integer + description: "`levelOrder` defines where that level exists in the hierarchy\ + \ of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy\ + \ (ie field -> 1) and higher numbers are at the bottom of the hierarchy\ + \ (ie plant -> 9). \n\nFor more information on Observation Levels, please\ + \ review the Observation Levels documentation. " + format: int32 + nullable: true + description: "The exact level and level code of an observation unit. \n\nFor\ + \ more information on Observation Levels, please review the Observation\ + \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ + Type of observation unit in textual form, usually one of the following: study,\ + \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ + \ types is possible but not recommended. \nThe observation unit type can not\ + \ be used to indicate sub-plant levels. However, observations can still be\ + \ made on the sub-plant level, as long as the details are indicated in the\ + \ associated observed variable (see observed variables). \nAlternatively,\ + \ it is possible to use samples for more detailed tracing of sub-plant units,\ + \ attaching the observations to them instead.\" " + ObservationUnitLevel: + type: object + properties: + levelCode: type: string - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string - locationDbId: - type: string - locationName: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string - programDbId: - type: string - programName: - type: string - seedLotDbId: - type: string - seedLotName: - type: string - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string - trialDbId: - type: string - trialName: - type: string - trialPUI: - type: string - description: "A representation of the physical entity being observed during\ - \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ - \ but it could include things like Fields, Blocks, or Samples." - ObservationUnitHierarchyLevel: - type: object - properties: - levelName: + description: "An ID code or number to represent a real thing that may or\ + \ may not be an an observation unit.\n
For example, if the 'levelName'\ + \ is 'plot', then the 'levelCode' would be the plot number or plot barcode.\ + \ If this plot is also considered an ObservationUnit, then the appropriate\ + \ observationUnitDbId should also be recorded.\n
If the 'levelName'\ + \ is 'field', then the 'levelCode' might be something like '3' or 'F3'\ + \ to indicate the third field at a research station. " + nullable: true + levelName: type: string + description: "A name for this level \n\n**Standard Level Names: study, field,\ + \ entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\ + \nFor more information on Observation Levels, please review the Observation Levels documentation. " + nullable: true levelOrder: type: integer + description: "`levelOrder` defines where that level exists in the hierarchy\ + \ of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy\ + \ (ie field -> 1) and higher numbers are at the bottom of the hierarchy\ + \ (ie plant -> 9). \n\nFor more information on Observation Levels, please\ + \ review the Observation Levels documentation. " format: int32 + nullable: true description: "The exact level and level code of an observation unit. \n\nFor\ \ more information on Observation Levels, please review the Observation\ @@ -2564,40 +4359,43 @@ components: \ associated observed variable (see observed variables). \nAlternatively,\ \ it is possible to use samples for more detailed tracing of sub-plant units,\ \ attaching the observations to them instead.\" " - ObservationUnitLevel: + ObservationUnitLevelRelationship: type: object properties: levelCode: type: string + description: "An ID code or number to represent a real thing that may or\ + \ may not be an an observation unit.\n
For example, if the 'levelName'\ + \ is 'plot', then the 'levelCode' would be the plot number or plot barcode.\ + \ If this plot is also considered an ObservationUnit, then the appropriate\ + \ observationUnitDbId should also be recorded.\n
If the 'levelName'\ + \ is 'field', then the 'levelCode' might be something like '3' or 'F3'\ + \ to indicate the third field at a research station. " + nullable: true levelName: type: string + description: "A name for this level \n\n**Standard Level Names: study, field,\ + \ entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\ + \nFor more information on Observation Levels, please review the Observation Levels documentation. " + nullable: true levelOrder: type: integer + description: "`levelOrder` defines where that level exists in the hierarchy\ + \ of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy\ + \ (ie field -> 1) and higher numbers are at the bottom of the hierarchy\ + \ (ie plant -> 9). \n\nFor more information on Observation Levels, please\ + \ review the Observation Levels documentation. " format: int32 - description: "The exact level and level code of an observation unit. \n\nFor\ - \ more information on Observation Levels, please review the Observation\ - \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ - Type of observation unit in textual form, usually one of the following: study,\ - \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ - \ types is possible but not recommended. \nThe observation unit type can not\ - \ be used to indicate sub-plant levels. However, observations can still be\ - \ made on the sub-plant level, as long as the details are indicated in the\ - \ associated observed variable (see observed variables). \nAlternatively,\ - \ it is possible to use samples for more detailed tracing of sub-plant units,\ - \ attaching the observations to them instead.\" " - ObservationUnitLevelRelationship: - type: object - properties: - levelCode: + nullable: true + observationUnitDbId: type: string - levelName: + observationUnitName: + type: string + observationUnitPUI: type: string - levelOrder: - type: integer - format: int32 - observationUnit: - $ref: "#/components/schemas/ObservationUnit" description: "Observation levels indicate the granularity level at which the\ \ measurements are taken. `levelName` \ndefines the level, `levelOrder` defines\ \ where that level exists in the hierarchy of levels. \n`levelOrder`s lower\ @@ -2609,9 +4407,6 @@ components: >Observation Levels documentation. \n\n**Standard Level Names: study,\ \ field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** " ObservationUnitNewRequest: - required: - - observationUnitDbId - - observationUnitDbId type: object properties: additionalInfo: @@ -2620,6 +4415,14 @@ components: type: string crossName: type: string + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" germplasmDbId: type: string germplasmName: @@ -2630,12 +4433,28 @@ components: type: string locationName: type: string - observationUnitDbId: - type: string observationUnitName: type: string + description: A human readable name for an observation unit + nullable: true observationUnitPUI: type: string + description: |- + A Permanent Unique Identifier for an observation unit + + MIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible. + nullable: true + observationUnitPosition: + type: array + description: "All positional and layout information related to this Observation\ + \ Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of\ + \ a spatial coordinate (georeference or relative) \nor level of observation\ + \ (plot 45, subblock 7, block 2) provided as a key-value pair of the form\ + \ type:value. \nLevels of observation must be consistent with those listed\ + \ in the Study section." + nullable: true + items: + $ref: "#/components/schemas/ObservationUnitPosition" programDbId: type: string programName: @@ -2650,6 +4469,15 @@ components: type: string studyPUI: type: string + treatments: + type: array + description: |- + List of treatments applied to an observation unit. + + MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. + nullable: true + items: + $ref: "#/components/schemas/ObservationTreatment" trialDbId: type: string trialName: @@ -2666,12 +4494,41 @@ components: type: string description: "The type of entry for this observation unit. ex. \"CHECK\"\ , \"TEST\", \"FILLER\"" + nullable: true enum: - CHECK - TEST - FILLER + geoCoordinates: + type: array + description: |- + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + nullable: true + items: + $ref: "#/components/schemas/GeoJSON" observationLevel: $ref: "#/components/schemas/ObservationUnitLevel" + observationLevelRelationships: + type: array + description: "Observation levels indicate the granularity level at which\ + \ the measurements are taken. `levelName` \ndefines the level, `levelOrder`\ + \ defines where that level exists in the hierarchy of levels. \n`levelOrder`s\ + \ lower numbers are at the top of the hierarchy (ie field > 0) and higher\ + \ numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode`\ + \ is an ID code for this level tag. Identify \nthis observation unit by\ + \ each level of the hierarchy where it exists. \n\nFor more information\ + \ on Observation Levels, please review the Observation Levels\ + \ documentation. \n\n**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** " + nullable: true + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" observationUnitDbId: type: string observationUnitName: @@ -2680,27 +4537,356 @@ components: type: string positionCoordinateX: type: string + description: The X position coordinate for an observation unit. Different + systems may use different coordinate systems. + nullable: true positionCoordinateXType: $ref: "#/components/schemas/PositionCoordinateType" positionCoordinateY: type: string + description: The Y position coordinate for an observation unit. Different + systems may use different coordinate systems. + nullable: true positionCoordinateYType: $ref: "#/components/schemas/PositionCoordinateType" description: All positional and layout information related to this Observation Unit + ObservationUnitRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + includeObservations: + type: boolean + description: "Use this parameter to include a list of observations embedded\ + \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ + \ your own risk. It may return large, unpaginated lists of observation\ + \ data. Only set this value to True if you are sure you need to." + example: false + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationUnitDbIds: + type: array + description: The unique id of an observation unit + items: + type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitNames: + type: array + description: The human readable identifier for an Observation Unit + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string ObservationUnitSearchRequest: type: object properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitNames: + type: array + description: The human readable identifier for an Observation Unit + items: + type: string + observationUnitDbIds: + type: array + description: The unique id of an observation unit + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string includeObservations: type: boolean + description: "Use this parameter to include a list of observations embedded\ + \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ + \ your own risk. It may return large, unpaginated lists of observation\ + \ data. Only set this value to True if you are sure you need to." + example: false + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string description: "A representation of the physical entity being observed during\ \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ \ but it could include things like Fields, Blocks, or Samples." ObservationVariable: + allOf: + - $ref: "#/components/schemas/ObservationVariableNewRequest" + - required: + - observationVariableDbId + type: object + properties: + observationVariableDbId: + type: string + description: |- + Variable unique identifier + + MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. + ObservationVariableNewRequest: required: - methodDbId - methodName - - observationVariableDbId - observationVariableName - scaleDbId - scaleName @@ -2711,16 +4897,46 @@ components: $ref: "#/components/schemas/AdditionalInfo" commonCropName: type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true + contextOfUse: + type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true + items: + type: string defaultValue: type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" growthStage: type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true institution: type: string + description: Name of institution submitting the variable + nullable: true language: type: string + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true methodDbId: type: string methodName: @@ -2729,10 +4945,17 @@ components: type: string observationVariableName: type: string + description: |- + Variable name (usually a short name) + + MIAPPE V1.1 (DM-84) Variable name - Name of the variable. observationVariablePUI: type: string - ontologyReferenceDbId: - type: string + description: "The Permanent Unique Identifier of a Observation Variable,\ + \ usually in the form of a URI" + nullable: true + ontologyReference: + $ref: "#/components/schemas/OntologyReference" scaleDbId: type: string scaleName: @@ -2741,80 +4964,407 @@ components: type: string scientist: type: string + description: Name of scientist submitting the variable. + nullable: true status: type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true submissionTimestamp: type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true + synonyms: + type: array + description: Other variable names + nullable: true + items: + type: string traitDbId: type: string traitName: type: string traitPUI: type: string - ObservationVariableNewRequest: - required: - - methodDbId - - methodName - - observationVariableDbId - - observationVariableDbId - - observationVariableName - - scaleDbId - - scaleName - - traitName + ObservationVariableParameters: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - defaultValue: - type: string - documentationURL: - type: string - growthStage: - type: string - institution: - type: string - language: - type: string - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string - observationVariableDbId: - type: string - observationVariableName: - type: string - observationVariablePUI: - type: string - ontologyReferenceDbId: - type: string - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string - scientist: - type: string - status: - type: string - submissionTimestamp: - type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + ObservationVariableRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string ObservationVariableSearchRequest: type: object - properties: {} + properties: + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string Ontology: + allOf: + - $ref: "#/components/schemas/OntologyNewRequest" + - required: + - ontologyDbId + type: object + properties: + ontologyDbId: + type: string + description: Ontology database unique identifier + description: The identifier and metadata needed to reference an external controlled + vocabulary + OntologyNewRequest: required: - - ontologyDbId - ontologyName type: object properties: @@ -2822,58 +5372,68 @@ components: $ref: "#/components/schemas/AdditionalInfo" authors: type: string + description: Ontology's list of authors (no specific format) + nullable: true copyright: type: string + description: Ontology copyright + nullable: true description: type: string + description: Human readable description of Ontology + nullable: true documentationURL: type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true licence: type: string + description: Ontology licence + nullable: true ontologyName: type: string + description: Ontology name version: type: string + description: Ontology version (no specific format) + nullable: true description: The identifier and metadata needed to reference an external controlled vocabulary - OntologyNewRequest: + OntologyParameters: + type: object + properties: + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + OntologyReference: required: - ontologyDbId - - ontologyDbId - ontologyName type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - authors: - type: string - copyright: - type: string - description: - type: string - documentationURL: - type: string - licence: - type: string + documentationLinks: + type: array + description: links to various ontology documentation + nullable: true + items: + $ref: "#/components/schemas/DocumentationLink" ontologyDbId: type: string ontologyName: type: string - version: - type: string - description: The identifier and metadata needed to reference an external controlled - vocabulary - OntologyReference: - required: - - ontology - type: object - properties: - ontology: - $ref: "#/components/schemas/Ontology" ontologyReferenceDbId: type: string + description: The ID which uniquely identifies a ontology reference + nullable: true version: type: string + description: Ontology version (no specific format) + nullable: true description: "MIAPPE V1.1 (DM-85) Variable accession number - Accession number\ \ of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession\ \ number - Accession number of the trait in a suitable controlled vocabulary\ @@ -2882,32 +5442,424 @@ components: \ Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number -\ \ Accession number of the scale in a suitable controlled vocabulary (Crop\ \ Ontology)." + OntologyRequest: + type: object + properties: + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + ontologyNames: + type: array + description: The human readable identifier for an ontology definition. + items: + type: string OntologyTerm: type: object properties: term: type: string + description: Ontology term - the label of the ontology term the termId is + pointing to. + nullable: true termURI: type: string + description: Ontology term identifier - the CURIE for an ontology term. + It differs from the standard GA4GH schema's :ref:`id ` in that it is a + CURIE pointing to an information resource outside of the scope of the + schema or its resource implementation. + nullable: true description: A pointer to an ontology used by a genomic reference - ParentType: - type: string - description: "The type of parent used during crossing. Accepted values for this\ - \ field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn\ - \ a pedigree record, the 'parentType' describes each parent of a particular\ - \ germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe\ - \ how this germplasm was crossed to generate a particular progeny. \\nFor\ - \ example, given a record for germplasm A, having a progeny B and C. The 'parentType'\ - \ field for progeny B item refers \\nto the 'parentType' of A toward B. The\ - \ 'parentType' field for progeny C item refers to the 'parentType' of A toward\ - \ C.\\nIn this way, A could be a male parent to B, but a female parent to\ - \ C. " - enum: - - MALE - - FEMALE - - SELF - - POPULATION - - CLONAL + PedigreeNodeRequest: + type: object + properties: + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + items: + type: string + includeFullTree: + type: boolean + description: "If this parameter is true, recursively include ALL of the\ + \ nodes available in this pedigree tree" + example: true + includeParents: + type: boolean + description: "If this parameter is true, include the array of parents in\ + \ the response" + example: true + includeProgeny: + type: boolean + description: "If this parameter is true, include the array of progeny in\ + \ the response" + example: true + includeSiblings: + type: boolean + description: "If this parameter is true, include the array of siblings in\ + \ the response" + example: true + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + items: + type: string + pedigreeDepth: + type: integer + description: "Recursively include this number of levels up the tree in the\ + \ response (parents, grand-parents, great-grand-parents, etc)" + format: int32 + example: 3 + progenyDepth: + type: integer + description: "Recursively include this number of levels down the tree in\ + \ the response (children, grand-children, great-grand-children, etc)" + format: int32 + example: 3 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + PersonRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + emailAddresses: + type: array + description: email address for this person + items: + type: string + firstNames: + type: array + description: Persons first name + items: + type: string + lastNames: + type: array + description: Persons last name + items: + type: string + mailingAddresses: + type: array + description: physical address of this person + items: + type: string + middleNames: + type: array + description: Persons middle name + items: + type: string + personDbIds: + type: array + description: Unique ID for this person + items: + type: string + phoneNumbers: + type: array + description: phone number of this person + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + userIDs: + type: array + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + items: + type: string + PlannedCrossRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + plannedCrossDbIds: + type: array + description: Search for Planned Cross with this unique id + items: + type: string + plannedCrossNames: + type: array + description: Search for Planned Cross with this human readable name + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + statuses: + type: array + description: "The status of this planned cross. Is it waiting to be performed\ + \ ('TODO'), has it been completed successfully ('DONE'), or has it not\ + \ been done on purpose ('SKIPPED')." + items: + type: string + enum: + - TODO + - DONE + - SKIPPED + PlateRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit + items: + type: string + plateBarcodes: + type: array + description: A unique identifier physically attached to the plate + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a plate of samples + items: + type: string + plateNames: + type: array + description: The human readable name of a plate of samples + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a sample + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related Samples + items: + type: string + sampleNames: + type: array + description: The human readable name of the sample + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string PositionCoordinateType: type: string description: "The type of positional coordinate. Must be one of the following\ @@ -2929,9 +5881,417 @@ components: - GRID_COL - MEASURED_ROW - MEASURED_COL + ProgramParameters: + type: object + properties: + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + ProgramRequest: + type: object + properties: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Programs + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + leadPersonDbIds: + type: array + description: The person DbIds of the program leader to search for + items: + type: string + leadPersonNames: + type: array + description: The names of the program leader to search for + items: + type: string + objectives: + type: array + description: A program objective to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + programTypes: + type: array + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding " + items: + type: string + description: |- + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding. + enum: + - STANDARD + - PROJECT + ReferenceBasesRequest: + type: object + properties: + end: + type: integer + description: "The end position (0-based, exclusive) of this query. Defaults\ + \ to the length of this `Reference`." + format: int32 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + start: + type: integer + description: |- + The start position (0-based) of this query. Defaults to 0. + Genomic positions are non-negative integers less than reference length. + Requests spanning the join of circular genomes are represented as + two requests one on each side of the join (position 0). + format: int32 + ReferenceRequest: + type: object + properties: + accessions: + type: array + description: "If specified, return the references for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + isDerived: + type: boolean + description: "A sequence X is said to be derived from source sequence Y,\ + \ if X and Y are of the same length and the per-base sequence divergence\ + \ at A/C/G/T bases is sufficiently small. Two sequences derived from the\ + \ same official sequence share the same coordinates and annotations, and\ + \ can be replaced with the official sequence for certain use cases." + format: boolean + maxLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 90000 + md5checksums: + type: array + description: "If specified, return the references for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + minLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 4000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: A list of IDs which uniquely identify `References` within the + given database server + items: + type: string + referenceSetDbIds: + type: array + description: A list of IDs which uniquely identify `ReferenceSets` within + the given database server + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ReferenceSetRequest: + type: object + properties: + accessions: + type: array + description: "If set, return the reference sets for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + assemblyPUIs: + type: array + description: "If set, return the reference sets for which the `assemblyId`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + md5checksums: + type: array + description: "If set, return the reference sets for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceSetDbIds: + type: array + description: The `ReferenceSets` to search. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + SampleRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an `ObservationUnit` + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a `Plate` of `Samples` + items: + type: string + plateNames: + type: array + description: The human readable name of a `Plate` of `Samples` + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a `Sample` + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related `Samples` + items: + type: string + sampleNames: + type: array + description: The human readable name of the `Sample` + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string Scale: + allOf: + - $ref: "#/components/schemas/ScaleNewRequest" + - required: + - scaleDbId + type: object + properties: + scaleDbId: + type: string + description: "Unique identifier of the scale. If left blank, the upload\ + \ system will automatically generate a scale ID." + description: "A Scale describes the units and acceptable values for an ObservationVariable.\ + \ \n
For example, an ObservationVariable might be defined with a Trait\ + \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ + . This variable would be distinct from a variable with the Scale \"inches\"\ + \ or \"pixels\"." + ScaleNewRequest: required: - - scaleDbId - scaleName type: object properties: @@ -2948,6 +6308,7 @@ components:

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

"Ordinal" - Ordinal scales are scales composed of ordered categories

"Text" - A free text is used to express the trait.

+ nullable: true enum: - Code - Date @@ -2958,15 +6319,37 @@ components: - Text decimalPlaces: type: integer + description: "For numerical, number of decimal places to be reported" format: int32 - ontologyReferenceDbId: - type: string + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + ontologyReference: + $ref: "#/components/schemas/OntologyReference" scaleName: type: string + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable scalePUI: type: string + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + nullable: true units: type: string + description: "This field can be used to describe the units used for this\ + \ scale. This should be the abbreviated \nform of the units, intended\ + \ to be displayed with every value using this scale. Usually this only\ + \ \napplies when `dataType` is Numeric, but could also be included for\ + \ other dataTypes when applicable." + nullable: true validValues: $ref: "#/components/schemas/ValidValues" description: "A Scale describes the units and acceptable values for an ObservationVariable.\ @@ -2974,89 +6357,322 @@ components: \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ . This variable would be distinct from a variable with the Scale \"inches\"\ \ or \"pixels\"." - ScaleNewRequest: - required: - - scaleDbId - - scaleDbId - - scaleName + ScaleRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - dataType: - type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array description: |- -

Class of the scale, entries can be

-

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

-

"Date" - The date class is for events expressed in a time format, See ISO 8601

-

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

-

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

-

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

-

"Ordinal" - Ordinal scales are scales composed of ordered categories

-

"Text" - A free text is used to express the trait.

- enum: - - Code - - Date - - Duration - - Nominal - - Numerical - - Ordinal - - Text - decimalPlaces: - type: integer - format: int32 - ontologyReferenceDbId: - type: string - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string - units: - type: string - validValues: - $ref: "#/components/schemas/ValidValues" - description: "A Scale describes the units and acceptable values for an ObservationVariable.\ - \ \n
For example, an ObservationVariable might be defined with a Trait\ - \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ - . This variable would be distinct from a variable with the Scale \"inches\"\ - \ or \"pixels\"." - Trait: - required: - - traitDbId - - traitName + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a scale. + items: + type: string + SeasonRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - attribute: - type: string - attributePUI: - type: string - entity: - type: string - entityPUI: - type: string - mainAbbreviation: - type: string - ontologyReferenceDbId: - type: string - status: - type: string - traitClass: - type: string - traitDescription: - type: string - traitName: - type: string - traitPUI: + seasonDbIds: + type: array + description: "The unique identifier for a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'." + items: + type: string + seasonNames: + type: array + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + items: + type: string + seasons: + type: array + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + items: + type: string + years: + type: array + description: The 4 digit year of a season. Example "2017" + items: + type: string + SeedLotRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seedLotDbIds: + type: array + description: Unique id for a seed lot on this server + items: + type: string + SortBy: + type: string + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + SortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + StudyParameters: + type: object + properties: + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + StudyRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Study is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: The ID which uniquely identifies a season + items: + type: string + sortBy: type: string - description: "A Trait describes what property is being observed. \n
For example,\ - \ an ObservationVariable might be defined with a Trait of \"plant height\"\ - , a Scale of \"meters\", and a Method of \"tape measure\". This variable would\ - \ be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\"\ - . " + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + studyCodes: + type: array + description: A short human readable code for a study + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + studyPUIs: + type: array + description: "Permanent unique identifier associated with study data. For\ + \ example, a URI or DOI" + items: + type: string + studyTypes: + type: array + description: "The type of study being performed. ex. \"Yield Trial\", etc" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + Trait: + allOf: + - $ref: "#/components/schemas/TraitNewRequest" + - type: object + properties: + traitDbId: + type: string + description: The ID which uniquely identifies a trait + nullable: true + description: "A Trait describes what property is being observed. \n
For\ + \ example, an ObservationVariable might be defined with a Trait of \"plant\ + \ height\", a Scale of \"meters\", and a Method of \"tape measure\". This\ + \ variable would be distinct from a variable with the Trait \"Leaf length\"\ + \ or \"Flower height\". " TraitDataType: type: string description: |- @@ -3078,48 +6694,309 @@ components: - Text TraitNewRequest: required: - - traitDbId - traitName type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" + alternativeAbbreviations: + type: array + description: "A list of shortened, human readable, names for a Trait. These\ + \ abbreviations are acceptable alternatives to the mainAbbreviation and\ + \ do not need to follow any formatting convention." + nullable: true + items: + type: string attribute: type: string + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + nullable: true attributePUI: type: string + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + nullable: true entity: type: string + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + nullable: true entityPUI: type: string + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A Trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the Entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" mainAbbreviation: type: string - ontologyReferenceDbId: - type: string + description: A shortened version of the human readable name for a Trait + nullable: true + ontologyReference: + $ref: "#/components/schemas/OntologyReference" status: type: string + description: "Trait status (examples: \"recommended\", \"obsolete\", \"\ + legacy\", etc.)" + nullable: true + synonyms: + type: array + description: Other trait names + nullable: true + items: + type: string traitClass: type: string - traitDbId: - type: string + description: |- + A classification to describe the type of trait and the context it should be considered in. +
examples- "morphological", "phenological", "agronomical", "physiological", "abiotic stress", "biotic stress", "biochemical", "quality traits", "fertility", etc. + nullable: true traitDescription: type: string + description: The description of a trait + nullable: true traitName: type: string + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation traitPUI: type: string + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + nullable: true description: "A Trait describes what property is being observed. \n
For example,\ \ an ObservationVariable might be defined with a Trait of \"plant height\"\ , a Scale of \"meters\", and a Method of \"tape measure\". This variable would\ \ be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\"\ . " + TraitRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a trait. + items: + type: string + TrialParameters: + type: object + properties: + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + TrialRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Trial is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + contactDbIds: + type: array + description: List of contact entities associated with this trial + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + searchDateRangeEnd: + type: string + description: "The end of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + searchDateRangeStart: + type: string + description: "The start of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + sortBy: + type: string + description: Name of the field to sort by. + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - asc + - ASC + - desc + - DESC + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + trialPUIs: + type: array + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + items: + type: string ValidValues: type: object properties: + categories: + type: array + description: List of possible values with optional labels + nullable: true + items: + $ref: "#/components/schemas/ValidValuesCategory" maximumValue: type: string + description: "Maximum value for numerical, date, and time scales. Typically\ + \ used for data capture control and QC." + nullable: true minimumValue: type: string + description: "Minimum value for numerical, date, and time scales. Typically\ + \ used for data capture control and QC." + nullable: true scaleDbId: type: string scaleName: @@ -3130,59 +7007,445 @@ components: ValidValuesCategory: type: object properties: - label: - type: string - validValues: - $ref: "#/components/schemas/ValidValues" - value: + label: + type: string + description: A text label for a category + nullable: true + value: + type: string + description: The actual value for a category + nullable: true + description: "If the Scale is a categorical type, these objects define the valid\ + \ options" + Variable: + required: + - methodDbId + - methodName + - scaleDbId + - scaleName + - traitName + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true + contextOfUse: + type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true + items: + type: string + defaultValue: + type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true + documentationURL: + type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + growthStage: + type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true + institution: + type: string + description: Name of institution submitting the variable + nullable: true + language: + type: string + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true + methodDbId: + type: string + methodName: + type: string + methodPUI: + type: string + ontologyReference: + $ref: "#/components/schemas/OntologyReference" + scaleDbId: + type: string + scaleName: + type: string + scalePUI: + type: string + scientist: + type: string + description: Name of scientist submitting the variable. + nullable: true + status: + type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true + submissionTimestamp: + type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true + synonyms: + type: array + description: Other variable names + nullable: true + items: + type: string + traitDbId: + type: string + traitName: + type: string + traitPUI: + type: string + description: "A unique combination of Trait, Method, and Scale to define a clear\ + \ context for an Observation." + VariableBaseClassParameters: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + VariantRequest: + type: object + properties: + callSetDbIds: + type: array + description: "**Deprecated in v2.1** Parameter unnecessary. Github issue\ + \ number #474 \n
Only return variant calls which belong to call sets\ + \ with these IDs. If unspecified, return all variants and no variant call\ + \ objects." + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + end: + type: integer + description: "The end of the window (0-based, exclusive) for which overlapping\ + \ variants should be returned." + format: int32 + example: 1500 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbId: type: string - description: "If the Scale is a categorical type, these objects define the valid\ - \ options" - Variable: - required: - - method - - scale - - trait + description: |- + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + example: 120a2d5c + referenceDbIds: + type: array + description: The unique identifier representing a genotype `Reference` + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype `ReferenceSet` + items: + type: string + start: + type: integer + description: "The beginning of the window (0-based, inclusive) for which\ + \ overlapping variants should be returned. Genomic positions are non-negative\ + \ integers less than reference length. Requests spanning the join of circular\ + \ genomes are represented as two requests one on each side of the join\ + \ (position 0)." + format: int32 + example: 100 + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` + items: + type: string + VariantSetRequest: type: object properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - contextOfUse: + callSetDbIds: type: array + description: The unique identifier representing a CallSet items: type: string - defaultValue: - type: string - documentationURL: - type: string - growthStage: - type: string - institution: - type: string - language: - type: string - method: - $ref: "#/components/schemas/Method" - ontologyReference: - $ref: "#/components/schemas/OntologyReference" - scale: - $ref: "#/components/schemas/Scale" - scientist: - type: string - status: - type: string - submissionTimestamp: - type: string - synonyms: + commonCropNames: type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: The unique identifier representing a genotype Reference + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype ReferenceSet + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantDbIds: + type: array + description: The unique identifier representing a Variant + items: + type: string + variantSetDbIds: + type: array + description: The unique identifier representing a VariantSet items: type: string - trait: - $ref: "#/components/schemas/Trait" - description: "A unique combination of Trait, Method, and Scale to define a clear\ - \ context for an Observation." basePagination: required: - currentPage @@ -3365,12 +7628,12 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/ObservationVariable" - SeedLotSingleResponse: + VariantSingleResponse: description: OK content: application/json: schema: - title: SeedLotSingleResponse + title: VariantSingleResponse required: - metadata - result @@ -3381,13 +7644,13 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/SeedLot" - VariantSingleResponse: + $ref: "#/components/schemas/Variant" + SeedLotSingleResponse: description: OK content: application/json: schema: - title: VariantSingleResponse + title: SeedLotSingleResponse required: - metadata - result @@ -3398,7 +7661,7 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Variant" + $ref: "#/components/schemas/SeedLot" "202AcceptedSearchResponse": description: Accepted content: @@ -3417,6 +7680,30 @@ components: searchResultsDbId: type: string example: 551ae08c + StudyStudyTypeListResponse: + description: OK + content: + application/json: + schema: + title: StudyStudyTypeListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: string StudySingleResponse: description: OK content: @@ -3752,6 +8039,23 @@ components: type: array items: $ref: "#/components/schemas/Season" + ReferenceBasesSingleResponse: + description: OK + content: + application/json: + schema: + title: ReferenceBasesSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ReferenceBases" ObservationUnitListResponse: description: OK content: @@ -4290,6 +8594,23 @@ components: type: array items: $ref: "#/components/schemas/Sample" + GermplasmMCPDSingleResponse: + description: OK + content: + application/json: + schema: + title: GermplasmMCPDSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/GermplasmMCPD" ReferenceSetListResponse: description: OK content: @@ -4438,12 +8759,12 @@ components: type: array items: $ref: "#/components/schemas/Study" - ScaleSingleResponse: + LinkageGroupListResponse: description: OK content: application/json: schema: - title: ScaleSingleResponse + title: LinkageGroupListResponse required: - metadata - result @@ -4454,13 +8775,20 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/Scale" - BreedingMethodSingleResponse: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/LinkageGroup" + ScaleSingleResponse: description: OK content: application/json: schema: - title: BreedingMethodSingleResponse + title: ScaleSingleResponse required: - metadata - result @@ -4471,7 +8799,7 @@ components: metadata: $ref: "#/components/schemas/metadata" result: - $ref: "#/components/schemas/BreedingMethod" + $ref: "#/components/schemas/Scale" CallListResponse: description: OK content: @@ -4496,6 +8824,23 @@ components: type: array items: $ref: "#/components/schemas/Call" + BreedingMethodSingleResponse: + description: OK + content: + application/json: + schema: + title: BreedingMethodSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/BreedingMethod" LocationSingleResponse: description: OK content: @@ -4643,6 +8988,30 @@ components: type: array items: $ref: "#/components/schemas/BreedingMethod" + GermplasmAttributeAttributeCategoryListResponse: + description: OK + content: + application/json: + schema: + title: GermplasmAttributeAttributeCategoryListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: string GermplasmAttributeValueSingleResponse: description: OK content: @@ -4823,6 +9192,18 @@ components: schema: type: integer example: 1000 + authorizationHeader: + name: Authorization + in: header + description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ + \ {token_string} " + required: false + style: simple + explode: false + schema: + pattern: ^Bearer .*$ + type: string + example: Bearer XXXX page: name: page in: query @@ -4851,18 +9232,6 @@ components: schema: type: string example: 33c27874 - authorizationHeader: - name: Authorization - in: header - description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ - \ {token_string} " - required: false - style: simple - explode: false - schema: - pattern: ^Bearer .*$ - type: string - example: Bearer XXXX securitySchemes: AuthorizationToken: type: http diff --git a/Specification/Generated/brapi_generated.graphqls b/Specification/Generated/brapi_generated.graphqls index 2886e710..17105737 100644 --- a/Specification/Generated/brapi_generated.graphqls +++ b/Specification/Generated/brapi_generated.graphqls @@ -58,7 +58,7 @@ interface Attribute implements Variable { A description of the way an Observation should be collected.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". """ - method: Method + methodDbIds: ID """ MIAPPE V1.1 @@ -75,7 +75,7 @@ interface Attribute implements Variable { A Scale describes the units and acceptable values for an ObservationVariable.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". """ - scale: Scale + scaleDbIds: ID "Name of scientist submitting the variable." scientist: String "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" @@ -88,7 +88,7 @@ interface Attribute implements Variable { A Trait describes what property is being observed.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". """ - trait: Trait + traitDbIds: ID } """ @@ -118,6 +118,80 @@ interface ObservationUnitHierarchyLevel { levelOrder: Int } +""" +The exact level and level code of an observation unit. + +For more information on Observation Levels, please review the Observation Levels documentation. + +MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. +The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). +Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead." +""" +interface ObservationUnitLevel implements ObservationUnitHierarchyLevel { + """ + An ID code or number to represent a real thing that may or may not be an an observation unit. +
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. +
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. + """ + levelCode: String + """ + A name for this level + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelName: String + """ + `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers + are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelOrder: Int +} + +""" +Observation levels indicate the granularity level at which the measurements are taken. `levelName` +defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. +`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are +at the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify +this observation unit by each level of the hierarchy where it exists. + +For more information on Observation Levels, please review the Observation Levels documentation. + +**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** +""" +interface ObservationUnitLevelRelationship { + """ + An ID code or number to represent a real thing that may or may not be an an observation unit. +
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. +
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. + """ + levelCode: String + """ + A name for this level + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelName: String + """ + `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers + are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelOrder: Int + """ + The an observation unit +
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. +
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response. + """ + observationUnitDbIds: ID +} + "A unique combination of Trait, Method, and Scale to define a clear context for an Observation." interface Variable { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." @@ -142,7 +216,7 @@ interface Variable { A description of the way an Observation should be collected.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". """ - method: Method + methodDbIds: ID """ MIAPPE V1.1 @@ -159,7 +233,7 @@ interface Variable { A Scale describes the units and acceptable values for an ObservationVariable.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". """ - scale: Scale + scaleDbIds: ID "Name of scientist submitting the variable." scientist: String "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" @@ -172,15 +246,16 @@ interface Variable { A Trait describes what property is being observed.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". """ - trait: Trait + traitDbIds: ID } union GeoJSONGeometry = GeoJSONPoint | GeoJSONPolygon "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." type AdditionalInfo { - "A free space containing any additional information related to a particular object." - additionalProperties: String + additionalInfo: AdditionalInfo + "Additional properties as a map of key-value pairs" + additionalProperties: [KeyValuePair] } "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." @@ -210,6 +285,15 @@ type AlleleMatrixListResponse { page: PageInfo } +type AlleleMatrixPagination { + "the dimension of the matrix being paginated" + dimension: Dimension + "the requested page number (zero indexed)" + page: Int + "the maximum number of elements per page in this dimension of the matrix" + pageSize: Int +} + "An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used." type Analysis { "Unique identifier for this analysis description" @@ -227,7 +311,7 @@ type Analysis { "The time at which this record was last updated, in ISO 8601 format." updated: String "Analysis associated with a variant set" - variantSet: VariantSet + variantSetDbIds: ID } "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other." @@ -247,7 +331,7 @@ type AvailableFormat { "The string used as a representation for missing data." unknownString: String "Formats associated with a variant set" - variantSet: VariantSet + variantSetDbIds: ID } "The techniques and protocol used to produce a Cross or Germplasm" @@ -279,7 +363,7 @@ type Call { If this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same. """ - callSet: CallSet + callSetDbIds: ID "Genotype Metadata are additional layers of metadata associated with each genotype." genotypeMetadata: [GenotypeMetadata] "The value of this genotype call" @@ -290,9 +374,9 @@ type Call { """ phaseSet: String "The ID of the variant this call belongs to." - variant: Variant + variantDbIds: ID "The unique identifier for a VariantSet" - variantSet: VariantSet + variantSetDbIds: ID } type CallListResponse { @@ -315,9 +399,9 @@ type CallSet { "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] "The Biosample entity the call set data was generated from." - sample: Sample + sampleDbIds: ID "The ID which uniquely identifies a study within the given database server" - study: Study + studyDbIds: ID "The time at which this call set was last updated" updated: String "The IDs of the variantSets this callSet has calls in." @@ -339,6 +423,42 @@ type CallsSearchResponse { searchResultsDbId: String } +"Information about the collection of a germplasm" +type CollectingInfo { + "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero]." + collectingDate: String + "Institutes which collected the sample" + collectingInstitutes: [Institute] + "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\")." + collectingMissionIdentifier: String + "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections." + collectingNumber: String + "Information about the location where the sample was collected" + collectingSite: CollectingSite +} + +"Information about the location where the sample was collected" +type CollectingSite { + "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown." + coordinateUncertainty: String + "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed." + elevation: String + "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known." + georeferencingMethod: String + "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975)." + latitudeDecimal: String + "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10" + latitudeDegrees: String + "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville)." + locationDescription: String + "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123)." + longitudeDecimal: String + "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076" + longitudeDegrees: String + "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum." + spatialReferenceSystem: String +} + "A persons contact information" type Contact { """ @@ -386,13 +506,13 @@ The mixture of germplasm present in the seed lot. """ type ContentMixture { "The cross for the germplasm using in this content mixture" - cross: Cross + crosDbIds: ID "The germplasm using in this content mixture" - germplasm: Germplasm + germplasmDbIds: ID "The percentage of the given germplasm in the seed lot mixture." mixturePercentage: Int "associated seedLot" - seedLot: SeedLot + seedLotDbIds: ID } "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present." @@ -408,7 +528,7 @@ type Cross { "the type of cross" crossType: CrossType "the unique identifier for a crossing project" - crossingProject: CrossingProject + crossingProjectDbIds: ID "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] "the first parent used in the cross" @@ -416,7 +536,7 @@ type Cross { "the second parent used in the cross" parent2: CrossParent "The Cross that was used in the planning of this one." - plannedCross: PlannedCross + plannedCrosDbIds: ID "The list of pollination events that occurred for this cross." pollinationEvents: [PollinationEvent] } @@ -424,7 +544,7 @@ type Cross { "A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'" type CrossAttribute { "a custom attributes associated with a cross" - cross: Cross + crosDbIds: ID "the human readable name of a cross attribute" crossAttributeName: String "the value of a cross attribute" @@ -439,9 +559,9 @@ type CrossListResponse { "The identifying information gor the parent material of a cross." type CrossParent { "the germplasm of the cross parent" - germplasm: Germplasm + germplasmDbIds: ID "the Observation Unit of the cross parent" - observationUnit: ObservationUnit + observationUnitDbIds: ID "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc." parentType: ParentType } @@ -466,7 +586,7 @@ type CrossingProject { """ potentialParents: [CrossParent] "the unique identifier for a program" - program: Program + programDbIds: ID } type CrossingProjectListResponse { @@ -526,7 +646,7 @@ type DataLink { "A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." type DataMatrix { "Data matrices associated with an alleleMatrix" - alleleMatrix: AlleleMatrix + alleleMatrixDbIds: ID "The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." dataMatrix: [[String]] """ @@ -554,7 +674,7 @@ type DatasetAuthorships { "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository." submissionDate: String "Dataset authorships associated with a trial" - trial: Trial + trialDbIds: ID } "Links to various ontology documentation" @@ -581,7 +701,21 @@ type Donor { """ donorInstituteCode: String "donors associated with a germplasm" - germplasm: Germplasm + germplasmDbIds: ID +} + +"Information about an accession donor" +type DonorInfo { + "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard." + donorAccessionNumber: String + "PUI (DOI mostly) of the accession in the donor system." + donorAccessionPui: String + """ + The identifying information for the entity acting as an accession donor +
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard. +
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available. + """ + donorInstitute: Institute } """ @@ -603,7 +737,7 @@ type EnvironmentParameter { "URI pointing to an ontology class for the parameter" parameterPUI: String "Environment parameters associated with a study" - study: Study + studyDbIds: ID "Unit of the value for this parameter" unit: String "URI pointing to an ontology class for the unit" @@ -651,7 +785,7 @@ type Event { "A list of the affected observation units. If this parameter is not given, it is understood that the event affected all units in the study" observationUnits(observationUnitsInput: ObservationUnitsInput, paging: PageInput): ObservationUnitListResponse "The study in which the event occurred" - study: Study + studyDbIds: ID } "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" @@ -667,7 +801,7 @@ type EventDateRange { """ endDate: String "associated event" - event: Event + eventDbIds: ID """ The beginning of a continuous or regularly repetitive event
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. @@ -690,7 +824,7 @@ type EventParameter { "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter." description: String "associated event" - event: Event + eventDbIds: ID """ The full name of an event parameter
ICASA "Variable_Name" @@ -724,7 +858,7 @@ type ExperimentalDesign { "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'." description: String "Experimental design associated with a study" - study: Study + studyDbIds: ID } type ExternalReference { @@ -746,6 +880,8 @@ type GenomeMap { documentationURL: String "The number of linkage groups present in a `GenomeMap`" linkageGroupCount: Int + "The linkage groups present in a `GenomeMap`" + linkageGroups: [LinkageGroup] "The unique identifier for a `GenomeMap`" mapDbId: String "The human readable identifier for a `GenomeMap`" @@ -755,7 +891,7 @@ type GenomeMap { "The number of markers present in a `GenomeMap`" markerCount: Int "markerPositions" - markerPositions: [MarkerPosition] + markerPositionDbId: [ID] "The date this `GenomeMap` was published" publishedDate: String "Full scientific binomial format name. This includes Genus, Species, and Sub-species" @@ -779,7 +915,7 @@ type GenomeMapsSearchResponse { "Genotype Metadata are additional layers of metadata associated with each genotype." type GenotypeMetadata { "Genotype metadata associated with a call" - call: Call + callDbIds: ID "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON." dataType: DataType """ @@ -882,7 +1018,7 @@ type Germplasm { "Supplemental text description for 'biologicalStatusOfAccessionCode'" biologicalStatusOfAccessionDescription: String "The unique identifier for the breeding method used to create this germplasm" - breedingMethod: BreedingMethod + breedingMethodDbIds: ID "A specific panel/collection/population name this germplasm belongs to." collection: String """ @@ -946,6 +1082,8 @@ type Germplasm { instituteCode: String "The name of the institute that maintains the material" instituteName: String + "The mulit-crop passport descriptors (MCPD) for this germplasm" + mcpd: GermplasmMCPD """ The cross name and optional selection history. @@ -1022,7 +1160,7 @@ type GermplasmAttribute { "The Permanent Unique Identifier of an Attribute, usually in the form of a URI" attributePUI: String "attributeValues" - attributeValues: [GermplasmAttributeValue] + attributeValueDbId: [ID] "Crop name (examples: \"Maize\", \"Wheat\")" commonCropName: String "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])" @@ -1043,7 +1181,7 @@ type GermplasmAttribute { A description of the way an Observation should be collected.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". """ - method: Method + methodDbIds: ID """ MIAPPE V1.1 @@ -1060,7 +1198,7 @@ type GermplasmAttribute { A Scale describes the units and acceptable values for an ObservationVariable.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". """ - scale: Scale + scaleDbIds: ID "Name of scientist submitting the variable." scientist: String "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" @@ -1073,7 +1211,7 @@ type GermplasmAttribute { A Trait describes what property is being observed.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". """ - trait: Trait + traitDbIds: ID } type GermplasmAttributeListResponse { @@ -1086,7 +1224,7 @@ type GermplasmAttributeValue { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo "The ID which uniquely identifies this attribute within the given database server" - attribute: GermplasmAttribute + attributeDbIds: ID "The ID which uniquely identifies this attribute value within the given database server" attributeValueDbId: String "The date the value of this attribute was determined for a given germplasm" @@ -1094,7 +1232,7 @@ type GermplasmAttributeValue { "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] "The ID which uniquely identifies a germplasm within the given database server" - germplasm: Germplasm + germplasmDbIds: ID "The value of this attribute for a given germplasm" value: String } @@ -1117,7 +1255,7 @@ type GermplasmAttributesSearchResponse { "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes." type GermplasmChild { "The child germplasm" - childGermplasm: Germplasm + childGermplasmDbIds: ID """ The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. @@ -1130,7 +1268,7 @@ type GermplasmChild { """ parentType: ParentType "associated pedigreeNode" - pedigreeNode: PedigreeNode + pedigreeNodeDbIds: ID } type GermplasmListResponse { @@ -1138,6 +1276,116 @@ type GermplasmListResponse { page: PageInfo } +"The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." +type GermplasmMCPD { + "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered names or other designations given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase." + accessionNames: [String] + """ + The unique identifier for a material or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + """ + accessionNumber: String + """ + The date a material or germplasm was acquired by the genebank + + MCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or "00" [double zero]. + """ + acquisitionDate: String + """ + MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. + + 10) Wild habitat + 11) Forest or woodland + 12) Shrubland + 13) Grassland + 14) Desert or tundra + 15) Aquatic habitat + 20) Farm or cultivated habitat + 21) Field + 22) Orchard + 23) Backyard, kitchen or home garden (urban, peri-urban or rural) + 24) Fallow land + 25) Pasture + 26) Farm store + 27) Threshing floor + 28) Park + 30) Market or shop + 40) Institute, Experimental station, Research organization, Genebank + 50) Seed company + 60) Weedy, disturbed or ruderal habitat + 61) Roadside + 62) Field margin + 99) Other (Elaborate in REMARKS field) + """ + acquisitionSourceCode: AcquisitionSourceCode + "MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. " + alternateIDs: [String] + "MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'." + ancestralData: String + """ + MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. + + 100) Wild + 110) Natural + 120) Semi-natural/wild + 130) Semi-natural/sown + 200) Weedy + 300) Traditional cultivar/landrace + 400) Breeding/research material + 410) Breeders line + 411) Synthetic population + 412) Hybrid + 413) Founder stock/base population + 414) Inbred line (parent of hybrid cultivar) + 415) Segregating population + 416) Clonal selection + 420) Genetic stock + 421) Mutant (e.g. induced/insertion mutants, tilling populations) + 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) + 423) Other genetic stocks (e.g. mapping populations) + 500) Advanced or improved cultivar (conventional breeding methods) + 600) GMO (by genetic engineering) + 999) Other (Elaborate in REMARKS field) + """ + biologicalStatusOfAccessionCode: BiologicalStatusOfAccessionCode + """ + A list of institutes that were involved with breeding a material/germplasm +
MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. +
MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available. + """ + breedingInstitutes: [Institute] + "Information about the collection of a germplasm" + collectingInfo: CollectingInfo + "MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\". " + commonCropName: String + "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers\" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\"." + countryOfOrigin: String + "Information about an accession donor" + donorInfo: DonorInfo + "MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required." + genus: String + "donors associated with a germplasm" + germplasmDbIds: ID + "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\"." + instituteCode: String + "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")" + mlsStatus: MlsStatus + "MCPD (v2.1) (REMARKS) 28. The remarks field is used to add notes or to elaborate on descriptors with value 99 or 999 (= Other). Prefix remarks with the field name they refer to and a colon (:) without space (e.g. COLLSRC:riverside). Distinct remarks referring to different fields are separated by semi-colons without space." + remarks: String + safetyDuplicateInstitutes: [Institute] + "MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" " + species: String + "MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name." + speciesAuthority: String + "MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) 10) Seed collection 11) Short term 12) Medium term 13) Long term 20) Field collection 30) In vitro collection 40) Cryo-preserved collection 50) DNA collection 99) Other (elaborate in REMARKS field)" + storageTypeCodes: [StorageTypeCode] + "MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\")." + subtaxon: String + "MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level." + subtaxonAuthority: String +} + "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm." type GermplasmOrigin { "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown." @@ -1152,13 +1400,13 @@ type GermplasmOrigin { """ coordinates: [GeoJSON] "associated germplasm" - germplasm: Germplasm + germplasmDbIds: ID } "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes." type GermplasmParent { "The parent germplasm" - parentGermplasm: Germplasm + parentGermplasmDbIds: ID """ The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. @@ -1171,7 +1419,7 @@ type GermplasmParent { """ parentType: ParentType "associated pedigreeNode" - pedigreeNode: PedigreeNode + pedigreeNodeDbIds: ID } type GermplasmSearchResponse { @@ -1185,8 +1433,6 @@ type GrowthFacility { PUI: String "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out." description: String - "Growth facility associated with a study" - study: Study } "The metadata for an image file that is connected to some phenotypic observation data." @@ -1201,6 +1447,8 @@ type Image { descriptiveOntologyTerms: [String] "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] + "The content of the image" + imageContent: String "The unique identifier of an image" imageDbId: String "The name of the image file. Might be the same as 'imageName', but could be different." @@ -1229,7 +1477,7 @@ type Image { "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc" mimeType: String "The related observation unit identifier, if relevant." - observationUnit: ObservationUnit + observationUnitDbIds: ID "A list of observation Ids this image is associated with, if applicable." observations(observationsInput: ObservationsInput, paging: PageInput): ObservationListResponse } @@ -1244,18 +1492,48 @@ type ImagesSearchResponse { searchResultsDbId: String } +"The details of an Institute or other simular entity." +type Institute { + "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space." + instituteAddress: String + "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space." + instituteCode: String + "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space." + instituteName: String +} + +"A key-value pair representing a single map entry" +type KeyValuePair { + key: String + value: String +} + "The date and time when this study was last modified" type LastUpdate { - "The date and time when this study was last modified" + "The ID which uniquely identifies a LastUpdate within the given database server" lastUpdateDbId: String "Last update associated with a study" - study: Study + studyDbIds: ID "The timestamp of the update." timestamp: String "The version of the update." version: String } +"a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group." +type LinkageGroup { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "The `GenomeMap` to which this `LinkageGroup` belongs " + genomeMapDbIds: ID + "The Uniquely Identifiable name of a `LinkageGroup`
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable." + linkageGroupName: String + "The number of markers associated with a `LinkageGroup`." + markerCount: Int + "The maximum position of a marker within a `LinkageGroup`." + maxPosition: Int +} + "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." type List { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." @@ -1277,7 +1555,7 @@ type List { "Human readable name of a List Owner. (usually a user or person)" listOwnerName: String "The unique identifier for a List Owner. (usually a user or person)" - listOwnerPerson: Person + listOwnerPersonDbIds: ID "The number of elements in a List" listSize: Int "The description of where a List originated from" @@ -1302,7 +1580,11 @@ type Location { abbreviation: String "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo - childLocations: [Location] + """ + The child locations that belong to this Location. + For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + """ + childLocationDbId: [ID] "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)" coordinateDescription: String "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown." @@ -1358,7 +1640,7 @@ type Location {
The Parent Location defines the encompassing Location that a smaller Location belongs to. For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. """ - parentLocation: Location + parentLocationDbIds: ID "Description of the accessibility of the location (ex. Public, Private)" siteStatus: String "Describes the approximate slope (height/distance) of a Location." @@ -1387,14 +1669,14 @@ type MarkerPosition { """ linkageGroupName: String "The ID which uniquely identifies a `GenomeMap`" - map: GenomeMap + mapDbIds: ID "The position of a marker or variant within a `LinkageGroup`" position: Int """ The ID which uniquely identifies a `Variant` within the given database server
A `Variant` can also represent a Marker """ - variant: Variant + variantDbIds: ID } type MarkerPositionListResponse { @@ -1419,7 +1701,7 @@ type MetadataField { "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"" fieldName: String "Formats associated with a variant set" - variantSet: VariantSet + variantSetDbIds: ID } """ @@ -1598,19 +1880,19 @@ type Observation { """ geoCoordinates: GeoJSON "The ID which uniquely identifies a germplasm" - germplasm: Germplasm + germplasmDbIds: ID "The ID which uniquely identifies an observation" observationDbId: String "The date and time when this observation was made" observationTimeStamp: String "The ID which uniquely identifies an observation unit" - observationUnit: ObservationUnit + observationUnitDbIds: ID "The ID which uniquely identifies an observation variable" - observationVariable: ObservationVariable + observationVariableDbIds: ID "The season for this Observation" - season: Season + seasonDbIds: ID "The ID which uniquely identifies a study within the given database server" - study: Study + studyDbIds: ID "The name or id of the user who uploaded the observation to the database system" uploadedBy: String "The value of the data collected as an observation" @@ -1637,7 +1919,7 @@ type ObservationTreatment { """ modality: String "associated observation Unit" - observationUnit: ObservationUnit + observationUnitDbIds: ID } "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." @@ -1645,13 +1927,13 @@ type ObservationUnit { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo "the unique identifier for a cross" - cross: Cross + crosDbIds: ID "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] "The ID which uniquely identifies a germplasm" - germplasm: Germplasm + germplasmDbIds: ID "The ID which uniquely identifies a location, associated with this study" - location: Location + locationDbIds: ID """ The ID which uniquely identifies an observation unit @@ -1675,11 +1957,11 @@ type ObservationUnit { """ observationUnitPosition: [ObservationUnitPosition] "The ID which uniquely identifies a program" - program: Program + programDbIds: ID "The unique identifier for the originating Seed Lot" - seedLot: SeedLot + seedLotDbIds: ID "The ID which uniquely identifies a study within the given database server" - study: Study + studyDbIds: ID """ List of treatments applied to an observation unit. @@ -1687,81 +1969,7 @@ type ObservationUnit { """ treatments: [ObservationTreatment] "The ID which uniquely identifies a trial" - trial: Trial -} - -""" -The exact level and level code of an observation unit. - -For more information on Observation Levels, please review the Observation Levels documentation. - -MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. -The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). -Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead." -""" -type ObservationUnitLevel implements ObservationUnitHierarchyLevel { - """ - An ID code or number to represent a real thing that may or may not be an an observation unit. -
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. -
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. - """ - levelCode: String - """ - A name for this level - - **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** - - For more information on Observation Levels, please review the Observation Levels documentation. - """ - levelName: String - """ - `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers - are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). - - For more information on Observation Levels, please review the Observation Levels documentation. - """ - levelOrder: Int -} - -""" -Observation levels indicate the granularity level at which the measurements are taken. `levelName` -defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. -`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are -at the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify -this observation unit by each level of the hierarchy where it exists. - -For more information on Observation Levels, please review the Observation Levels documentation. - -**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** -""" -type ObservationUnitLevelRelationship { - """ - An ID code or number to represent a real thing that may or may not be an an observation unit. -
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. -
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. - """ - levelCode: String - """ - A name for this level - - **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** - - For more information on Observation Levels, please review the Observation Levels documentation. - """ - levelName: String - """ - `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers - are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). - - For more information on Observation Levels, please review the Observation Levels documentation. - """ - levelOrder: Int - """ - The an observation unit -
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. -
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response. - """ - observationUnit: ObservationUnit + trialDbIds: ID } type ObservationUnitListResponse { @@ -1805,7 +2013,7 @@ type ObservationUnitPosition { """ observationLevelRelationships: [ObservationUnitLevelRelationship] "associated observation Unit" - observationUnit: ObservationUnit + observationUnitDbIds: ID "The X position coordinate for an observation unit. Different systems may use different coordinate systems." positionCoordinateX: String "The type of positional coordinate used for the X coordinate of the position." @@ -1844,7 +2052,7 @@ type ObservationVariable implements Variable { A description of the way an Observation should be collected.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". """ - method: Method + methodDbIds: ID """ Variable unique identifier @@ -1875,7 +2083,7 @@ type ObservationVariable implements Variable { A Scale describes the units and acceptable values for an ObservationVariable.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". """ - scale: Scale + scaleDbIds: ID "Name of scientist submitting the variable." scientist: String "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" @@ -1888,7 +2096,7 @@ type ObservationVariable implements Variable { A Trait describes what property is being observed.
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". """ - trait: Trait + traitDbIds: ID } type ObservationVariableListResponse { @@ -1943,7 +2151,7 @@ type OntologyReference { "links to various ontology documentation" documentationLinks: [DocumentationLink] "The Ontology for this reference" - ontology: Ontology + ontologyDbIds: ID "The ID which uniquely identifies a ontology reference" ontologyReferenceDbId: String "Ontology version (no specific format)" @@ -1968,7 +2176,7 @@ type PageInfo { "Pagination info for the matrix" type Pagination { "Pagination associated with an alleleMatrix" - alleleMatrix: AlleleMatrix + alleleMatrixDbIds: ID "The dimension of the matrix being paginated" dimension: Dimension "the requested page number (zero indexed)" @@ -1989,9 +2197,9 @@ type PedigreeNode { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo "The unique identifier for the breeding method used to create this germplasm" - breedingMethod: BreedingMethod + breedingMethodDbIds: ID "The crossing project used to generate this germplasm" - crossingProject: CrossingProject + crossingProjectDbIds: ID "The year the parents were originally crossed" crossingYear: Int "Human readable name used for display purposes" @@ -2001,7 +2209,7 @@ type PedigreeNode { "The code representing the family of this germplasm" familyCode: String "The ID which uniquely identifies a germplasm" - germplasm: Germplasm + germplasmDbIds: ID """ A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. @@ -2024,7 +2232,7 @@ type PedigreeNode {
Siblings share at least one parent with the given germplasm.
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response. """ - siblings: [Germplasm] + siblingDbId: [ID] } type PedigreeNodeListResponse { @@ -2080,7 +2288,7 @@ type PlannedCross { "the type of cross" crossType: CrossType "the unique identifier for a crossing project" - crossingProject: CrossingProject + crossingProjectDbIds: ID "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] "the first parent used in the cross" @@ -2120,13 +2328,13 @@ type Plate { "A human readable name for a `Plate`" plateName: String "The ID which uniquely identifies a `Program` within the given database server" - program: Program + programDbIds: ID "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" sampleType: SampleType "The ID which uniquely identifies a `Study` within the given database server" - study: Study + studyDbIds: ID "The ID which uniquely identifies a `Trial` within the given database server" - trial: Trial + trialDbIds: ID } type PlateListResponse { @@ -2142,7 +2350,7 @@ type PlatesSearchResponse { "A Pollination Event that was used or attempted for a Cross." type PollinationEvent { "The Cross associated with this Pollination Event" - cross: Cross + crosDbIds: ID "The unique identifier for this pollination event" pollinationNumber: String "True if the pollination was successful" @@ -2166,7 +2374,7 @@ type Program { "Information describing the grant or funding source for this program" fundingInformation: String "The unique identifier of the program leader" - leadPerson: Person + leadPersonDbIds: ID "The primary objective of the program" objective: String "The ID which uniquely identifies the program" @@ -2198,7 +2406,7 @@ type Publication { "The publication reference." publicationReference: String "Publications associated with a trial" - trial: Trial + trialDbIds: ID } type Query { @@ -2394,6 +2602,8 @@ type Query { type Reference { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + bases: ReferenceBases "Common name for the crop" commonCropName: String "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." @@ -2409,19 +2619,29 @@ type Reference { "The human readable name of a `Reference` within a `ReferenceSet`." referenceName: String "The unique identifier for a `ReferenceSet`" - referenceSet: ReferenceSet + referenceSetDbIds: ID "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`." sourceAccessions: [String] "The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from." sourceDivergence: Float "All known corresponding Germplasm" - sourceGermplasm: [Germplasm] + sourceGermplasmDbId: [ID] "The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the `getReferenceBases()` method to obtain sequence bases for a `Reference` instead of attempting to retrieve this URI." sourceURI: String "An ontology term describing an attribute." species: OntologyTerm "variants" - variants: [Variant] + variantDbId: [ID] +} + +"A string representation of the `Reference` base alleles." +type ReferenceBases { + "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there are not any additional results." + nextPageToken: String + "The offset position (0-based) of the given sequence from the start of this `Reference`. This value will differ for each page in a request." + offset: Int + "A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`." + sequence: String } type ReferenceListResponse { @@ -2452,24 +2672,24 @@ type ReferenceSet { hexadecimal string. """ md5checksum: String + "references" + referenceDbIds: ID "The unique identifier for a ReferenceSet" referenceSetDbId: String "The human readable name of a ReferenceSet" referenceSetName: String - "references" - references: Reference "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`." sourceAccessions: [String] "All known corresponding Germplasm" - sourceGermplasm: [Germplasm] + sourceGermplasmDbId: [ID] "Specifies a FASTA format file/string." sourceURI: String "An ontology term describing an attribute." species: OntologyTerm - "variantSets" - variantSets: [VariantSet] "variants" - variants: [Variant] + variantDbId: [ID] + "variantSets" + variantSetDbId: [ID] } type ReferenceSetListResponse { @@ -2491,19 +2711,19 @@ type ReferencesSearchResponse { type Sample { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo - callSets: [CallSet] + callSetDbId: [ID] "The Column identifier for this `Sample` location in the `Plate`" column: Int "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] "The ID which uniquely identifies a `Germplasm`" - germplasm: Germplasm + germplasmDbIds: ID "The ID which uniquely identifies an `ObservationUnit`" - observationUnit: ObservationUnit + observationUnitDbIds: ID "The ID which uniquely identifies a `Plate` of `Sample`" - plate: Plate + plateDbIds: ID "The ID which uniquely identifies a `Program` within the given database server" - program: Program + programDbIds: ID "The Row identifier for this `Sample` location in the `Plate`" row: String "A unique identifier physically attached to the `Sample`" @@ -2535,7 +2755,7 @@ type Sample { "The type of `Sample` taken. ex. 'DNA', 'RNA', 'Tissue', etc" sampleType: String "The ID which uniquely identifies a `Study` within the given database server" - study: Study + studyDbIds: ID "The name or identifier of the entity which took the `Sample` from the field" takenBy: String """ @@ -2544,7 +2764,7 @@ type Sample { """ tissueType: String "The ID which uniquely identifies a `Trial` within the given database server" - trial: Trial + trialDbIds: ID "The Well identifier for this `Sample` location in the `Plate`. Usually a concatenation of Row and Column, or just a number if the `Samples` are not part of an ordered `Plate`." well: String } @@ -2658,14 +2878,12 @@ type SeedLot { createdDate: String "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] - "fromSeedLotTransactions" - fromSeedLotTransactions: [SeedLotTransaction] "The timestamp for the last update to this Seed Lot (including transactions)" lastUpdated: String "The unique identifier for a Location" - location: Location + locationDbIds: ID "The unique DbId of the breeding program this Seed Lot belongs to" - program: Program + programDbIds: ID "Unique DbId for the Seed Lot" seedLotDbId: String "A general description of this Seed Lot" @@ -2676,8 +2894,8 @@ type SeedLot { sourceCollection: String "Description the storage location" storageLocation: String - "toSeedLotTransactions" - toSeedLotTransactions: [SeedLotTransaction] + "The complete history of transactions for this seed lot. This includes seed increases, seed usage (planting), and trading with other breeding programs." + transactions: [SeedLotTransaction] "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)" units: String } @@ -2696,9 +2914,9 @@ type SeedLotTransaction { "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] "The identifier for the Seed Lot being transferred out of" - fromSeedLot: SeedLot + fromSeedLotDbIds: ID "The identifier for the Seed Lot being transferred into" - toSeedLot: SeedLot + toSeedLotDbIds: ID "Unique DbId for the Seed Lot Transaction" transactionDbId: String "A general description of this Seed Lot Transaction" @@ -2735,7 +2953,7 @@ type StorageType { "A supplemental text description of the storage type" description: String "associated germplasm" - germplasm: Germplasm + germplasmDbIds: ID } type StudiesSearchResponse { @@ -2782,7 +3000,7 @@ type Study { "The usage license associated with the study data" license: String "The unique identifier for a Location" - location: Location + locationDbIds: ID """ Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. @@ -2835,7 +3053,7 @@ type Study { "The type of study being performed. ex. \"Yield Trial\", etc" studyType: String "The ID which uniquely identifies a trial" - trial: Trial + trialDbIds: ID } type StudyListResponse { @@ -2846,7 +3064,7 @@ type StudyListResponse { "Alternative names or IDs used to reference this germplasm" type Synonym { "associated germplasm" - germplasm: Germplasm + germplasmDbIds: ID "Alternative name or ID used to reference this germplasm" synonym: String "A descriptive classification for this synonym" @@ -2860,7 +3078,7 @@ MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species lev """ type TaxonId { "associated germplasm" - germplasm: Germplasm + germplasmDbIds: ID "The human readable name of the taxonomy provider" sourceName: String "The identifier (name, ID, URI) of a particular taxonomy within the source provider" @@ -2952,12 +3170,12 @@ type Trial { "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] "A program identifier to search for" - program: Program + programDbIds: ID "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended." publications: [Publication] "The date this trial started" startDate: String - studies: [Study] + studyDbId: [ID] """ The ID which uniquely identifies a trial @@ -2999,7 +3217,7 @@ type ValidValues { "Minimum value for numerical, date, and time scales. Typically used for data capture control and QC." minimumValue: String "associated scale" - scale: Scale + scaleDbIds: ID } "If the Scale is a categorical type, these objects define the valid options" @@ -3047,13 +3265,13 @@ type Variant { "True if all filters for this variant passed. VCF column 7 \"FILTER\" value PASS." filtersPassed: Boolean "markerPositions" - markerPositions: [MarkerPosition] - "The unique identifier for a Reference" - reference: Reference + markerPositionDbId: [ID] "The reference bases for this variant. They start at the given start position." referenceBases: String + "The unique identifier for a Reference" + referenceDbIds: ID "The unique identifier for a ReferenceSet" - referenceSet: ReferenceSet + referenceSetDbIds: ID """ This field is optional and may be ignored if there is no relevant map or reference to be associated with.
The start position at which this variant occurs (0-based). This corresponds to the first base of the string @@ -3070,7 +3288,7 @@ type Variant { "A human readable name associated with a `Variant`" variantNames: [String] "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted." - variantSet: VariantSet + variantSetDbIds: ID """ The "variant_type" is used to denote e.g. structural variants. Examples: @@ -3110,9 +3328,9 @@ type VariantSet { """ metadataFields: [MetadataField] "The ID of the reference set that describes the sequences used by the variants in this set." - referenceSet: ReferenceSet + referenceSetDbIds: ID "The ID of the dataset this variant set belongs to." - study: Study + studyDbIds: ID "The number of Variants included in this VariantSet" variantCount: Int "The unique identifier for a VariantSet" @@ -3138,6 +3356,57 @@ type VariantsSearchResponse { searchResultsDbId: String } +""" +MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. + +10) Wild habitat +11) Forest or woodland +12) Shrubland +13) Grassland +14) Desert or tundra +15) Aquatic habitat +20) Farm or cultivated habitat +21) Field +22) Orchard +23) Backyard, kitchen or home garden (urban, peri-urban or rural) +24) Fallow land +25) Pasture +26) Farm store +27) Threshing floor +28) Park +30) Market or shop +40) Institute, Experimental station, Research organization, Genebank +50) Seed company +60) Weedy, disturbed or ruderal habitat +61) Roadside +62) Field margin +99) Other (Elaborate in REMARKS field) +""" +enum AcquisitionSourceCode { + N10 + N11 + N12 + N13 + N14 + N15 + N20 + N21 + N22 + N23 + N24 + N25 + N26 + N27 + N28 + N30 + N40 + N50 + N60 + N61 + N62 + N99 +} + """ MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. @@ -3213,7 +3482,7 @@ enum DataFormat { tabular } -"The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON." +"The type of field represented in this data matrix. This is intended to help parse the data out of JSON." enum DataType { boolean float @@ -3221,7 +3490,7 @@ enum DataType { string } -"The dimension of the matrix being paginated" +"the dimension of the matrix being paginated" enum Dimension { CALLSETS VARIANTS @@ -3264,6 +3533,14 @@ enum ListType { variants } +"MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")" +enum MlsStatus { + N0 + N1 + N99 + blank +} + "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. " enum ParentType { CLONAL @@ -3334,21 +3611,27 @@ enum SampleType { TISSUE } -""" -The 2 digit code representing the type of storage this germplasm is kept in at a genebank. - -MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) - -10) Seed collection -11) Short term -12) Medium term -13) Long term -20) Field collection -30) In vitro collection -40) Cryo-preserved collection -50) DNA collection -99) Other (elaborate in REMARKS field) -""" +"Name of the field to sort by." +enum SortBy { + locationDbId + programDbId + programName + seasonDbId + studyDbId + studyLocation + studyName + studyType + trialDbId +} + +"Sort order direction. Ascending/Descending." +enum SortOrder { + ASC + DESC + asc + desc +} + enum StorageTypeCode { N10 N11 @@ -3382,10 +3665,7 @@ enum TraitDataType { } "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." -input AdditionalInfoInput { - "A free space containing any additional information related to a particular object." - additionalProperties: String -} +scalar AdditionalInfoInput "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." input AlleleMatrixInput { @@ -3582,6 +3862,42 @@ input CallsInput { variantSetDbIds: [String] } +"Information about the collection of a germplasm" +input CollectingInfoInput { + "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero]." + collectingDate: String + "Institutes which collected the sample" + collectingInstitutes: [InstituteInput] + "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\")." + collectingMissionIdentifier: String + "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections." + collectingNumber: String + "Information about the location where the sample was collected" + collectingSite: CollectingSiteInput +} + +"Information about the location where the sample was collected" +input CollectingSiteInput { + "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown." + coordinateUncertainty: String + "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed." + elevation: String + "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known." + georeferencingMethod: String + "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975)." + latitudeDecimal: String + "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10" + latitudeDegrees: String + "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville)." + locationDescription: String + "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123)." + longitudeDecimal: String + "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076" + longitudeDegrees: String + "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum." + spatialReferenceSystem: String +} + "A persons contact information" input ContactInput { """ @@ -3867,6 +4183,20 @@ input DocumentationLinkInput { type: DocumentationLinkType } +"Information about an accession donor" +input DonorInfoInput { + "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard." + donorAccessionNumber: String + "PUI (DOI mostly) of the accession in the donor system." + donorAccessionPui: String + """ + The identifying information for the entity acting as an accession donor +
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard. +
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available. + """ + donorInstitute: InstituteInput +} + "Identifier assigned to an accession by the material donor." input DonorInput { """ @@ -4053,6 +4383,8 @@ input GenomeMapInput { documentationURL: String "The number of linkage groups present in a `GenomeMap`" linkageGroupCount: Int + "The linkage groups present in a `GenomeMap`" + linkageGroups: [LinkageGroupInput] "The unique identifier for a `GenomeMap`" mapDbId: String "The human readable identifier for a `GenomeMap`" @@ -4085,7 +4417,7 @@ input GenomeMapsInput { "The ID which uniquely identifies a `GenomeMap`" mapDbIds: [String] "The DOI or other permanent identifier for a `GenomeMap`" - mapPUI: [String] + mapPUIs: [String] """ A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. @@ -4566,6 +4898,8 @@ input GermplasmInput { instituteCode: String "The name of the institute that maintains the material" instituteName: String + "The mulit-crop passport descriptors (MCPD) for this germplasm" + mcpd: GermplasmMCPDInput "observationUnits" observationUnits: [ObservationUnitInput] "observations" @@ -4643,6 +4977,116 @@ input GermplasmInput { taxonIds: [TaxonIdInput] } +"The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." +input GermplasmMCPDInput { + "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered names or other designations given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase." + accessionNames: [String] + """ + The unique identifier for a material or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + """ + accessionNumber: String + """ + The date a material or germplasm was acquired by the genebank + + MCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or "00" [double zero]. + """ + acquisitionDate: String + """ + MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. + + 10) Wild habitat + 11) Forest or woodland + 12) Shrubland + 13) Grassland + 14) Desert or tundra + 15) Aquatic habitat + 20) Farm or cultivated habitat + 21) Field + 22) Orchard + 23) Backyard, kitchen or home garden (urban, peri-urban or rural) + 24) Fallow land + 25) Pasture + 26) Farm store + 27) Threshing floor + 28) Park + 30) Market or shop + 40) Institute, Experimental station, Research organization, Genebank + 50) Seed company + 60) Weedy, disturbed or ruderal habitat + 61) Roadside + 62) Field margin + 99) Other (Elaborate in REMARKS field) + """ + acquisitionSourceCode: AcquisitionSourceCode + "MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. " + alternateIDs: [String] + "MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'." + ancestralData: String + """ + MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. + + 100) Wild + 110) Natural + 120) Semi-natural/wild + 130) Semi-natural/sown + 200) Weedy + 300) Traditional cultivar/landrace + 400) Breeding/research material + 410) Breeders line + 411) Synthetic population + 412) Hybrid + 413) Founder stock/base population + 414) Inbred line (parent of hybrid cultivar) + 415) Segregating population + 416) Clonal selection + 420) Genetic stock + 421) Mutant (e.g. induced/insertion mutants, tilling populations) + 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) + 423) Other genetic stocks (e.g. mapping populations) + 500) Advanced or improved cultivar (conventional breeding methods) + 600) GMO (by genetic engineering) + 999) Other (Elaborate in REMARKS field) + """ + biologicalStatusOfAccessionCode: BiologicalStatusOfAccessionCode + """ + A list of institutes that were involved with breeding a material/germplasm +
MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. +
MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available. + """ + breedingInstitutes: [InstituteInput] + "Information about the collection of a germplasm" + collectingInfo: CollectingInfoInput + "MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\". " + commonCropName: String + "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers\" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\"." + countryOfOrigin: String + "Information about an accession donor" + donorInfo: DonorInfoInput + "MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required." + genus: String + "donors associated with a germplasm" + germplasm: GermplasmInput + "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\"." + instituteCode: String + "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")" + mlsStatus: MlsStatus + "MCPD (v2.1) (REMARKS) 28. The remarks field is used to add notes or to elaborate on descriptors with value 99 or 999 (= Other). Prefix remarks with the field name they refer to and a colon (:) without space (e.g. COLLSRC:riverside). Distinct remarks referring to different fields are separated by semi-colons without space." + remarks: String + safetyDuplicateInstitutes: [InstituteInput] + "MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" " + species: String + "MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name." + speciesAuthority: String + "MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) 10) Seed collection 11) Short term 12) Medium term 13) Long term 20) Field collection 30) In vitro collection 40) Cryo-preserved collection 50) DNA collection 99) Other (elaborate in REMARKS field)" + storageTypeCodes: [StorageTypeCode] + "MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\")." + subtaxon: String + "MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level." + subtaxonAuthority: String +} + "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm." input GermplasmOriginInput { "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown." @@ -4701,6 +5145,8 @@ input ImageInput { descriptiveOntologyTerms: [String] "Filter by External References" externalReferences: [ExternalReferenceInput] + "The content of the image" + imageContent: String "The unique identifier of an image" imageDbId: String "The name of the image file. Might be the same as 'imageName', but could be different." @@ -4790,9 +5236,19 @@ input ImagesInput { programNames: [String] } +"The details of an Institute or other simular entity." +input InstituteInput { + "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space." + instituteAddress: String + "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space." + instituteCode: String + "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space." + instituteName: String +} + "The date and time when this study was last modified" input LastUpdateInput { - "The date and time when this study was last modified" + "The ID which uniquely identifies a LastUpdate within the given database server" lastUpdateDbId: String "Last update associated with a study" study: StudyInput @@ -4802,6 +5258,20 @@ input LastUpdateInput { version: String } +"a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group." +input LinkageGroupInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "The `GenomeMap` to which this `LinkageGroup` belongs " + genomeMap: GenomeMapInput + "The Uniquely Identifiable name of a `LinkageGroup`
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable." + linkageGroupName: String + "The number of markers associated with a `LinkageGroup`." + markerCount: Int + "The maximum position of a marker within a `LinkageGroup`." + maxPosition: Int +} + "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." input ListInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." @@ -4833,6 +5303,14 @@ input ListInput { } input ListsInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] "Define the end for an interval of time and only include Lists that are created within this interval." dateCreatedRangeEnd: String "Define the beginning for an interval of time and only include Lists that are created within this interval." @@ -4852,6 +5330,20 @@ input ListsInput { "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)" listSources: [String] listType: ListType + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] } "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." @@ -4860,6 +5352,10 @@ input LocationInput { abbreviation: String "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput + """ + The child locations that belong to this Location. + For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + """ childLocations: [LocationInput] "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)" coordinateDescription: String @@ -5091,6 +5587,8 @@ input MethodsInput { Use `GET /commoncropnames` to find the list of available crops on a server. """ commonCropNames: [String] + "The unique identifier for a method." + methodDbIds: [String] "The unique identifier for an observation variable." observationVariableDbIds: [String] """ @@ -5113,8 +5611,6 @@ input MethodsInput { Use `GET /programs` to find the list of available programs on a server. """ programNames: [String] - "The unique identifier for a method." - scaleDbIds: [String] } "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." @@ -5409,6 +5905,51 @@ input ObservationUnitsInput { observationLevels: [ObservationUnitLevelInput] "The unique id of an observation unit" observationUnitDbIds: [String] + """ + The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` + or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelCodes: [String] + """ + The Observation Unit Level. Returns only the observation unit of the specified Level. +
References ObservationUnit->observationUnitPosition->observationLevel->levelName +
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelNames: [String] + """ + The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. + References ObservationUnit->observationUnitPosition->observationLevel->levelOrder +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelOrders: [String] + """ + The Observation Unit Level Code. +
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelRelationshipCodes: [String] + """ + The observationUnitDbId associated with a particular level and code. +
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelRelationshipDbIds: [String] + """ + The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. +
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. +
Use this parameter to identify groups of observation units that share a relationship level. +
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelRelationshipNames: [String] + """ + The Observation Unit Level Order Number. +
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelRelationshipOrders: [String] "The human readable identifier for an Observation Unit" observationUnitNames: [String] "The DbIds of Variables to search for" @@ -5636,6 +6177,51 @@ input ObservationsInput { observationTimeStampRangeStart: String "The unique id of an Observation Unit" observationUnitDbIds: [String] + """ + The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` + or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelCodes: [String] + """ + The Observation Unit Level. Returns only the observation unit of the specified Level. +
References ObservationUnit->observationUnitPosition->observationLevel->levelName +
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelNames: [String] + """ + The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. + References ObservationUnit->observationUnitPosition->observationLevel->levelOrder +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelOrders: [String] + """ + The Observation Unit Level Code. +
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelRelationshipCodes: [String] + """ + The observationUnitDbId associated with a particular level and code. +
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelRelationshipDbIds: [String] + """ + The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. +
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. +
Use this parameter to identify groups of observation units that share a relationship level. +
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelRelationshipNames: [String] + """ + The Observation Unit Level Order Number. +
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder +
For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationUnitLevelRelationshipOrders: [String] "The DbIds of Variables to search for" observationVariableDbIds: [String] "The names of Variables to search for" @@ -6034,7 +6620,7 @@ input PlatesInput { Use `GET /commoncropnames` to find the list of available crops on a server. """ commonCropNames: [String] - "The ID which uniquely identifies a germplasm" + "List of IDs which uniquely identify germplasm to search for" germplasmDbIds: [String] "List of human readable names to identify germplasm to search for" germplasmNames: [String] @@ -6178,10 +6764,22 @@ input PublicationInput { trial: TrialInput } +"A string representation of the `Reference` base alleles." +input ReferenceBasesInput { + "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there are not any additional results." + nextPageToken: String + "The offset position (0-based) of the given sequence from the start of this `Reference`. This value will differ for each page in a request." + offset: Int + "A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`." + sequence: String +} + "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." input ReferenceInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + bases: ReferenceBasesInput "Common name for the crop" commonCropName: String "Filter by External References" @@ -6422,7 +7020,7 @@ input SamplesInput { Use `GET /commoncropnames` to find the list of available crops on a server. """ commonCropNames: [String] - "The ID which uniquely identifies a `Germplasm`" + "List of IDs which uniquely identify germplasm to search for" germplasmDbIds: [String] "List of human readable names to identify germplasm to search for" germplasmNames: [String] @@ -6592,8 +7190,6 @@ input SeedLotInput { createdDate: String "Filter by External References" externalReferences: [ExternalReferenceInput] - "fromSeedLotTransactions" - fromSeedLotTransactions: [SeedLotTransactionInput] "The timestamp for the last update to this Seed Lot (including transactions)" lastUpdated: String "The unique identifier for a Location" @@ -6612,8 +7208,8 @@ input SeedLotInput { sourceCollection: String "Description the storage location" storageLocation: String - "toSeedLotTransactions" - toSeedLotTransactions: [SeedLotTransactionInput] + "The complete history of transactions for this seed lot. This includes seed increases, seed usage (planting), and trading with other breeding programs." + transactions: [SeedLotTransactionInput] "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)" units: String } @@ -6740,6 +7336,10 @@ input StudiesInput { programNames: [String] "The ID which uniquely identifies a season" seasonDbIds: [String] + "Name of the field to sort by." + sortBy: SortBy + "Sort order direction. Ascending/Descending." + sortOrder: SortOrder "A short human readable code for a study" studyCodes: [String] "List of study identifiers to search for" @@ -7102,6 +7702,10 @@ input TrialsInput { - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate` """ searchDateRangeStart: String + "Name of the field to sort by." + sortBy: SortBy + "Sort order direction. Ascending/Descending." + sortOrder: SortOrder "List of study identifiers to search for" studyDbIds: [String] "List of study names to filter search results" diff --git a/Specification/Generated/brapi_generated.json b/Specification/Generated/brapi_generated.json index f7370c40..2ac94fcd 100644 --- a/Specification/Generated/brapi_generated.json +++ b/Specification/Generated/brapi_generated.json @@ -12,7 +12,17 @@ ], "summary" : "Get a filtered list of BreedingMethod", "description" : "Get a list of BreedingMethod", - "parameters" : [ ], + "parameters" : [ + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/BreedingMethodListResponse" @@ -65,7 +75,7 @@ } }, { - "name" : "expandHomozygote", + "name" : "expandHomozygotes", "in" : "query", "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", "required" : false, @@ -100,6 +110,9 @@ "type" : "string" } }, + { + "$ref" : "#/components/parameters/pageToken" + }, { "$ref" : "#/components/parameters/page" }, @@ -134,15 +147,6 @@ "summary" : "Get a filtered list of CallSet", "description" : "Get a list of CallSet", "parameters" : [ - { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "germplasmDbId", "in" : "query", @@ -152,69 +156,6 @@ "type" : "string" } }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "sampleDbId", "in" : "query", @@ -224,15 +165,6 @@ "type" : "string" } }, - { - "name" : "sampleName", - "in" : "query", - "description" : "A list of human readable names associated with `Samples`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "callSetDbId", "in" : "query", @@ -260,9 +192,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -321,15 +250,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "crossingProjectDbId", "in" : "query", @@ -366,9 +286,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -415,7 +332,11 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/CrossNewRequest" + "type" : "object", + "additionalProperties" : { + "$ref" : "#/components/schemas/CrossNewRequest" + }, + "example" : "{_1={additionalInfo={}, crossAttributes=[{}], crossDbId=15187888, crossName=15a57676, crossType={}, crossingProject={}, externalReferences=[{}], parent1={}, parent2={}, plannedCross={}, pollinationEvents=[{}], observationUnits=[{}]}, _2={additionalInfo={}, crossAttributes=[{}], crossDbId=15187889, crossName=15a57677, crossType={}, crossingProject={}, externalReferences=[{}], parent1={}, parent2={}, plannedCross={}, pollinationEvents=[{}], observationUnits=[{}]}}" } } } @@ -450,7 +371,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/CrossNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/CrossNewRequest" + } } } } @@ -497,15 +421,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "crossingProjectDbId", "in" : "query", @@ -525,7 +440,7 @@ } }, { - "name" : "includePotentialParent", + "name" : "includePotentialParents", "in" : "query", "description" : "If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object.", "required" : false, @@ -533,9 +448,6 @@ "type" : "boolean" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -582,7 +494,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/CrossingProjectNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/CrossingProjectNewRequest" + } } } } @@ -620,15 +535,6 @@ "type" : "string" } }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "observationUnitDbId", "in" : "query", @@ -662,7 +568,8 @@ "description" : "Filter based on an Event start date.", "required" : false, "schema" : { - "type" : "string" + "type" : "string", + "format" : "date-time" } }, { @@ -671,7 +578,8 @@ "description" : "Filter based on an Event start date.", "required" : false, "schema" : { - "type" : "string" + "type" : "string", + "format" : "date-time" } }, { @@ -726,15 +634,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -744,15 +643,6 @@ "type" : "string" } }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "trialDbId", "in" : "query", @@ -762,15 +652,6 @@ "type" : "string" } }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "mapDbId", "in" : "query", @@ -877,15 +758,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -895,15 +767,6 @@ "type" : "string" } }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "trialDbId", "in" : "query", @@ -913,15 +776,6 @@ "type" : "string" } }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "germplasmPUI", "in" : "query", @@ -949,24 +803,6 @@ "type" : "string" } }, - { - "name" : "familyCode", - "in" : "query", - "description" : "A familyCode representing the family this germplasm belongs to.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "instituteCode", - "in" : "query", - "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "binomialName", "in" : "query", @@ -977,7 +813,7 @@ } }, { - "name" : "genu", + "name" : "genus", "in" : "query", "description" : "List of Genus names to identify germplasm", "required" : false, @@ -986,7 +822,7 @@ } }, { - "name" : "specy", + "name" : "species", "in" : "query", "description" : "List of Species names to identify germplasm", "required" : false, @@ -1021,9 +857,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -1070,7 +903,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/GermplasmNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/GermplasmNewRequest" + } } } } @@ -1243,9 +1079,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -1292,7 +1125,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/GermplasmAttributeNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/GermplasmAttributeNewRequest" + } } } } @@ -1339,15 +1175,6 @@ "type" : "string" } }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "programDbId", "in" : "query", @@ -1357,15 +1184,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "attributeValueDbId", "in" : "query", @@ -1394,67 +1212,10 @@ } }, { - "name" : "ontologyDbId", - "in" : "query", - "description" : "List of ontology IDs to search for", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/externalReferenceId" }, { - "name" : "methodDbId", - "in" : "query", - "description" : "List of methods to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "scaleDbId", - "in" : "query", - "description" : "List of scales to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "traitDbId", - "in" : "query", - "description" : "List of trait unique ID to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "traitClass", - "in" : "query", - "description" : "List of trait classes to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "dataType", - "in" : "query", - "description" : "List of scale data types to filter search results", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/TraitDataType" - } - }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, - { - "$ref" : "#/components/parameters/externalReferenceId" - }, - { - "$ref" : "#/components/parameters/externalReferenceSource" + "$ref" : "#/components/parameters/externalReferenceSource" }, { "$ref" : "#/components/parameters/page" @@ -1496,7 +1257,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/GermplasmAttributeValueNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueNewRequest" + } } } } @@ -1543,15 +1307,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "descriptiveOntologyTerm", "in" : "query", @@ -1561,63 +1316,6 @@ "type" : "string" } }, - { - "name" : "imageFileName", - "in" : "query", - "description" : "Image file names to search for.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "imageFileSizeMax", - "in" : "query", - "description" : "A maximum image file size to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, - { - "name" : "imageFileSizeMin", - "in" : "query", - "description" : "A minimum image file size to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, - { - "name" : "imageHeightMax", - "in" : "query", - "description" : "A maximum image height to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, - { - "name" : "imageHeightMin", - "in" : "query", - "description" : "A minimum image height to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, - { - "name" : "imageLocation", - "in" : "query", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" - } - }, { "name" : "imageName", "in" : "query", @@ -1627,53 +1325,6 @@ "type" : "string" } }, - { - "name" : "imageTimeStampRangeEnd", - "in" : "query", - "description" : "The latest timestamp to search for.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "imageTimeStampRangeStart", - "in" : "query", - "description" : "The earliest timestamp to search for.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "imageWidthMax", - "in" : "query", - "description" : "A maximum image width to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, - { - "name" : "imageWidthMin", - "in" : "query", - "description" : "A minimum image width to search for.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, - { - "name" : "mimeType", - "in" : "query", - "description" : "A set of image file types to search for.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "observationDbId", "in" : "query", @@ -1701,9 +1352,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -1750,7 +1398,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/ImageNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ImageNewRequest" + } } } } @@ -1780,36 +1431,18 @@ "description" : "Get a list of List", "parameters" : [ { - "name" : "dateCreatedRangeStart", - "in" : "query", - "description" : "Define the beginning for an interval of time and only include Lists that are created within this interval.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "dateCreatedRangeEnd", - "in" : "query", - "description" : "Define the end for an interval of time and only include Lists that are created within this interval.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "dateModifiedRangeStart", + "name" : "commonCropName", "in" : "query", - "description" : "Define the beginning for an interval of time and only include Lists that are modified within this interval.", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "dateModifiedRangeEnd", + "name" : "programDbId", "in" : "query", - "description" : "Define the end for an interval of time and only include Lists that are modified within this interval.", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "required" : false, "schema" : { "type" : "string" @@ -1833,24 +1466,6 @@ "type" : "string" } }, - { - "name" : "listOwnerName", - "in" : "query", - "description" : "An array of names for the people or entities who are responsible for a set of Lists", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "listOwnerPersonDbId", - "in" : "query", - "description" : "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "listSource", "in" : "query", @@ -1868,9 +1483,6 @@ "$ref" : "#/components/schemas/ListType" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -1917,7 +1529,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/ListNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ListNewRequest" + } } } } @@ -1983,126 +1598,43 @@ } }, { - "name" : "programName", + "name" : "locationType", "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The type of location this represents (ex. Breeding Location, Storage Location, etc)", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "abbreviation", + "name" : "parentLocationDbId", "in" : "query", - "description" : "A list of shortened human readable names for a set of Locations", + "description" : "The unique identifier for a Location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "altitudeMin", - "in" : "query", - "description" : "The minimum altitude to search for", - "required" : false, - "schema" : { - "type" : "number" - } - }, - { - "name" : "altitudeMax", - "in" : "query", - "description" : "The maximum altitude to search for", - "required" : false, - "schema" : { - "type" : "number" - } - }, - { - "name" : "countryCode", + "name" : "parentLocationName", "in" : "query", - "description" : "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec", + "description" : "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "countryName", - "in" : "query", - "description" : "The full name of the country to search for", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/externalReferenceId" }, { - "name" : "coordinate", - "in" : "query", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" - } + "$ref" : "#/components/parameters/externalReferenceSource" }, { - "name" : "instituteAddress", - "in" : "query", - "description" : "The street address of the institute to search for", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/page" }, { - "name" : "instituteName", - "in" : "query", - "description" : "The name of the institute to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "locationType", - "in" : "query", - "description" : "The type of location this represents (ex. Breeding Location, Storage Location, etc)", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "parentLocationDbId", - "in" : "query", - "description" : "The unique identifier for a Location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "parentLocationName", - "in" : "query", - "description" : "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, - { - "$ref" : "#/components/parameters/externalReferenceId" - }, - { - "$ref" : "#/components/parameters/externalReferenceSource" - }, - { - "$ref" : "#/components/parameters/page" - }, - { - "$ref" : "#/components/parameters/pageSize" + "$ref" : "#/components/parameters/pageSize" }, { "$ref" : "#/components/parameters/authorizationHeader" @@ -2138,7 +1670,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/LocationNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/LocationNewRequest" + } } } } @@ -2162,7 +1697,7 @@ "/markerpositions" : { "get" : { "tags" : [ - "MarkerPositions" + "Genome Maps" ], "summary" : "Get a filtered list of MarkerPosition", "description" : "Get a list of MarkerPosition", @@ -2276,16 +1811,7 @@ } }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "scaleDbId", + "name" : "methodDbId", "in" : "query", "description" : "The unique identifier for a method.", "required" : false, @@ -2302,9 +1828,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -2351,7 +1874,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/MethodNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/MethodNewRequest" + } } } } @@ -2398,15 +1924,6 @@ "type" : "string" } }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "locationDbId", "in" : "query", @@ -2416,15 +1933,6 @@ "type" : "string" } }, - { - "name" : "locationName", - "in" : "query", - "description" : "A human readable names to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "observationVariableDbId", "in" : "query", @@ -2435,111 +1943,111 @@ } }, { - "name" : "observationVariableName", + "name" : "programDbId", "in" : "query", - "description" : "The names of Variables to search for", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationVariablePUI", + "name" : "studyDbId", "in" : "query", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "description" : "List of study identifiers to search for", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "programDbId", + "name" : "trialDbId", "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The ID which uniquely identifies a trial to search for", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "programName", + "name" : "observationDbId", "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The unique id of an Observation", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "studyDbId", + "name" : "observationUnitDbId", "in" : "query", - "description" : "List of study identifiers to search for", + "description" : "The unique id of an Observation Unit", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "studyName", + "name" : "observationUnitLevelName", "in" : "query", - "description" : "List of study names to filter search results", + "description" : "The Observation Unit Level. Returns only the observation unit of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "trialDbId", + "name" : "observationUnitLevelOrder", "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "trialName", + "name" : "observationUnitLevelCode", "in" : "query", - "description" : "The human readable name of a trial to search for", + "description" : "The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationDbId", + "name" : "observationUnitLevelRelationshipName", "in" : "query", - "description" : "The unique id of an Observation", + "description" : "The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. \n
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. \n
Use this parameter to identify groups of observation units that share a relationship level. \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationUnitDbId", + "name" : "observationUnitLevelRelationshipOrder", "in" : "query", - "description" : "The unique id of an Observation Unit", + "description" : "The Observation Unit Level Order Number. \n
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationLevel", + "name" : "observationUnitLevelRelationshipCode", "in" : "query", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "description" : "The Observation Unit Level Code. \n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { - "$ref" : "#/components/schemas/ObservationUnitLevel" + "type" : "string" } }, { - "name" : "observationLevelRelationship", + "name" : "observationUnitLevelRelationshipDbId", "in" : "query", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "description" : "The observationUnitDbId associated with a particular level and code.\n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + "type" : "string" } }, { @@ -2548,7 +2056,8 @@ "description" : "Timestamp range end", "required" : false, "schema" : { - "type" : "string" + "type" : "string", + "format" : "date-time" } }, { @@ -2557,7 +2066,8 @@ "description" : "Timestamp range start", "required" : false, "schema" : { - "type" : "string" + "type" : "string", + "format" : "date-time" } }, { @@ -2569,9 +2079,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -2618,7 +2125,11 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/ObservationNewRequest" + "type" : "object", + "additionalProperties" : { + "$ref" : "#/components/schemas/ObservationNewRequest" + }, + "example" : "{_1={additionalInfo={}, collector=1835c514, externalReferences=[{}], geoCoordinates={}, germplasm={}, observationDbId=5cbd4c1c, observationTimeStamp=2020-08-12T18:10:40.413Z, observationUnit={}, observationVariable={}, season={}, study={}, uploadedBy=3fc74c0a, value=4ee59cb0, images=[{}]}, _2={additionalInfo={}, collector=1835c515, externalReferences=[{}], geoCoordinates={}, germplasm={}, observationDbId=5cbd4c1d, observationTimeStamp=2020-08-12T18:10:40.413Z, observationUnit={}, observationVariable={}, season={}, study={}, uploadedBy=3fc74c0b, value=4ee59cb1, images=[{}]}}" } } } @@ -2653,7 +2164,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/ObservationNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ObservationNewRequest" + } } } } @@ -2700,15 +2214,6 @@ "type" : "string" } }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "locationDbId", "in" : "query", @@ -2718,15 +2223,6 @@ "type" : "string" } }, - { - "name" : "locationName", - "in" : "query", - "description" : "A human readable names to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -2737,115 +2233,106 @@ } }, { - "name" : "studyName", + "name" : "programDbId", "in" : "query", - "description" : "List of study names to filter search results", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationVariableDbId", + "name" : "trialDbId", "in" : "query", - "description" : "The DbIds of Variables to search for", + "description" : "The ID which uniquely identifies a trial to search for", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationVariableName", + "name" : "observationUnitDbId", "in" : "query", - "description" : "The names of Variables to search for", + "description" : "The unique id of an observation unit", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationVariablePUI", + "name" : "observationUnitName", "in" : "query", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "description" : "The human readable identifier for an Observation Unit", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "programDbId", + "name" : "observationUnitLevelName", "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The Observation Unit Level. Returns only the observation unit of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "programName", + "name" : "observationUnitLevelOrder", "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "trialDbId", + "name" : "observationUnitLevelCode", "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "trialName", + "name" : "observationUnitLevelRelationshipName", "in" : "query", - "description" : "The human readable name of a trial to search for", + "description" : "The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. \n
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. \n
Use this parameter to identify groups of observation units that share a relationship level. \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationUnitDbId", + "name" : "observationUnitLevelRelationshipOrder", "in" : "query", - "description" : "The unique id of an observation unit", + "description" : "The Observation Unit Level Order Number. \n
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationUnitName", + "name" : "observationUnitLevelRelationshipCode", "in" : "query", - "description" : "The human readable identifier for an Observation Unit", + "description" : "The Observation Unit Level Code. \n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationLevel", - "in" : "query", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/ObservationUnitLevel" - } - }, - { - "name" : "observationLevelRelationship", + "name" : "observationUnitLevelRelationshipDbId", "in" : "query", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "description" : "The observationUnitDbId associated with a particular level and code.\n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "required" : false, "schema" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + "type" : "string" } }, { - "name" : "includeObservation", + "name" : "includeObservations", "in" : "query", "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", "required" : false, @@ -2862,9 +2349,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -2911,7 +2395,11 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/ObservationUnitNewRequest" + "type" : "object", + "additionalProperties" : { + "$ref" : "#/components/schemas/ObservationUnitNewRequest" + }, + "example" : "{_1={additionalInfo={}, cross={}, externalReferences=[{}], germplasm={}, location={}, observationUnitDbId=59ce1af8, observationUnitName=5a5b18e6, observationUnitPUI=491c6d6d, observationUnitPosition=[{}], program={}, seedLot={}, study={}, treatments=[{}], trial={}, samples=[{}], events=[{}], images=[{}], observations=[{}]}, _2={additionalInfo={}, cross={}, externalReferences=[{}], germplasm={}, location={}, observationUnitDbId=59ce1af9, observationUnitName=5a5b18e7, observationUnitPUI=491c6d6e, observationUnitPosition=[{}], program={}, seedLot={}, study={}, treatments=[{}], trial={}, samples=[{}], events=[{}], images=[{}], observations=[{}]}}" } } } @@ -2946,7 +2434,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/ObservationUnitNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ObservationUnitNewRequest" + } } } } @@ -3020,33 +2511,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "trialDbId", "in" : "query", @@ -3056,15 +2520,6 @@ "type" : "string" } }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -3137,15 +2592,6 @@ "type" : "string" } }, - { - "name" : "dataType", - "in" : "query", - "description" : "List of scale data types to filter search results", - "required" : false, - "schema" : { - "$ref" : "#/components/schemas/TraitDataType" - } - }, { "name" : "traitClass", "in" : "query", @@ -3183,55 +2629,16 @@ } }, { - "name" : "traitAttribute", - "in" : "query", - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/externalReferenceId" }, { - "name" : "traitAttributePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/externalReferenceSource" }, { - "name" : "traitEntity", - "in" : "query", - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/page" }, { - "name" : "traitEntityPUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, - { - "$ref" : "#/components/parameters/externalReferenceId" - }, - { - "$ref" : "#/components/parameters/externalReferenceSource" - }, - { - "$ref" : "#/components/parameters/page" - }, - { - "$ref" : "#/components/parameters/pageSize" + "$ref" : "#/components/parameters/pageSize" }, { "$ref" : "#/components/parameters/authorizationHeader" @@ -3267,7 +2674,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/ObservationVariableNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ObservationVariableNewRequest" + } } } } @@ -3354,7 +2764,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/OntologyNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/OntologyNewRequest" + } } } } @@ -3419,15 +2832,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -3437,15 +2841,6 @@ "type" : "string" } }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "trialDbId", "in" : "query", @@ -3455,15 +2850,6 @@ "type" : "string" } }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "germplasmPUI", "in" : "query", @@ -3500,15 +2886,6 @@ "type" : "string" } }, - { - "name" : "instituteCode", - "in" : "query", - "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "binomialName", "in" : "query", @@ -3519,7 +2896,7 @@ } }, { - "name" : "genu", + "name" : "genus", "in" : "query", "description" : "List of Genus names to identify germplasm", "required" : false, @@ -3528,7 +2905,7 @@ } }, { - "name" : "specy", + "name" : "species", "in" : "query", "description" : "List of Species names to identify germplasm", "required" : false, @@ -3546,7 +2923,7 @@ } }, { - "name" : "includeParent", + "name" : "includeParents", "in" : "query", "description" : "If this parameter is true, include the array of parents in the response", "required" : false, @@ -3555,7 +2932,7 @@ } }, { - "name" : "includeSibling", + "name" : "includeSiblings", "in" : "query", "description" : "If this parameter is true, include the array of siblings in the response", "required" : false, @@ -3601,9 +2978,6 @@ "format" : "int32" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -3650,7 +3024,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/PedigreeNode" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/PedigreeNode" + } } } } @@ -3697,24 +3074,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "emailAddress", - "in" : "query", - "description" : "email address for this person", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "firstName", "in" : "query", @@ -3733,24 +3092,6 @@ "type" : "string" } }, - { - "name" : "mailingAddress", - "in" : "query", - "description" : "physical address of this person", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "middleName", - "in" : "query", - "description" : "Persons middle name", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "personDbId", "in" : "query", @@ -3760,15 +3101,6 @@ "type" : "string" } }, - { - "name" : "phoneNumber", - "in" : "query", - "description" : "phone number of this person", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "userID", "in" : "query", @@ -3778,9 +3110,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -3827,7 +3156,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/PersonNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/PersonNewRequest" + } } } } @@ -3874,15 +3206,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "crossingProjectDbId", "in" : "query", @@ -3933,9 +3256,6 @@ ] } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -3982,7 +3302,11 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/PlannedCross" + "type" : "object", + "additionalProperties" : { + "$ref" : "#/components/schemas/PlannedCross" + }, + "example" : "{_1={additionalInfo={}, crossType={}, crossingProject={}, externalReferences=[{}], parent1={}, parent2={}, plannedCrossDbId=47edd16c, plannedCrossName=487acf5a, status={}, crosses=[{}]}, _2={additionalInfo={}, crossType={}, crossingProject={}, externalReferences=[{}], parent1={}, parent2={}, plannedCrossDbId=47edd16d, plannedCrossName=487acf5b, status={}, crosses=[{}]}}" } } } @@ -4017,7 +3341,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/PlannedCross" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/PlannedCross" + } } } } @@ -4064,15 +3391,6 @@ "type" : "string" } }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "programDbId", "in" : "query", @@ -4082,15 +3400,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -4100,15 +3409,6 @@ "type" : "string" } }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "trialDbId", "in" : "query", @@ -4118,15 +3418,6 @@ "type" : "string" } }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "observationUnitDbId", "in" : "query", @@ -4154,15 +3445,6 @@ "type" : "string" } }, - { - "name" : "plateBarcode", - "in" : "query", - "description" : "A unique identifier physically attached to the plate", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "sampleDbId", "in" : "query", @@ -4190,18 +3472,6 @@ "type" : "string" } }, - { - "name" : "germplasmDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -4248,7 +3518,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/PlateNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/PlateNewRequest" + } } } } @@ -4313,33 +3586,6 @@ "type" : "string" } }, - { - "name" : "leadPersonDbId", - "in" : "query", - "description" : "The person DbIds of the program leader to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "leadPersonName", - "in" : "query", - "description" : "The names of the program leader to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "objectife", - "in" : "query", - "description" : "A program objective to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "programType", "in" : "query", @@ -4347,15 +3593,13 @@ "required" : false, "schema" : { "type" : "string", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding.", "enum" : [ "STANDARD", "PROJECT" ] } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -4402,7 +3646,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/ProgramNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ProgramNewRequest" + } } } } @@ -4440,24 +3687,6 @@ "type" : "string" } }, - { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "programDbId", "in" : "query", @@ -4467,15 +3696,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -4485,15 +3705,6 @@ "type" : "string" } }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "trialDbId", "in" : "query", @@ -4503,15 +3714,6 @@ "type" : "string" } }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "accession", "in" : "query", @@ -4554,7 +3756,8 @@ "description" : "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", "required" : false, "schema" : { - "type" : "boolean" + "type" : "boolean", + "format" : "boolean" } }, { @@ -4577,9 +3780,6 @@ "format" : "int32" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -4629,24 +3829,6 @@ "type" : "string" } }, - { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "programDbId", "in" : "query", @@ -4656,15 +3838,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -4674,15 +3847,6 @@ "type" : "string" } }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "trialDbId", "in" : "query", @@ -4692,15 +3856,6 @@ "type" : "string" } }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "accession", "in" : "query", @@ -4737,9 +3892,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -4798,15 +3950,6 @@ "type" : "string" } }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "programDbId", "in" : "query", @@ -4816,15 +3959,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -4834,15 +3968,6 @@ "type" : "string" } }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "trialDbId", "in" : "query", @@ -4852,15 +3977,6 @@ "type" : "string" } }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "observationUnitDbId", "in" : "query", @@ -4915,18 +4031,6 @@ "type" : "string" } }, - { - "name" : "germplasmDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a `Germplasm`", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -4973,7 +4077,11 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/SampleNewRequest" + "type" : "object", + "additionalProperties" : { + "$ref" : "#/components/schemas/SampleNewRequest" + }, + "example" : "{_1={additionalInfo={}, callSets=[{}], column=10, externalReferences=[{}], germplasm={}, observationUnit={}, plate={}, program={}, row=00358167, sampleBarcode=6a6db74b, sampleDescription=3388964f, sampleDbId=079d6d5e, sampleGroupId=70fcb311, sampleName=082a6b4c, samplePUI=08863647, sampleTimestamp=2020-08-12T18:10:40.413Z, sampleType=0889ec7d, study={}, takenBy=599da043, tissueType=4d105e22, trial={}, well=06bc78f3}, _2={additionalInfo={}, callSets=[{}], column=20, externalReferences=[{}], germplasm={}, observationUnit={}, plate={}, program={}, row=00358168, sampleBarcode=6a6db74c, sampleDescription=33889650, sampleDbId=079d6d5f, sampleGroupId=70fcb312, sampleName=082a6b4d, samplePUI=08863648, sampleTimestamp=2020-08-12T18:10:40.413Z, sampleType=0889ec7e, study={}, takenBy=599da044, tissueType=4d105e23, trial={}, well=06bc78f4}}" } } } @@ -5008,7 +4116,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/SampleNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/SampleNewRequest" + } } } } @@ -5064,15 +4175,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "scaleDbId", "in" : "query", @@ -5091,9 +4193,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -5140,7 +4239,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/ScaleNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ScaleNewRequest" + } } } } @@ -5245,7 +4347,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/Season" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Season" + } } } } @@ -5310,15 +4415,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "seedLotDbId", "in" : "query", @@ -5346,9 +4442,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -5395,7 +4488,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/SeedLotNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/SeedLotNewRequest" + } } } } @@ -5442,15 +4538,6 @@ "type" : "string" } }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "locationDbId", "in" : "query", @@ -5460,15 +4547,6 @@ "type" : "string" } }, - { - "name" : "locationName", - "in" : "query", - "description" : "A human readable names to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "programDbId", "in" : "query", @@ -5478,15 +4556,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -5514,15 +4583,6 @@ "type" : "string" } }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "observationVariableDbId", "in" : "query", @@ -5533,25 +4593,7 @@ } }, { - "name" : "observationVariableName", - "in" : "query", - "description" : "The names of Variables to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "observationVariablePUI", - "in" : "query", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "actife", + "name" : "active", "in" : "query", "description" : "A flag to indicate if a Study is currently active and ongoing", "required" : false, @@ -5596,7 +4638,41 @@ } }, { - "$ref" : "#/components/parameters/externalReferenceID" + "name" : "sortBy", + "in" : "query", + "description" : "Name of the field to sort by.", + "required" : false, + "schema" : { + "type" : "string", + "description" : "Name of the field to sort by.", + "enum" : [ + "studyDbId", + "trialDbId", + "programDbId", + "locationDbId", + "seasonDbId", + "studyType", + "studyName", + "studyLocation", + "programName" + ] + } + }, + { + "name" : "sortOrder", + "in" : "query", + "description" : "Sort order direction. Ascending/Descending.", + "required" : false, + "schema" : { + "type" : "string", + "description" : "Sort order direction. Ascending/Descending.", + "enum" : [ + "asc", + "ASC", + "desc", + "DESC" + ] + } }, { "$ref" : "#/components/parameters/externalReferenceId" @@ -5644,7 +4720,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/StudyNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/StudyNewRequest" + } } } } @@ -5700,15 +4779,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "traitDbId", "in" : "query", @@ -5727,9 +4797,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -5776,7 +4843,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/TraitNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/TraitNewRequest" + } } } } @@ -5824,143 +4894,123 @@ } }, { - "name" : "locationName", + "name" : "programDbId", "in" : "query", - "description" : "A human readable names to search for", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationVariableDbId", + "name" : "studyDbId", "in" : "query", - "description" : "The DbIds of Variables to search for", + "description" : "List of study identifiers to search for", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationVariableName", + "name" : "trialDbId", "in" : "query", - "description" : "The names of Variables to search for", + "description" : "The ID which uniquely identifies a trial to search for", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationVariablePUI", + "name" : "trialName", "in" : "query", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "description" : "The human readable name of a trial to search for", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "programDbId", + "name" : "active", "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "A flag to indicate if a Trial is currently active and ongoing", "required" : false, "schema" : { - "type" : "string" + "type" : "boolean" } }, { - "name" : "programName", + "name" : "contactDbId", "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of contact entities associated with this trial", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "studyDbId", + "name" : "searchDateRangeStart", "in" : "query", - "description" : "List of study identifiers to search for", + "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", "required" : false, "schema" : { - "type" : "string" + "type" : "string", + "format" : "date" } }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "actife", - "in" : "query", - "description" : "A flag to indicate if a Trial is currently active and ongoing", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, - { - "name" : "contactDbId", + "name" : "searchDateRangeEnd", "in" : "query", - "description" : "List of contact entities associated with this trial", + "description" : "The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", "required" : false, "schema" : { - "type" : "string" + "type" : "string", + "format" : "date" } }, { - "name" : "searchDateRangeStart", + "name" : "trialPUI", "in" : "query", - "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "description" : "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "searchDateRangeEnd", + "name" : "sortBy", "in" : "query", - "description" : "The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "description" : "Name of the field to sort by.", "required" : false, "schema" : { - "type" : "string" + "type" : "string", + "description" : "Name of the field to sort by.", + "enum" : [ + "trialDbId", + "trialName", + "programDbId", + "programName", + "locationDbId", + "startDate", + "endDate" + ] } }, { - "name" : "trialPUI", + "name" : "sortOrder", "in" : "query", - "description" : "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", + "description" : "Sort order direction. Ascending/Descending.", "required" : false, "schema" : { - "type" : "string" + "type" : "string", + "description" : "Sort order direction. Ascending/Descending.", + "enum" : [ + "asc", + "ASC", + "desc", + "DESC" + ] } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -6007,7 +5057,10 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/TrialNewRequest" + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/TrialNewRequest" + } } } } @@ -6036,88 +5089,6 @@ "summary" : "Get a filtered list of Variant", "description" : "Get a list of Variant", "parameters" : [ - { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "callSetDbId", - "in" : "query", - "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "end", - "in" : "query", - "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { "name" : "referenceDbId", "in" : "query", @@ -6127,15 +5098,6 @@ "type" : "string" } }, - { - "name" : "referenceDbId", - "in" : "query", - "description" : "The unique identifier representing a genotype `Reference`", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "referenceSetDbId", "in" : "query", @@ -6145,16 +5107,6 @@ "type" : "string" } }, - { - "name" : "start", - "in" : "query", - "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { "name" : "variantDbId", "in" : "query", @@ -6173,15 +5125,15 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, { "$ref" : "#/components/parameters/externalReferenceSource" }, + { + "$ref" : "#/components/parameters/pageToken" + }, { "$ref" : "#/components/parameters/page" }, @@ -6234,15 +5186,6 @@ "type" : "string" } }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "studyDbId", "in" : "query", @@ -6261,24 +5204,6 @@ "type" : "string" } }, - { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "callSetDbId", "in" : "query", @@ -6306,15 +5231,6 @@ "type" : "string" } }, - { - "name" : "referenceDbId", - "in" : "query", - "description" : "The unique identifier representing a genotype Reference", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "referenceSetDbId", "in" : "query", @@ -6324,9 +5240,6 @@ "type" : "string" } }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -6359,16 +5272,27 @@ } } }, - "/breedingmethods/{breedingMethodDbId}" : { + "/attributes/categories" : { "get" : { "tags" : [ - "Germplasm" + "GermplasmAttributes" + ], + "summary" : "Get the attributeCategories of GermplasmAttribute", + "description" : "List all available GermplasmAttribute attributeCategories", + "parameters" : [ + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } ], - "summary" : "Get the details of a specific BreedingMethod", - "description" : "Get details for a BreedingMethod", "responses" : { "200" : { - "$ref" : "#/components/responses/BreedingMethodSingleResponse" + "$ref" : "#/components/responses/GermplasmAttributeAttributeCategoryListResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -6382,16 +5306,27 @@ } } }, - "/callsets/{callSetDbId}" : { + "/studytypes" : { "get" : { "tags" : [ - "CallSets" + "Studies" + ], + "summary" : "Get the studyTypes of Study", + "description" : "List all available Study studyTypes", + "parameters" : [ + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } ], - "summary" : "Get the details of a specific CallSet", - "description" : "Get details for a CallSet", "responses" : { "200" : { - "$ref" : "#/components/responses/CallSetSingleResponse" + "$ref" : "#/components/responses/StudyStudyTypeListResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -6405,43 +5340,105 @@ } } }, - "/callsets/{callSetDbId}/calls" : { + "/breedingmethods/{breedingMethodDbId}" : { "get" : { "tags" : [ - "Calls" + "Germplasm" ], - "summary" : "Get a filtered list of Call", - "description" : "Get a list of Call", + "summary" : "Get the details of a specific BreedingMethod", + "description" : "Get details for a BreedingMethod", "parameters" : [ { - "name" : "callSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "required" : false, + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "breedingMethodDbId", + "in" : "path", + "description" : "the unique identifier for this breeding method", + "required" : true, "schema" : { "type" : "string" } - }, - { - "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variant` within the given database server", - "required" : false, + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/BreedingMethodSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/callsets/{callSetDbId}" : { + "get" : { + "tags" : [ + "CallSets" + ], + "summary" : "Get the details of a specific CallSet", + "description" : "Get details for a CallSet", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "callSetDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a CallSet within the given database server", + "required" : true, "schema" : { "type" : "string" } + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallSetSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/callsets/{callSetDbId}/calls" : { + "get" : { + "tags" : [ + "CallSets" + ], + "summary" : "Get a filtered list of Call", + "description" : "Get a list of Call", + "parameters" : [ { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "required" : false, + "name" : "callSetDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a CallSet within the given database server", + "required" : true, "schema" : { "type" : "string" } }, { - "name" : "expandHomozygote", + "name" : "expandHomozygotes", "in" : "query", "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", "required" : false, @@ -6482,6 +5479,9 @@ { "$ref" : "#/components/parameters/pageSize" }, + { + "$ref" : "#/components/parameters/pageToken" + }, { "$ref" : "#/components/parameters/authorizationHeader" } @@ -6498,6 +5498,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -6509,6 +5512,20 @@ ], "summary" : "Get the details of a specific CrossingProject", "description" : "Get details for a CrossingProject", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "crossingProjectDbId", + "in" : "path", + "description" : "The unique identifier for a crossing project", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/CrossingProjectSingleResponse" @@ -6521,6 +5538,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -6533,6 +5553,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "crossingProjectDbId", + "in" : "path", + "description" : "The unique identifier for a crossing project", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -6556,6 +5585,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -6567,6 +5599,20 @@ ], "summary" : "Get the details of a specific GenomeMap", "description" : "Get details for a GenomeMap", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "mapDbId", + "in" : "path", + "description" : "The unique identifier for a `GenomeMap`", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/GenomeMapSingleResponse" @@ -6579,6 +5625,55 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/maps/{mapDbId}/linkagegroups" : { + "get" : { + "tags" : [ + "GenomeMaps" + ], + "summary" : "Get a filtered list of LinkageGroup", + "description" : "Get a list of LinkageGroup", + "parameters" : [ + { + "name" : "mapDbId", + "in" : "path", + "description" : "The unique identifier for a `GenomeMap`", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/LinkageGroupListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -6590,6 +5685,20 @@ ], "summary" : "Get the details of a specific Germplasm", "description" : "Get details for a Germplasm", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "germplasmDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/GermplasmSingleResponse" @@ -6602,6 +5711,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -6614,6 +5726,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "germplasmDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -6637,6 +5758,49 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/germplasm/{germplasmDbId}/mcpd" : { + "get" : { + "tags" : [ + "Germplasm" + ], + "summary" : "Get the details of a specific GermplasmMCPD", + "description" : "Get details for a GermplasmMCPD", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "germplasmDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmMCPDSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -6648,6 +5812,20 @@ ], "summary" : "Get the details of a specific GermplasmAttribute", "description" : "Get details for a GermplasmAttribute", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "attributeDbId", + "in" : "path", + "description" : "The ID which uniquely identifies this attribute within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/GermplasmAttributeSingleResponse" @@ -6660,6 +5838,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -6672,6 +5853,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "attributeDbId", + "in" : "path", + "description" : "The ID which uniquely identifies this attribute within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -6695,6 +5885,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -6706,6 +5899,20 @@ ], "summary" : "Get the details of a specific GermplasmAttributeValue", "description" : "Get details for a GermplasmAttributeValue", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "attributeValueDbId", + "in" : "path", + "description" : "The ID which uniquely identifies this attribute value within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/GermplasmAttributeValueSingleResponse" @@ -6718,6 +5925,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -6730,6 +5940,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "attributeValueDbId", + "in" : "path", + "description" : "The ID which uniquely identifies this attribute value within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -6753,6 +5972,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -6764,6 +5986,20 @@ ], "summary" : "Get the details of a specific Image", "description" : "Get details for a Image", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "imageDbId", + "in" : "path", + "description" : "The unique identifier of an image", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ImageSingleResponse" @@ -6776,6 +6012,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -6788,6 +6027,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "imageDbId", + "in" : "path", + "description" : "The unique identifier of an image", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -6811,17 +6059,84 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } }, - "/lists/{listDbId}" : { - "get" : { + "/images/{imageDbId}/imagecontent" : { + "put" : { "tags" : [ - "Lists" + "Images" + ], + "summary" : "Update the details for an existing string", + "description" : "Update the details for an existing string", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "imageDbId", + "in" : "path", + "description" : "The unique identifier of an image", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], + "requestBody" : { + "content" : { + "image/*" : { + "schema" : { + "type" : "string", + "format" : "binary" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/lists/{listDbId}" : { + "get" : { + "tags" : [ + "Lists" + ], + "summary" : "Get the details of a specific List", + "description" : "Get details for a List", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "listDbId", + "in" : "path", + "description" : "The unique identifier for a List", + "required" : true, + "schema" : { + "type" : "string" + } + } ], - "summary" : "Get the details of a specific List", - "description" : "Get details for a List", "responses" : { "200" : { "$ref" : "#/components/responses/ListSingleResponse" @@ -6834,6 +6149,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -6846,6 +6164,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "listDbId", + "in" : "path", + "description" : "The unique identifier for a List", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -6869,6 +6196,58 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/lists/{listDbId}/data" : { + "post" : { + "tags" : [ + "Lists" + ], + "summary" : "Create new string", + "description" : "Add new string to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "listDbId", + "in" : "path", + "description" : "The unique identifier for a List", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "string" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -6880,6 +6259,20 @@ ], "summary" : "Get the details of a specific Location", "description" : "Get details for a Location", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "locationDbId", + "in" : "path", + "description" : "The unique identifier for a Location", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/LocationSingleResponse" @@ -6892,6 +6285,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -6904,6 +6300,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "locationDbId", + "in" : "path", + "description" : "The unique identifier for a Location", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -6927,6 +6332,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -6938,6 +6346,20 @@ ], "summary" : "Get the details of a specific Method", "description" : "Get details for a Method", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "methodDbId", + "in" : "path", + "description" : "Method unique identifier", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/MethodSingleResponse" @@ -6950,6 +6372,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -6962,6 +6387,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "methodDbId", + "in" : "path", + "description" : "Method unique identifier", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -6985,6 +6419,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -6996,6 +6433,20 @@ ], "summary" : "Get the details of a specific Observation", "description" : "Get details for a Observation", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "observationDbId", + "in" : "path", + "description" : "The ID which uniquely identifies an observation", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ObservationSingleResponse" @@ -7008,6 +6459,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7019,6 +6473,20 @@ ], "summary" : "Get the details of a specific ObservationUnit", "description" : "Get details for a ObservationUnit", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "observationUnitDbId", + "in" : "path", + "description" : "The ID which uniquely identifies an observation unit\n\nMIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. ", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ObservationUnitSingleResponse" @@ -7031,6 +6499,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7042,6 +6513,20 @@ ], "summary" : "Get the details of a specific ObservationVariable", "description" : "Get details for a ObservationVariable", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "observationVariableDbId", + "in" : "path", + "description" : "Variable unique identifier\n\nMIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation.", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ObservationVariableSingleResponse" @@ -7054,6 +6539,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -7066,6 +6554,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "observationVariableDbId", + "in" : "path", + "description" : "Variable unique identifier\n\nMIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation.", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -7089,6 +6586,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7100,6 +6600,20 @@ ], "summary" : "Get the details of a specific Ontology", "description" : "Get details for a Ontology", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "ontologyDbId", + "in" : "path", + "description" : "Ontology database unique identifier", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/OntologySingleResponse" @@ -7112,6 +6626,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -7124,6 +6641,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "ontologyDbId", + "in" : "path", + "description" : "Ontology database unique identifier", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -7147,6 +6673,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7158,6 +6687,20 @@ ], "summary" : "Get the details of a specific Person", "description" : "Get details for a Person", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "personDbId", + "in" : "path", + "description" : "Unique ID for a person", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/PersonSingleResponse" @@ -7170,6 +6713,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -7182,6 +6728,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "personDbId", + "in" : "path", + "description" : "Unique ID for a person", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -7205,6 +6760,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7216,6 +6774,20 @@ ], "summary" : "Get the details of a specific Plate", "description" : "Get details for a Plate", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "plateDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a `Plate`", + "required" : false, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/PlateSingleResponse" @@ -7228,6 +6800,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7239,6 +6814,20 @@ ], "summary" : "Get the details of a specific Program", "description" : "Get details for a Program", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "programDbId", + "in" : "path", + "description" : "The ID which uniquely identifies the program", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ProgramSingleResponse" @@ -7251,6 +6840,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -7263,6 +6855,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "programDbId", + "in" : "path", + "description" : "The ID which uniquely identifies the program", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -7286,6 +6887,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7297,8 +6901,22 @@ ], "summary" : "Get the details of a specific Reference", "description" : "Get details for a Reference", - "responses" : { - "200" : { + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "referenceDbId", + "in" : "path", + "description" : "The unique identifier for a `Reference`", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], + "responses" : { + "200" : { "$ref" : "#/components/responses/ReferenceSingleResponse" }, "400" : { @@ -7309,6 +6927,78 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/references/{referenceDbId}/bases" : { + "get" : { + "tags" : [ + "References" + ], + "summary" : "Get the details of a specific ReferenceBases", + "description" : "Get details for a ReferenceBases", + "parameters" : [ + { + "name" : "start", + "in" : "query", + "description" : "The start position (0-based) of this query. Defaults to 0.\nGenomic positions are non-negative integers less than reference length.\nRequests spanning the join of circular genomes are represented as\ntwo requests one on each side of the join (position 0).", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "end", + "in" : "query", + "description" : "The end position (0-based, exclusive) of this query. Defaults to the length of this `Reference`.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "pageToken", + "in" : "query", + "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "referenceDbId", + "in" : "path", + "description" : "The unique identifier for a `Reference`", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceBasesSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7320,6 +7010,20 @@ ], "summary" : "Get the details of a specific ReferenceSet", "description" : "Get details for a ReferenceSet", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "referenceSetDbId", + "in" : "path", + "description" : "The unique identifier for a ReferenceSet", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ReferenceSetSingleResponse" @@ -7332,6 +7036,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7343,6 +7050,20 @@ ], "summary" : "Get the details of a specific Sample", "description" : "Get details for a Sample", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "sampleDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a `Sample`\n
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample.", + "required" : false, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/SampleSingleResponse" @@ -7355,6 +7076,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7366,6 +7090,20 @@ ], "summary" : "Get the details of a specific Scale", "description" : "Get details for a Scale", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "scaleDbId", + "in" : "path", + "description" : "Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID.", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ScaleSingleResponse" @@ -7378,6 +7116,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -7390,6 +7131,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "scaleDbId", + "in" : "path", + "description" : "Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID.", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -7413,6 +7163,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7424,6 +7177,20 @@ ], "summary" : "Get the details of a specific Season", "description" : "Get details for a Season", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "seasonDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/SeasonSingleResponse" @@ -7436,6 +7203,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -7448,6 +7218,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "seasonDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -7471,6 +7250,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7482,6 +7264,20 @@ ], "summary" : "Get the details of a specific SeedLot", "description" : "Get details for a SeedLot", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "seedLotDbId", + "in" : "path", + "description" : "Unique DbId for the Seed Lot", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/SeedLotSingleResponse" @@ -7494,6 +7290,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -7506,6 +7305,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "seedLotDbId", + "in" : "path", + "description" : "Unique DbId for the Seed Lot", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -7529,6 +7337,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7540,6 +7351,20 @@ ], "summary" : "Get the details of a specific Study", "description" : "Get details for a Study", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "studyDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a study within the given database server\n\nMIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution.", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/StudySingleResponse" @@ -7552,6 +7377,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -7564,6 +7392,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "studyDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a study within the given database server\n\nMIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution.", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -7587,6 +7424,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7598,6 +7438,20 @@ ], "summary" : "Get the details of a specific Trait", "description" : "Get details for a Trait", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "traitDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a trait", + "required" : false, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/TraitSingleResponse" @@ -7610,6 +7464,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -7622,6 +7479,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "traitDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a trait", + "required" : false, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -7645,6 +7511,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7656,6 +7525,20 @@ ], "summary" : "Get the details of a specific Trial", "description" : "Get details for a Trial", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "trialDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a trial\n\nMIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution.", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/TrialSingleResponse" @@ -7668,6 +7551,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -7680,6 +7566,15 @@ "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "trialDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a trial\n\nMIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution.", + "required" : true, + "schema" : { + "type" : "string" + } } ], "requestBody" : { @@ -7703,6 +7598,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7714,6 +7612,20 @@ ], "summary" : "Get the details of a specific Variant", "description" : "Get details for a Variant", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "variantDbId", + "in" : "path", + "description" : "The ID which uniquely identifies a `Variant`", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/VariantSingleResponse" @@ -7726,6 +7638,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7733,40 +7648,22 @@ "/variants/{variantDbId}/calls" : { "get" : { "tags" : [ - "Calls" + "Variants" ], "summary" : "Get a filtered list of Call", "description" : "Get a list of Call", "parameters" : [ - { - "name" : "callSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variant` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "required" : false, + "in" : "path", + "description" : "The ID which uniquely identifies a `Variant`", + "required" : true, "schema" : { "type" : "string" } }, { - "name" : "expandHomozygote", + "name" : "expandHomozygotes", "in" : "query", "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", "required" : false, @@ -7807,6 +7704,9 @@ { "$ref" : "#/components/parameters/pageSize" }, + { + "$ref" : "#/components/parameters/pageToken" + }, { "$ref" : "#/components/parameters/authorizationHeader" } @@ -7823,6 +7723,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7834,11 +7737,25 @@ ], "summary" : "Get the details of a specific VariantSet", "description" : "Get details for a VariantSet", - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantSetSingleResponse" + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" }, - "400" : { + { + "name" : "variantSetDbId", + "in" : "path", + "description" : "The unique identifier for a VariantSet", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetSingleResponse" + }, + "400" : { "$ref" : "#/components/responses/400BadRequest" }, "401" : { @@ -7846,6 +7763,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7853,40 +7773,22 @@ "/variantsets/{variantSetDbId}/calls" : { "get" : { "tags" : [ - "Calls" + "VariantSets" ], "summary" : "Get a filtered list of Call", "description" : "Get a list of Call", "parameters" : [ - { - "name" : "callSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variant` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "required" : false, + "in" : "path", + "description" : "The unique identifier for a VariantSet", + "required" : true, "schema" : { "type" : "string" } }, { - "name" : "expandHomozygote", + "name" : "expandHomozygotes", "in" : "query", "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", "required" : false, @@ -7927,6 +7829,9 @@ { "$ref" : "#/components/parameters/pageSize" }, + { + "$ref" : "#/components/parameters/pageToken" + }, { "$ref" : "#/components/parameters/authorizationHeader" } @@ -7943,6 +7848,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -7950,106 +7858,16 @@ "/variantsets/{variantSetDbId}/callsets" : { "get" : { "tags" : [ - "CallSets" + "VariantSets" ], "summary" : "Get a filtered list of CallSet", "description" : "Get a list of CallSet", "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "sampleDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Samples` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "sampleName", - "in" : "query", - "description" : "A list of human readable names associated with `Samples`", - "required" : false, + "name" : "variantSetDbId", + "in" : "path", + "description" : "The unique identifier for a VariantSet", + "required" : true, "schema" : { "type" : "string" } @@ -8072,24 +7890,6 @@ "type" : "string" } }, - { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, - { - "$ref" : "#/components/parameters/externalReferenceId" - }, - { - "$ref" : "#/components/parameters/externalReferenceSource" - }, { "$ref" : "#/components/parameters/page" }, @@ -8112,6 +7912,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -8119,193 +7922,85 @@ "/variantsets/{variantSetDbId}/variants" : { "get" : { "tags" : [ - "Variants" + "VariantSets" ], "summary" : "Get a filtered list of Variant", "description" : "Get a list of Variant", "parameters" : [ { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, + "name" : "variantSetDbId", + "in" : "path", + "description" : "The unique identifier for a VariantSet", + "required" : true, "schema" : { "type" : "string" } }, { - "name" : "programDbId", + "name" : "variantDbId", "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "A list of IDs which uniquely identify `Variants`", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "programName", - "in" : "query", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/page" }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/pageSize" }, { - "name" : "studyName", - "in" : "query", - "description" : "List of study names to filter search results", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/pageToken" }, { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantListResponse" }, - { - "name" : "trialName", - "in" : "query", - "description" : "The human readable name of a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } + "400" : { + "$ref" : "#/components/responses/400BadRequest" }, - { - "name" : "callSetDbId", - "in" : "query", - "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", - "required" : false, - "schema" : { - "type" : "string" - } + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/search/allelematrix" : { + "post" : { + "tags" : [ + "AlleleMatrix" + ], + "summary" : "Submit a search request for `AlleleMatrix`", + "description" : "Submit a search request for `AlleleMatrix`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ { - "name" : "end", - "in" : "query", - "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/AlleleMatrixSearchRequest" + } } - }, - { - "name" : "referenceDbId", - "in" : "query", - "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "referenceDbId", - "in" : "query", - "description" : "The unique identifier representing a genotype `Reference`", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "referenceSetDbId", - "in" : "query", - "description" : "The unique identifier representing a genotype `ReferenceSet`", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "start", - "in" : "query", - "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, - { - "name" : "variantDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `Variants`", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "variantSetDbId", - "in" : "query", - "description" : "A list of IDs which uniquely identify `VariantSets`", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, - { - "$ref" : "#/components/parameters/externalReferenceId" - }, - { - "$ref" : "#/components/parameters/externalReferenceSource" - }, - { - "$ref" : "#/components/parameters/page" - }, - { - "$ref" : "#/components/parameters/pageSize" - }, - { - "$ref" : "#/components/parameters/authorizationHeader" - } - ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/allelematrix" : { - "post" : { - "tags" : [ - "AlleleMatrix" - ], - "summary" : "Submit a search request for `AlleleMatrix`", - "description" : "Submit a search request for `AlleleMatrix`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/AlleleMatrixListResponse" + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/AlleleMatrixListResponse" }, "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" @@ -8329,6 +8024,20 @@ ], "summary" : "Submit a search request for `Call`", "description" : "Submit a search request for `Call`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/CallListResponse" @@ -8355,6 +8064,20 @@ ], "summary" : "Submit a search request for `CallSet`", "description" : "Submit a search request for `CallSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallSetSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/CallSetListResponse" @@ -8381,6 +8104,20 @@ ], "summary" : "Submit a search request for `Germplasm`", "description" : "Submit a search request for `Germplasm`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasm/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/GermplasmListResponse" @@ -8407,6 +8144,20 @@ ], "summary" : "Submit a search request for `GermplasmAttribute`", "description" : "Submit a search request for `GermplasmAttribute`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/GermplasmAttributeListResponse" @@ -8433,6 +8184,20 @@ ], "summary" : "Submit a search request for `GermplasmAttributeValue`", "description" : "Submit a search request for `GermplasmAttributeValue`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/GermplasmAttributeValueSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" @@ -8459,6 +8224,20 @@ ], "summary" : "Submit a search request for `Image`", "description" : "Submit a search request for `Image`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ImageSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/ImageListResponse" @@ -8485,6 +8264,20 @@ ], "summary" : "Submit a search request for `List`", "description" : "Submit a search request for `List`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ListSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/ListListResponse" @@ -8511,6 +8304,20 @@ ], "summary" : "Submit a search request for `Location`", "description" : "Submit a search request for `Location`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/location/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/LocationSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/LocationListResponse" @@ -8533,10 +8340,24 @@ "/search/markerpositions" : { "post" : { "tags" : [ - "MarkerPositions" + "Genome Maps" ], "summary" : "Submit a search request for `MarkerPosition`", "description" : "Submit a search request for `MarkerPosition`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/markerPosition/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/MarkerPositionSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/MarkerPositionListResponse" @@ -8563,6 +8384,20 @@ ], "summary" : "Submit a search request for `Observation`", "description" : "Submit a search request for `Observation`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/ObservationListResponse" @@ -8589,6 +8424,20 @@ ], "summary" : "Submit a search request for `ObservationUnit`", "description" : "Submit a search request for `ObservationUnit`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationUnitSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/ObservationUnitListResponse" @@ -8615,6 +8464,20 @@ ], "summary" : "Submit a search request for `ObservationVariable`", "description" : "Submit a search request for `ObservationVariable`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationVariableSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/ObservationVariableListResponse" @@ -8641,6 +8504,20 @@ ], "summary" : "Submit a search request for `PedigreeNode`", "description" : "Submit a search request for `PedigreeNode`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/pedigreeNode/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PedigreeNodeSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/PedigreeNodeListResponse" @@ -8667,6 +8544,20 @@ ], "summary" : "Submit a search request for `Person`", "description" : "Submit a search request for `Person`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/person/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PersonSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/PersonListResponse" @@ -8693,6 +8584,20 @@ ], "summary" : "Submit a search request for `Plate`", "description" : "Submit a search request for `Plate`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/PlateSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/PlateListResponse" @@ -8719,6 +8624,20 @@ ], "summary" : "Submit a search request for `Program`", "description" : "Submit a search request for `Program`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/program/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ProgramSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/ProgramListResponse" @@ -8745,6 +8664,20 @@ ], "summary" : "Submit a search request for `Reference`", "description" : "Submit a search request for `Reference`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/reference/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ReferenceSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/ReferenceListResponse" @@ -8771,6 +8704,20 @@ ], "summary" : "Submit a search request for `ReferenceSet`", "description" : "Submit a search request for `ReferenceSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/referenceSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ReferenceSetSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/ReferenceSetListResponse" @@ -8797,6 +8744,20 @@ ], "summary" : "Submit a search request for `Sample`", "description" : "Submit a search request for `Sample`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/sample/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/SampleListResponse" @@ -8823,6 +8784,20 @@ ], "summary" : "Submit a search request for `Study`", "description" : "Submit a search request for `Study`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/StudySearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/StudyListResponse" @@ -8849,6 +8824,20 @@ ], "summary" : "Submit a search request for `Trial`", "description" : "Submit a search request for `Trial`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/TrialSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/TrialListResponse" @@ -8875,6 +8864,20 @@ ], "summary" : "Submit a search request for `Variant`", "description" : "Submit a search request for `Variant`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variant/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/VariantSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/VariantListResponse" @@ -8901,6 +8904,20 @@ ], "summary" : "Submit a search request for `VariantSet`", "description" : "Submit a search request for `VariantSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variantSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/VariantSetSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/VariantSetListResponse" @@ -8927,6 +8944,20 @@ ], "summary" : "Submit a search request for `AlleleMatrix`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `AlleleMatrix` search request
\nClients should submit a search request using the corresponding `POST /search/alleleMatrix` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/AlleleMatrixListResponse" @@ -8950,6 +8981,26 @@ ], "summary" : "Submit a search request for `Call`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Call` search request
\nClients should submit a search request using the corresponding `POST /search/call` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/CallListResponse" @@ -8973,6 +9024,26 @@ ], "summary" : "Submit a search request for `CallSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `CallSet` search request
\nClients should submit a search request using the corresponding `POST /search/callSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/CallSetListResponse" @@ -8996,6 +9067,26 @@ ], "summary" : "Submit a search request for `Germplasm`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasm/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Germplasm` search request
\nClients should submit a search request using the corresponding `POST /search/germplasm` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/GermplasmListResponse" @@ -9019,6 +9110,26 @@ ], "summary" : "Submit a search request for `GermplasmAttribute`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `GermplasmAttribute` search request
\nClients should submit a search request using the corresponding `POST /search/germplasmAttribute` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/GermplasmAttributeListResponse" @@ -9042,6 +9153,26 @@ ], "summary" : "Submit a search request for `GermplasmAttributeValue`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `GermplasmAttributeValue` search request
\nClients should submit a search request using the corresponding `POST /search/germplasmAttributeValue` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" @@ -9065,6 +9196,26 @@ ], "summary" : "Submit a search request for `Image`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Image` search request
\nClients should submit a search request using the corresponding `POST /search/image` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ImageListResponse" @@ -9088,13 +9239,33 @@ ], "summary" : "Submit a search request for `List`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `List` search request
\nClients should submit a search request using the corresponding `POST /search/list` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/ListListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, "401" : { "$ref" : "#/components/responses/401Unauthorized" }, @@ -9111,6 +9282,26 @@ ], "summary" : "Submit a search request for `Location`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/location/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Location` search request
\nClients should submit a search request using the corresponding `POST /search/location` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/LocationListResponse" @@ -9130,10 +9321,30 @@ "/search/markerpositions/{searchResultsDbId}" : { "get" : { "tags" : [ - "MarkerPositions" + "Genome Maps" ], "summary" : "Submit a search request for `MarkerPosition`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/markerPosition/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `MarkerPosition` search request
\nClients should submit a search request using the corresponding `POST /search/markerPosition` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/MarkerPositionListResponse" @@ -9157,6 +9368,26 @@ ], "summary" : "Submit a search request for `Observation`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Observation` search request
\nClients should submit a search request using the corresponding `POST /search/observation` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ObservationListResponse" @@ -9180,6 +9411,26 @@ ], "summary" : "Submit a search request for `ObservationUnit`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `ObservationUnit` search request
\nClients should submit a search request using the corresponding `POST /search/observationUnit` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ObservationUnitListResponse" @@ -9203,6 +9454,26 @@ ], "summary" : "Submit a search request for `ObservationVariable`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `ObservationVariable` search request
\nClients should submit a search request using the corresponding `POST /search/observationVariable` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ObservationVariableListResponse" @@ -9226,6 +9497,26 @@ ], "summary" : "Submit a search request for `PedigreeNode`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/pedigreeNode/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `PedigreeNode` search request
\nClients should submit a search request using the corresponding `POST /search/pedigreeNode` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/PedigreeNodeListResponse" @@ -9249,6 +9540,26 @@ ], "summary" : "Submit a search request for `Person`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/person/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Person` search request
\nClients should submit a search request using the corresponding `POST /search/person` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/PersonListResponse" @@ -9272,6 +9583,26 @@ ], "summary" : "Submit a search request for `Plate`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Plate` search request
\nClients should submit a search request using the corresponding `POST /search/plate` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/PlateListResponse" @@ -9295,6 +9626,26 @@ ], "summary" : "Submit a search request for `Program`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/program/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Program` search request
\nClients should submit a search request using the corresponding `POST /search/program` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ProgramListResponse" @@ -9318,6 +9669,26 @@ ], "summary" : "Submit a search request for `Reference`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/reference/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Reference` search request
\nClients should submit a search request using the corresponding `POST /search/reference` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ReferenceListResponse" @@ -9341,6 +9712,26 @@ ], "summary" : "Submit a search request for `ReferenceSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/referenceSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `ReferenceSet` search request
\nClients should submit a search request using the corresponding `POST /search/referenceSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/ReferenceSetListResponse" @@ -9364,6 +9755,26 @@ ], "summary" : "Submit a search request for `Sample`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/sample/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Sample` search request
\nClients should submit a search request using the corresponding `POST /search/sample` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/SampleListResponse" @@ -9387,6 +9798,26 @@ ], "summary" : "Submit a search request for `Study`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Study` search request
\nClients should submit a search request using the corresponding `POST /search/study` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/StudyListResponse" @@ -9410,6 +9841,26 @@ ], "summary" : "Submit a search request for `Trial`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Trial` search request
\nClients should submit a search request using the corresponding `POST /search/trial` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/TrialListResponse" @@ -9433,11 +9884,31 @@ ], "summary" : "Submit a search request for `Variant`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variant/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `Variant` search request
\nClients should submit a search request using the corresponding `POST /search/variant` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "responses" : { - "200" : { - "$ref" : "#/components/responses/VariantListResponse" + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } }, - "400" : { + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantListResponse" + }, + "400" : { "$ref" : "#/components/responses/400BadRequest" }, "401" : { @@ -9456,6 +9927,26 @@ ], "summary" : "Submit a search request for `VariantSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variantSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "description" : "Get the results of a `VariantSet` search request
\nClients should submit a search request using the corresponding `POST /search/variantSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "searchResultsDbId", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], "responses" : { "200" : { "$ref" : "#/components/responses/VariantSetListResponse" @@ -9475,72 +9966,367 @@ }, "components" : { "schemas" : { + "AcquisitionSourceCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)", + "enum" : [ + "10", + "11", + "12", + "13", + "14", + "15", + "20", + "21", + "22", + "23", + "24", + "25", + "26", + "27", + "28", + "30", + "40", + "50", + "60", + "61", + "62", + "99" + ] + }, "AdditionalInfo" : { + "type" : "string", + "additionalProperties" : { + "description" : "A free space containing any additional information related to a particular object." + }, + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "nullable" : true + }, + "AlleleMatrix" : { "type" : "object", "properties" : { - "additionalProperties" : { - "type" : "string" + "dataMatrices" : { + "type" : "array", + "description" : "The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/DataMatrix" + } + }, + "expandHomozygotes" : { + "type" : "boolean", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "nullable" : true + }, + "pagination" : { + "type" : "array", + "description" : "Pagination for the matrix", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Pagination" + } + }, + "sepPhased" : { + "type" : "string", + "description" : "The string used as a separator for phased allele calls.", + "nullable" : true + }, + "sepUnphased" : { + "type" : "string", + "description" : "The string used as a separator for unphased allele calls.", + "nullable" : true + }, + "unknownString" : { + "type" : "string", + "description" : "The string used as a representation for missing data.", + "nullable" : true } }, - "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + "description" : "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." }, - "AlleleMatrix" : { - "required" : [ - "callSetDbIds", - "variantSetDbIds" - ], + "AlleleMatrixPagination" : { + "type" : "object", + "properties" : { + "dimension" : { + "type" : "string", + "description" : "the dimension of the matrix being paginated", + "example" : "VARIANTS", + "enum" : [ + "CALLSETS", + "VARIANTS" + ] + }, + "page" : { + "type" : "integer", + "description" : "the requested page number (zero indexed)", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "the maximum number of elements per page in this dimension of the matrix", + "format" : "int32", + "example" : 500 + } + } + }, + "AlleleMatrixRequest" : { "type" : "object", "properties" : { "callSetDbIds" : { "type" : "array", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "items" : { + "type" : "string" + } + }, + "dataMatrixAbbreviations" : { + "type" : "array", + "description" : "`dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "items" : { + "type" : "string" + } + }, + "dataMatrixNames" : { + "type" : "array", + "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", "items" : { "type" : "string" } }, "expandHomozygotes" : { - "type" : "boolean" + "type" : "boolean", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "example" : true + }, + "germplasmDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Germplasm` within the given database server", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "A list of human readable `Germplasm` names", + "items" : { + "type" : "string" + } + }, + "germplasmPUIs" : { + "type" : "array", + "description" : "A list of permanent unique identifiers associated with `Germplasm`", + "items" : { + "type" : "string" + } + }, + "pagination" : { + "type" : "array", + "description" : "Pagination for the matrix", + "items" : { + "type" : "object", + "properties" : { + "dimension" : { + "type" : "string", + "description" : "the dimension of the matrix being paginated", + "example" : "VARIANTS", + "enum" : [ + "CALLSETS", + "VARIANTS" + ] + }, + "page" : { + "type" : "integer", + "description" : "the requested page number (zero indexed)", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "the maximum number of elements per page in this dimension of the matrix", + "format" : "int32", + "example" : 500 + } + } + } + }, + "positionRanges" : { + "type" : "array", + "description" : "The postion range to search\n
\nUses the format \":-\" where is the chromosome name, is \nthe starting position of the range, and is the ending position of the range", + "items" : { + "type" : "string" + } + }, + "preview" : { + "type" : "boolean", + "description" : "Default Value = false\n
\nIf 'preview' is set to true, then the server should only return the lists of 'callSetDbIds', \n'variantDbIds', and 'variantSetDbIds'. The server should not return any matrix data. This\nis intended to be a preview and give the client a sense of how large the matrix returned will be\n
\nIf 'preview' is set to false or not set (default), then the server should return all the matrix\ndata as requested.", + "example" : true + }, + "sampleDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "items" : { + "type" : "string" + } }, "sepPhased" : { - "type" : "string" + "type" : "string", + "description" : "The string used as a separator for phased allele calls.", + "example" : "|" }, "sepUnphased" : { - "type" : "string" + "type" : "string", + "description" : "The string used as a separator for unphased allele calls.", + "example" : "/" }, "unknownString" : { - "type" : "string" + "type" : "string", + "description" : "The string used as a representation for missing data.", + "example" : "." }, "variantDbIds" : { "type" : "array", + "description" : "A list of IDs which uniquely identify `Variants` within the given database server", "items" : { "type" : "string" } }, "variantSetDbIds" : { "type" : "array", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", "items" : { "type" : "string" } } - }, - "description" : "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." + } }, "AlleleMatrixSearchRequest" : { "type" : "object", "properties" : { - "expandHomozygotes" : { - "type" : "boolean" + "germplasmDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Germplasm` within the given database server", + "items" : { + "type" : "string" + } }, "preview" : { - "type" : "boolean" + "type" : "boolean", + "description" : "Default Value = false\n
\nIf 'preview' is set to true, then the server should only return the lists of 'callSetDbIds', \n'variantDbIds', and 'variantSetDbIds'. The server should not return any matrix data. This\nis intended to be a preview and give the client a sense of how large the matrix returned will be\n
\nIf 'preview' is set to false or not set (default), then the server should return all the matrix\ndata as requested.", + "example" : true }, - "sepPhased" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "A list of human readable `Germplasm` names", + "items" : { + "type" : "string" + } }, - "sepUnphased" : { - "type" : "string" + "pagination" : { + "type" : "array", + "description" : "Pagination for the matrix", + "items" : { + "type" : "object", + "properties" : { + "dimension" : { + "type" : "string", + "description" : "the dimension of the matrix being paginated", + "example" : "VARIANTS", + "enum" : [ + "CALLSETS", + "VARIANTS" + ] + }, + "page" : { + "type" : "integer", + "description" : "the requested page number (zero indexed)", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "the maximum number of elements per page in this dimension of the matrix", + "format" : "int32", + "example" : 500 + } + } + } }, "unknownString" : { - "type" : "string" + "type" : "string", + "description" : "The string used as a representation for missing data.", + "example" : "." + }, + "germplasmPUIs" : { + "type" : "array", + "description" : "A list of permanent unique identifiers associated with `Germplasm`", + "items" : { + "type" : "string" + } + }, + "positionRanges" : { + "type" : "array", + "description" : "The postion range to search\n
\nUses the format \":-\" where is the chromosome name, is \nthe starting position of the range, and is the ending position of the range", + "items" : { + "type" : "string" + } + }, + "sampleDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "items" : { + "type" : "string" + } + }, + "dataMatrixAbbreviations" : { + "type" : "array", + "description" : "`dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "items" : { + "type" : "string" + } + }, + "expandHomozygotes" : { + "type" : "boolean", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "example" : true + }, + "variantDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "items" : { + "type" : "string" + } + }, + "callSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "items" : { + "type" : "string" + } + }, + "dataMatrixNames" : { + "type" : "array", + "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "items" : { + "type" : "string" + } + }, + "sepPhased" : { + "type" : "string", + "description" : "The string used as a separator for phased allele calls.", + "example" : "|" + }, + "sepUnphased" : { + "type" : "string", + "description" : "The string used as a separator for unphased allele calls.", + "example" : "/" } }, "description" : "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." @@ -9552,28 +10338,44 @@ "type" : "object", "properties" : { "analysisDbId" : { - "type" : "string" + "type" : "string", + "description" : "Unique identifier for this analysis description", + "nullable" : true }, "analysisName" : { - "type" : "string" + "type" : "string", + "description" : "A human readable name for this analysis", + "nullable" : true }, "created" : { - "type" : "string" + "type" : "string", + "description" : "The time at which this record was created, in ISO 8601 format.", + "format" : "date-time", + "nullable" : true }, "description" : { - "type" : "string" + "type" : "string", + "description" : "A human readable description of the analysis", + "nullable" : true }, "software" : { "type" : "array", + "description" : "The software run to generate this analysis.", + "nullable" : true, "items" : { "type" : "string" } }, "type" : { - "type" : "string" + "type" : "string", + "description" : "The type of analysis.", + "nullable" : true }, "updated" : { - "type" : "string" + "type" : "string", + "description" : "The time at which this record was last updated, in ISO 8601 format.", + "format" : "date-time", + "nullable" : true }, "variantSetDbId" : { "type" : "string" @@ -9587,9 +10389,11 @@ "Attribute" : { "required" : [ "attributeName", - "method", - "scale", - "trait" + "methodDbId", + "methodName", + "scaleDbId", + "scaleName", + "traitName" ], "type" : "object", "properties" : { @@ -9597,70 +10401,129 @@ "$ref" : "#/components/schemas/AdditionalInfo" }, "attributeCategory" : { - "type" : "string" + "type" : "string", + "description" : "General category for the attribute. very similar to Trait class.", + "example" : "Morphological" }, "attributeDbId" : { - "type" : "string" + "type" : "string", + "description" : "The ID which uniquely identifies this attribute within the given database server" }, "attributeDescription" : { - "type" : "string" + "type" : "string", + "description" : "A human readable description of this attribute", + "example" : "Height of the plant measured in meters by a tape" }, "attributeName" : { - "type" : "string" + "type" : "string", + "description" : "A human readable name for this attribute", + "example" : "Plant Height 1" }, "attributePUI" : { - "type" : "string" + "type" : "string", + "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", + "example" : "http://my-traits.com/trait/CO_123:0008012" }, "commonCropName" : { - "type" : "string" + "type" : "string", + "description" : "Crop name (examples: \"Maize\", \"Wheat\")", + "nullable" : true }, "contextOfUse" : { "type" : "array", + "description" : "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])", + "nullable" : true, "items" : { "type" : "string" } }, "defaultValue" : { - "type" : "string" + "type" : "string", + "description" : "Variable default value. (examples: \"red\", \"2.3\", etc.)", + "nullable" : true }, "documentationURL" : { - "type" : "string" + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, "growthStage" : { - "type" : "string" + "type" : "string", + "description" : "Growth stage at which measurement is made (examples: \"flowering\")", + "nullable" : true }, "institution" : { - "type" : "string" + "type" : "string", + "description" : "Name of institution submitting the variable", + "nullable" : true }, "language" : { + "type" : "string", + "description" : "2 letter ISO 639-1 code for the language of submission of the variable.", + "nullable" : true + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { "type" : "string" }, - "method" : { - "$ref" : "#/components/schemas/Method" + "methodPUI" : { + "type" : "string" }, "ontologyReference" : { "$ref" : "#/components/schemas/OntologyReference" }, - "scale" : { - "$ref" : "#/components/schemas/Scale" + "scaleDbId" : { + "type" : "string" }, - "scientist" : { + "scaleName" : { "type" : "string" }, - "status" : { + "scalePUI" : { "type" : "string" }, + "scientist" : { + "type" : "string", + "description" : "Name of scientist submitting the variable.", + "nullable" : true + }, + "status" : { + "type" : "string", + "description" : "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)", + "nullable" : true + }, "submissionTimestamp" : { - "type" : "string" + "type" : "string", + "description" : "Timestamp when the Variable was added (ISO 8601)", + "format" : "date-time", + "nullable" : true }, "synonyms" : { "type" : "array", + "description" : "Other variable names", + "nullable" : true, "items" : { "type" : "string" } }, - "trait" : { - "$ref" : "#/components/schemas/Trait" + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" } } }, @@ -9670,6 +10533,7 @@ "dataFormat" : { "type" : "string", "description" : "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)", + "nullable" : true, "enum" : [ "DartSeq", "VCF", @@ -9679,11 +10543,14 @@ ] }, "expandHomozygotes" : { - "type" : "boolean" + "type" : "boolean", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "nullable" : true }, "fileFormat" : { "type" : "string", "description" : "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response.", + "nullable" : true, "enum" : [ "text/csv", "text/tsv", @@ -9693,16 +10560,25 @@ ] }, "fileURL" : { - "type" : "string" + "type" : "string", + "description" : "A URL which indicates the location of the file version of this VariantSet. Could be a static file URL or an API endpoint which generates the file.", + "format" : "uri", + "nullable" : true }, "sepPhased" : { - "type" : "string" + "type" : "string", + "description" : "The string used as a separator for phased allele calls.", + "nullable" : true }, "sepUnphased" : { - "type" : "string" + "type" : "string", + "description" : "The string used as a separator for unphased allele calls.", + "nullable" : true }, "unknownString" : { - "type" : "string" + "type" : "string", + "description" : "The string used as a representation for missing data.", + "nullable" : true }, "variantSetDbId" : { "type" : "string" @@ -9713,26 +10589,57 @@ }, "description" : "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other." }, + "BiologicalStatusOfAccessionCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "enum" : [ + "100", + "110", + "120", + "130", + "200", + "300", + "400", + "410", + "411", + "412", + "413", + "414", + "415", + "416", + "420", + "421", + "422", + "423", + "500", + "600", + "999" + ] + }, "BreedingMethod" : { "required" : [ - "abbreviation", - "breedingMethodDbId", - "breedingMethodName", - "description" + "breedingMethodDbId" ], "type" : "object", "properties" : { "abbreviation" : { - "type" : "string" + "type" : "string", + "description" : "A shortened version of the human readable name for a Breeding Method", + "nullable" : true }, "breedingMethodDbId" : { - "type" : "string" + "type" : "string", + "description" : "the unique identifier for this breeding method" }, "breedingMethodName" : { - "type" : "string" + "type" : "string", + "description" : "the human readable identifier for this breeding method", + "nullable" : true }, "description" : { - "type" : "string" + "type" : "string", + "description" : "human readable description of the breeding method", + "nullable" : true } }, "description" : "The techniques and protocol used to produce a Cross or Germplasm" @@ -9754,11 +10661,23 @@ "callSetName" : { "type" : "string" }, + "genotypeMetadata" : { + "type" : "array", + "description" : "Genotype Metadata are additional layers of metadata associated with each genotype.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/GenotypeMetadata" + } + }, "genotypeValue" : { - "type" : "string" + "type" : "string", + "description" : "The value of this genotype call", + "nullable" : true }, "phaseSet" : { - "type" : "string" + "type" : "string", + "description" : "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string.", + "nullable" : true }, "variantDbId" : { "type" : "string" @@ -9772,20 +10691,95 @@ }, "description" : "A `Call` represents the determination of genotype with respect to a particular `Variant`. \n\nIt may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345." }, - "CallSearchRequest" : { + "CallRequest" : { "type" : "object", "properties" : { + "callSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "items" : { + "type" : "string" + } + }, "expandHomozygotes" : { - "type" : "boolean" + "type" : "boolean", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "example" : true }, "sepPhased" : { - "type" : "string" + "type" : "string", + "description" : "The string used as a separator for phased allele calls.", + "example" : "|" }, "sepUnphased" : { - "type" : "string" + "type" : "string", + "description" : "The string used as a separator for unphased allele calls.", + "example" : "/" }, "unknownString" : { - "type" : "string" + "type" : "string", + "description" : "The string used as a representation for missing data.", + "example" : "." + }, + "variantDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Variant` within the given database server", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "items" : { + "type" : "string" + } + } + } + }, + "CallSearchRequest" : { + "type" : "object", + "properties" : { + "variantSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "items" : { + "type" : "string" + } + }, + "unknownString" : { + "type" : "string", + "description" : "The string used as a representation for missing data.", + "example" : "." + }, + "expandHomozygotes" : { + "type" : "boolean", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "example" : true + }, + "variantDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Variant` within the given database server", + "items" : { + "type" : "string" + } + }, + "callSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "items" : { + "type" : "string" + } + }, + "sepPhased" : { + "type" : "string", + "description" : "The string used as a separator for phased allele calls.", + "example" : "|" + }, + "sepUnphased" : { + "type" : "string", + "description" : "The string used as a separator for unphased allele calls.", + "example" : "/" } }, "description" : "A `Call` represents the determination of genotype with respect to a particular `Variant`. \n\nIt may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345." @@ -9800,13 +10794,27 @@ "$ref" : "#/components/schemas/AdditionalInfo" }, "callSetDbId" : { - "type" : "string" + "type" : "string", + "description" : "The ID which uniquely identifies a CallSet within the given database server" }, "callSetName" : { - "type" : "string" + "type" : "string", + "description" : "The human readable name which identifies a germplasm within the given database server", + "nullable" : true }, "created" : { - "type" : "string" + "type" : "string", + "description" : "The date this call set was created", + "format" : "date-time", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, "sampleDbId" : { "type" : "string" @@ -9827,3008 +10835,9403 @@ "type" : "string" }, "updated" : { - "type" : "string" - }, - "variantSetDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } + "type" : "string", + "description" : "The time at which this call set was last updated", + "format" : "date-time", + "nullable" : true } }, "description" : "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample" }, - "CallSetSearchRequest" : { - "type" : "object", - "properties" : { }, - "description" : "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample" - }, - "Contact" : { - "required" : [ - "contactDbId" - ], + "CallSetRequest" : { "type" : "object", "properties" : { - "contactDbId" : { - "type" : "string" + "callSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "items" : { + "type" : "string" + } }, - "email" : { - "type" : "string" + "callSetNames" : { + "type" : "array", + "description" : "A list of human readable names associated with `CallSets`", + "items" : { + "type" : "string" + } }, - "instituteName" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "name" : { - "type" : "string" + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "orcid" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "type" : { - "type" : "string" - } - }, - "description" : "A persons contact information" - }, - "ContentMixture" : { - "type" : "object", - "properties" : { - "crossDbId" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "crossName" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "germplasmDbId" : { - "type" : "string" + "sampleDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "items" : { + "type" : "string" + } }, - "germplasmName" : { - "type" : "string" + "sampleNames" : { + "type" : "array", + "description" : "A list of human readable names associated with `Samples`", + "items" : { + "type" : "string" + } }, - "germplasmPUI" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "mixturePercentage" : { - "type" : "integer", - "format" : "int32" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "seedLotDbId" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "seedLotName" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "items" : { + "type" : "string" + } } - }, - "description" : "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100." - }, - "ContentTypes" : { - "type" : "string", - "enum" : [ - "application/json", - "text/csv", - "text/tsv", - "application/flapjack" - ] - }, - "Context" : { - "title" : "context", - "type" : "array", - "description" : "The JSON-LD Context is used to provide JSON-LD definitions to each field in a JSON object. By providing an array of context file urls, a BrAPI response object becomes JSON-LD compatible. \n\nFor more information, see https://w3c.github.io/json-ld-syntax/#the-context", - "example" : [ - "https://brapi.org/jsonld/context/metadata.jsonld" - ], - "items" : { - "type" : "string", - "format" : "uri" } }, - "Cross" : { - "required" : [ - "crossDbId" - ], + "CallSetSearchRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "crossName" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "crossType" : { - "$ref" : "#/components/schemas/CrossType" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "crossingProjectDbId" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "crossingProjectName" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "parent1" : { - "$ref" : "#/components/schemas/CrossParent" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "parent2" : { - "$ref" : "#/components/schemas/CrossParent" + "sampleDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "items" : { + "type" : "string" + } }, - "plannedCrossDbId" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "plannedCrossName" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "items" : { + "type" : "string" + } + }, + "callSetNames" : { + "type" : "array", + "description" : "A list of human readable names associated with `CallSets`", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "sampleNames" : { + "type" : "array", + "description" : "A list of human readable names associated with `Samples`", + "items" : { + "type" : "string" + } + }, + "callSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "items" : { + "type" : "string" + } } }, - "description" : "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present." + "description" : "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample" }, - "CrossAttribute" : { + "CollectingInfo" : { "type" : "object", "properties" : { - "crossAttributeName" : { - "type" : "string" + "collectingDate" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "format" : "date", + "nullable" : true }, - "crossAttributeValue" : { - "type" : "string" + "collectingInstitutes" : { + "type" : "array", + "description" : "Institutes which collected the sample", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Institute" + } }, - "crossDbId" : { - "type" : "string" + "collectingMissionIdentifier" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\").", + "nullable" : true, + "example" : "CIATFOR_052" }, - "crossName" : { - "type" : "string" + "collectingNumber" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections.", + "nullable" : true, + "example" : "ab109909" + }, + "collectingSite" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string", + "description" : "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown.", + "nullable" : true, + "example" : "20" + }, + "elevation" : { + "type" : "string", + "description" : "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed.", + "nullable" : true, + "example" : "35" + }, + "georeferencingMethod" : { + "type" : "string", + "description" : "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known.", + "nullable" : true, + "example" : "WGS84" + }, + "latitudeDecimal" : { + "type" : "string", + "description" : "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975).", + "nullable" : true, + "example" : "+42.445295" + }, + "latitudeDegrees" : { + "type" : "string", + "description" : "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10", + "nullable" : true, + "example" : "42 26 43.1 N" + }, + "locationDescription" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville).", + "nullable" : true, + "example" : "South east hill near institute buildings" + }, + "longitudeDecimal" : { + "type" : "string", + "description" : "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123).", + "nullable" : true, + "example" : "-076.471934" + }, + "longitudeDegrees" : { + "type" : "string", + "description" : "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076", + "nullable" : true, + "example" : "76 28 19.0 W" + }, + "spatialReferenceSystem" : { + "type" : "string", + "description" : "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum.", + "nullable" : true, + "example" : "WGS84" + } + }, + "description" : "Information about the location where the sample was collected", + "nullable" : true } }, - "description" : "A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'" + "description" : "Information about the collection of a germplasm" }, - "CrossNewRequest" : { - "required" : [ - "crossDbId", - "crossDbId" - ], + "CollectingSite" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "crossDbId" : { - "type" : "string" + "coordinateUncertainty" : { + "type" : "string", + "description" : "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown.", + "nullable" : true, + "example" : "20" }, - "crossName" : { - "type" : "string" + "elevation" : { + "type" : "string", + "description" : "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed.", + "nullable" : true, + "example" : "35" }, - "crossType" : { - "$ref" : "#/components/schemas/CrossType" + "georeferencingMethod" : { + "type" : "string", + "description" : "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known.", + "nullable" : true, + "example" : "WGS84" }, - "crossingProjectDbId" : { - "type" : "string" + "latitudeDecimal" : { + "type" : "string", + "description" : "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975).", + "nullable" : true, + "example" : "+42.445295" }, - "crossingProjectName" : { - "type" : "string" + "latitudeDegrees" : { + "type" : "string", + "description" : "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10", + "nullable" : true, + "example" : "42 26 43.1 N" }, - "parent1" : { - "$ref" : "#/components/schemas/CrossParent" + "locationDescription" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville).", + "nullable" : true, + "example" : "South east hill near institute buildings" }, - "parent2" : { - "$ref" : "#/components/schemas/CrossParent" + "longitudeDecimal" : { + "type" : "string", + "description" : "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123).", + "nullable" : true, + "example" : "-076.471934" }, - "plannedCrossDbId" : { - "type" : "string" + "longitudeDegrees" : { + "type" : "string", + "description" : "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076", + "nullable" : true, + "example" : "76 28 19.0 W" }, - "plannedCrossName" : { - "type" : "string" + "spatialReferenceSystem" : { + "type" : "string", + "description" : "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum.", + "nullable" : true, + "example" : "WGS84" } }, - "description" : "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present." + "description" : "Information about the location where the sample was collected" }, - "CrossParent" : { + "CommonCropNamesParameters" : { "type" : "object", "properties" : { - "germplasm" : { - "$ref" : "#/components/schemas/Germplasm" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, - "parentType" : { - "$ref" : "#/components/schemas/ParentType" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } } - }, - "description" : "The identifying information gor the parent material of a cross." + } }, - "CrossType" : { - "type" : "string", - "description" : "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'.", - "enum" : [ - "BIPARENTAL", - "SELF", - "OPEN_POLLINATED", - "BULK", - "BULK_SELFED", - "BULK_OPEN_POLLINATED", - "DOUBLE_HAPLOID" - ] - }, - "CrossingProject" : { + "Contact" : { "required" : [ - "crossingProjectDbId", - "crossingProjectName" + "contactDbId" ], "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "contactDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies this contact\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended." }, - "commonCropName" : { - "type" : "string" + "email" : { + "type" : "string", + "description" : "The contacts email address\n\nMIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person.", + "nullable" : true }, - "crossingProjectDescription" : { - "type" : "string" + "instituteName" : { + "type" : "string", + "description" : "The name of the institution which this contact is part of\n\nMIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to", + "nullable" : true }, - "crossingProjectName" : { - "type" : "string" + "name" : { + "type" : "string", + "description" : "The full name of this contact person\n\nMIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications)", + "nullable" : true }, - "programDbId" : { - "type" : "string" + "orcid" : { + "type" : "string", + "description" : "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended.", + "nullable" : true }, - "programName" : { - "type" : "string" + "type" : { + "type" : "string", + "description" : "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation", + "nullable" : true } }, - "description" : "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented." + "description" : "A persons contact information" }, - "CrossingProjectNewRequest" : { - "required" : [ - "crossingProjectDbId", - "crossingProjectDbId", - "crossingProjectName" - ], + "ContentMixture" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "crossDbId" : { + "type" : "string" }, - "commonCropName" : { + "crossName" : { "type" : "string" }, - "crossingProjectDbId" : { + "germplasmDbId" : { "type" : "string" }, - "crossingProjectDescription" : { + "germplasmName" : { "type" : "string" }, - "crossingProjectName" : { + "germplasmPUI" : { "type" : "string" }, - "programDbId" : { + "mixturePercentage" : { + "type" : "integer", + "description" : "The percentage of the given germplasm in the seed lot mixture.", + "format" : "int32", + "nullable" : true + }, + "seedLotDbId" : { "type" : "string" }, - "programName" : { + "seedLotName" : { "type" : "string" } }, - "description" : "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented." + "description" : "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100." }, - "DataLink" : { + "ContentTypes" : { + "type" : "string", + "enum" : [ + "application/json", + "text/csv", + "text/tsv", + "application/flapjack" + ] + }, + "Context" : { + "title" : "context", + "type" : "array", + "description" : "The JSON-LD Context is used to provide JSON-LD definitions to each field in a JSON object. By providing an array of context file urls, a BrAPI response object becomes JSON-LD compatible. \n\nFor more information, see https://w3c.github.io/json-ld-syntax/#the-context", + "example" : [ + "https://brapi.org/jsonld/context/metadata.jsonld" + ], + "items" : { + "type" : "string", + "format" : "uri" + } + }, + "Cross" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/CrossNewRequest" + }, + { + "required" : [ + "crossDbId" + ], + "type" : "object", + "properties" : { + "crossDbId" : { + "type" : "string", + "description" : "the unique identifier for a cross" + } + }, + "description" : "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present." + } + ] + }, + "CrossAttribute" : { "type" : "object", "properties" : { - "dataFormat" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "fileFormat" : { - "type" : "string" - }, - "name" : { - "type" : "string" - }, - "provenance" : { - "type" : "string" + "crossAttributeName" : { + "type" : "string", + "description" : "the human readable name of a cross attribute", + "nullable" : true }, - "scientificType" : { - "type" : "string" + "crossAttributeValue" : { + "type" : "string", + "description" : "the value of a cross attribute", + "nullable" : true }, - "url" : { + "crossDbId" : { "type" : "string" }, - "version" : { + "crossName" : { "type" : "string" } }, - "description" : "A link to extra data files associated with this study. Extra data could include notes, images, and reference data." + "description" : "A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'" }, - "DataMatrix" : { + "CrossNewRequest" : { "type" : "object", "properties" : { - "alleleMatrix" : { - "$ref" : "#/components/schemas/AlleleMatrix" + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" }, - "dataMatrix" : { + "crossAttributes" : { "type" : "array", + "description" : "Set of custom attributes associated with a cross", + "nullable" : true, "items" : { - "type" : "array", - "items" : { - "type" : "string" - } + "$ref" : "#/components/schemas/CrossAttribute" } }, - "dataMatrixAbbreviation" : { - "type" : "string" + "crossName" : { + "type" : "string", + "description" : "the human readable name for a cross", + "nullable" : true }, - "dataMatrixName" : { - "type" : "string" + "crossType" : { + "$ref" : "#/components/schemas/CrossType" }, - "dataType" : { - "type" : "string", - "description" : "The type of field represented in this data matrix. This is intended to help parse the data out of JSON.", - "enum" : [ - "string", - "integer", - "float", - "boolean" - ] - } - }, - "description" : "A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." - }, - "DatasetAuthorships" : { - "type" : "object", - "properties" : { - "datasetPUI" : { + "crossingProjectDbId" : { "type" : "string" }, - "license" : { + "crossingProjectName" : { "type" : "string" }, - "publicReleaseDate" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "submissionDate" : { - "type" : "string" + "parent1" : { + "$ref" : "#/components/schemas/CrossParent" }, - "trialDbId" : { - "type" : "string" + "parent2" : { + "$ref" : "#/components/schemas/CrossParent" }, - "trialName" : { + "plannedCrossDbId" : { "type" : "string" }, - "trialPUI" : { + "plannedCrossName" : { "type" : "string" + }, + "pollinationEvents" : { + "type" : "array", + "description" : "The list of pollination events that occurred for this cross.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/PollinationEvent" + } } }, - "description" : "License and citation information for the data in this trial" + "description" : "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present." }, - "DocumentationLink" : { + "CrossParent" : { "type" : "object", "properties" : { - "URL" : { + "germplasmDbId" : { "type" : "string" }, - "ontologyReferenceDbId" : { + "germplasmName" : { "type" : "string" }, - "type" : { - "type" : "string", - "description" : "The type of documentation, which can be OBO Foundry, an RDF term or a webpage.", - "enum" : [ - "OBO", - "RDF", - "WEBPAGE" - ] - } - }, - "description" : "Links to various ontology documentation" - }, - "Donor" : { - "type" : "object", - "properties" : { - "donorAccessionNumber" : { + "germplasmPUI" : { "type" : "string" }, - "donorInstituteCode" : { + "observationUnitDbId" : { "type" : "string" }, - "germplasmDbId" : { + "observationUnitName" : { "type" : "string" }, - "germplasmName" : { + "observationUnitPUI" : { "type" : "string" }, - "germplasmPUI" : { - "type" : "string" + "parentType" : { + "$ref" : "#/components/schemas/ParentType" } }, - "description" : "Identifier assigned to an accession by the material donor." + "description" : "The identifying information gor the parent material of a cross." }, - "EnvironmentParameter" : { - "required" : [ - "description", - "environmentParametersDbId", - "parameterName" - ], + "CrossRequest" : { "type" : "object", "properties" : { - "description" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "environmentParametersDbId" : { - "type" : "string" + "crossDbIds" : { + "type" : "array", + "description" : "Search for Cross with this unique id", + "items" : { + "type" : "string" + } }, - "parameterName" : { - "type" : "string" + "crossNames" : { + "type" : "array", + "description" : "Search for Cross with this human readable name", + "items" : { + "type" : "string" + } }, - "parameterPUI" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" + "crossingProjectDbIds" : { + "type" : "array", + "description" : "Search for Crossing Projects with this unique id", + "items" : { + "type" : "string" + } }, - "unit" : { - "type" : "string" + "crossingProjectNames" : { + "type" : "array", + "description" : "The human readable name for a crossing project", + "items" : { + "type" : "string" + } }, - "unitPUI" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "value" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + } + } + }, + "CrossStatus" : { + "type" : "string", + "enum" : [ + "TODO", + "DONE", + "SKIPPED" + ] + }, + "CrossType" : { + "type" : "string", + "description" : "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'.", + "enum" : [ + "BIPARENTAL", + "SELF", + "OPEN_POLLINATED", + "BULK", + "BULK_SELFED", + "BULK_OPEN_POLLINATED", + "DOUBLE_HAPLOID" + ] + }, + "CrossingProject" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/CrossingProjectNewRequest" }, - "valuePUI" : { - "type" : "string" + { + "required" : [ + "crossingProjectDbId" + ], + "type" : "object", + "properties" : { + "crossingProjectDbId" : { + "type" : "string", + "description" : "The unique identifier for a crossing project" + } + }, + "description" : "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented." } - }, - "description" : "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)." + ] }, - "Event" : { + "CrossingProjectNewRequest" : { "required" : [ - "eventDbId", - "eventType" + "crossingProjectName" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "eventDbId" : { - "type" : "string" - }, - "eventDescription" : { - "type" : "string" + "commonCropName" : { + "type" : "string", + "description" : "the common name of a crop (for multi-crop systems)", + "nullable" : true }, - "eventType" : { - "type" : "string" + "crossingProjectDescription" : { + "type" : "string", + "description" : "the description for a crossing project", + "nullable" : true }, - "eventTypeDbId" : { - "type" : "string" + "crossingProjectName" : { + "type" : "string", + "description" : "The human readable name for a crossing project" }, - "observationUnitDbIds" : { + "externalReferences" : { "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, "items" : { - "type" : "string" + "$ref" : "#/components/schemas/ExternalReference" } }, - "studyDbId" : { - "type" : "string" + "potentialParents" : { + "type" : "array", + "description" : "A list of all the potential parents in the crossing block, available in the crossing project\n
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/CrossParent" + } }, - "studyName" : { + "programDbId" : { "type" : "string" }, - "studyPUI" : { + "programName" : { "type" : "string" } }, - "description" : "An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. \n
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other" + "description" : "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented." }, - "EventDateRange" : { + "CrossingProjectRequest" : { "type" : "object", "properties" : { - "discreteDates" : { + "commonCropNames" : { "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "endDate" : { - "type" : "string" + "crossingProjectDbIds" : { + "type" : "array", + "description" : "Search for Crossing Projects with this unique id", + "items" : { + "type" : "string" + } }, - "eventDbId" : { - "type" : "string" + "crossingProjectNames" : { + "type" : "array", + "description" : "The human readable name for a crossing project", + "items" : { + "type" : "string" + } }, - "startDate" : { - "type" : "string" + "includePotentialParents" : { + "type" : "boolean", + "description" : "If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object." + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } } - }, - "description" : "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" + } }, - "EventParameter" : { + "DataFormat" : { + "type" : "string", + "description" : "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)", + "enum" : [ + "DartSeq", + "VCF", + "Hapmap", + "tabular", + "JSON" + ] + }, + "DataLink" : { "type" : "object", "properties" : { - "code" : { - "type" : "string" + "dataFormat" : { + "type" : "string", + "description" : "The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", + "nullable" : true }, "description" : { - "type" : "string" + "type" : "string", + "description" : "The general description of this data link\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", + "nullable" : true }, - "eventDbId" : { - "type" : "string" + "fileFormat" : { + "type" : "string", + "description" : "The MIME type of the file (ie text/csv, application/excel, application/zip).\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", + "nullable" : true }, "name" : { - "type" : "string" + "type" : "string", + "description" : "The name of the external data link\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file.", + "nullable" : true }, - "units" : { - "type" : "string" + "provenance" : { + "type" : "string", + "description" : "The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow.", + "nullable" : true }, - "value" : { - "type" : "string" + "scientificType" : { + "type" : "string", + "description" : "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc", + "nullable" : true }, - "valueDescription" : { - "type" : "string" + "url" : { + "type" : "string", + "description" : "URL describing the location of this data file to view or download\n\nMIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission.", + "format" : "uri", + "nullable" : true }, - "valuesByDate" : { + "version" : { + "type" : "string", + "description" : "The version number for this data \n\nMIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data).", + "nullable" : true + } + }, + "description" : "A link to extra data files associated with this study. Extra data could include notes, images, and reference data." + }, + "DataMatrix" : { + "type" : "object", + "properties" : { + "dataMatrix" : { "type" : "array", + "description" : "The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows.", + "nullable" : true, "items" : { - "type" : "string" + "type" : "array", + "items" : { + "type" : "string" + } } + }, + "dataMatrixAbbreviation" : { + "type" : "string", + "description" : "The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word \"GT\" is reserved for the allele matrix. Examples of other metadata matrices include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard.", + "nullable" : true + }, + "dataMatrixName" : { + "type" : "string", + "description" : "The name of the field represented in this data matrix. The key word \"Genotype\" is reserved for the allele matrix. Examples of other metadata matrices include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard.", + "nullable" : true + }, + "dataType" : { + "type" : "string", + "description" : "The type of field represented in this data matrix. This is intended to help parse the data out of JSON.", + "nullable" : true, + "enum" : [ + "string", + "integer", + "float", + "boolean" + ] } }, - "description" : "Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event." + "description" : "A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." }, - "ExperimentalDesign" : { + "DataType" : { + "type" : "string", + "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", + "enum" : [ + "string", + "integer", + "float", + "boolean" + ] + }, + "DatasetAuthorships" : { "type" : "object", "properties" : { - "PUI" : { - "type" : "string" + "datasetPUI" : { + "type" : "string", + "description" : "The DOI or other permanent unique identifier for this published dataset", + "nullable" : true }, - "description" : { - "type" : "string" + "license" : { + "type" : "string", + "description" : "MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended.", + "nullable" : true }, - "studyDbId" : { + "publicReleaseDate" : { + "type" : "string", + "description" : "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described.", + "nullable" : true + }, + "submissionDate" : { + "type" : "string", + "description" : "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository.", + "nullable" : true + }, + "trialDbId" : { "type" : "string" }, - "studyName" : { + "trialName" : { "type" : "string" }, - "studyPUI" : { + "trialPUI" : { "type" : "string" } }, - "description" : "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology" + "description" : "License and citation information for the data in this trial" }, - "ExternalReference" : { + "Dimension" : { + "type" : "string", + "description" : "The dimension of the matrix being paginated", + "enum" : [ + "CALLSETS", + "VARIANTS" + ] + }, + "DocumentationLink" : { "type" : "object", "properties" : { - "referenceId" : { - "type" : "string" + "URL" : { + "type" : "string", + "description" : "The URL or URI to the documentation", + "format" : "uri", + "nullable" : true }, - "referenceSource" : { - "type" : "string" + "type" : { + "type" : "string", + "description" : "The type of documentation, which can be OBO Foundry, an RDF term or a webpage.", + "nullable" : true, + "enum" : [ + "OBO", + "RDF", + "WEBPAGE" + ] } - } + }, + "description" : "Links to various ontology documentation" }, - "GenomeMap" : { - "required" : [ - "commonCropName", - "mapDbId", - "type" - ], + "DocumentationLinkType" : { + "type" : "string", + "description" : "The type of documentation, which can be OBO Foundry, an RDF term or a webpage.", + "enum" : [ + "OBO", + "RDF", + "WEBPAGE" + ] + }, + "Donor" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "donorAccessionNumber" : { + "type" : "string", + "description" : "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", + "nullable" : true }, - "comments" : { + "donorInstituteCode" : { + "type" : "string", + "description" : "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", + "nullable" : true + }, + "germplasmDbId" : { "type" : "string" }, - "commonCropName" : { + "germplasmName" : { "type" : "string" }, - "documentationURL" : { + "germplasmPUI" : { "type" : "string" + } + }, + "description" : "Identifier assigned to an accession by the material donor." + }, + "DonorInfo" : { + "type" : "object", + "properties" : { + "donorAccessionNumber" : { + "type" : "string", + "description" : "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", + "nullable" : true, + "example" : "A0090204" }, - "linkageGroupCount" : { - "type" : "integer", - "format" : "int32" + "donorAccessionPui" : { + "type" : "string", + "description" : "PUI (DOI mostly) of the accession in the donor system.", + "nullable" : true, + "example" : "http://pui.per/accession/A0010025" }, - "mapDbId" : { - "type" : "string" + "donorInstitute" : { + "$ref" : "#/components/schemas/Institute" + } + }, + "description" : "Information about an accession donor" + }, + "EntryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ + "CHECK", + "TEST", + "FILLER" + ] + }, + "EnvironmentParameter" : { + "required" : [ + "description", + "environmentParametersDbId", + "parameterName" + ], + "type" : "object", + "properties" : { + "description" : { + "type" : "string", + "description" : "Human-readable value of the environment parameter (defined above) constant within the experiment" }, - "mapName" : { - "type" : "string" + "environmentParametersDbId" : { + "type" : "string", + "description" : "Human-readable value of the environment parameter (defined above) constant within the experiment" }, - "mapPUI" : { - "type" : "string" + "parameterName" : { + "type" : "string", + "description" : "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. " }, - "markerCount" : { - "type" : "integer", - "format" : "int32" + "parameterPUI" : { + "type" : "string", + "description" : "URI pointing to an ontology class for the parameter", + "nullable" : true }, - "publishedDate" : { + "studyDbId" : { "type" : "string" }, - "scientificName" : { + "studyName" : { "type" : "string" }, - "type" : { + "studyPUI" : { "type" : "string" }, "unit" : { - "type" : "string" + "type" : "string", + "description" : "Unit of the value for this parameter", + "nullable" : true + }, + "unitPUI" : { + "type" : "string", + "description" : "URI pointing to an ontology class for the unit", + "nullable" : true + }, + "value" : { + "type" : "string", + "description" : "Numerical or categorical value\n\nMIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment.", + "nullable" : true + }, + "valuePUI" : { + "type" : "string", + "description" : "URI pointing to an ontology class for the parameter value", + "nullable" : true } }, - "description" : "The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map." + "description" : "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)." }, - "GenotypeMetadata" : { + "Event" : { + "required" : [ + "eventDbId", + "eventType" + ], "type" : "object", "properties" : { - "call" : { - "$ref" : "#/components/schemas/Call" + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" }, - "dataType" : { + "eventDateRange" : { + "type" : "array", + "description" : "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/EventDateRange" + } + }, + "eventDbId" : { "type" : "string", - "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", - "enum" : [ - "string", - "integer", - "float", - "boolean" - ] + "description" : "Internal database identifier" }, - "fieldAbbreviation" : { + "eventDescription" : { + "type" : "string", + "description" : "A detailed, human-readable description of this event\n
MIAPPE V1.1 (DM-67) Event description - Description of the event, including details such as amount applied and possibly duration of the event. ", + "nullable" : true + }, + "eventParameters" : { + "type" : "array", + "description" : "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/EventParameter" + } + }, + "eventType" : { + "type" : "string", + "description" : "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology).", + "nullable" : true + }, + "eventTypeDbId" : { + "type" : "string", + "description" : "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology).", + "nullable" : true + }, + "studyDbId" : { "type" : "string" }, - "fieldName" : { + "studyName" : { "type" : "string" }, - "fieldValue" : { + "studyPUI" : { "type" : "string" } }, - "description" : "Genotype Metadata are additional layers of metadata associated with each genotype." + "description" : "An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. \n
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other" }, - "GeoJSON" : { + "EventDateRange" : { "type" : "object", "properties" : { - "geometry" : { - "$ref" : "#/components/schemas/GeoJSONGeometry" + "discreteDates" : { + "type" : "array", + "description" : "A list of dates when the event occurred\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", + "nullable" : true, + "items" : { + "type" : "string", + "format" : "date-time" + } }, - "type" : { + "endDate" : { + "type" : "string", + "description" : "The end of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", + "format" : "date-time", + "nullable" : true + }, + "eventDbId" : { "type" : "string" - } - }, - "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." - }, - "GeoJSONGeometry" : { - "oneOf" : [ - { - "required" : [ - "coordinateDbIds", - "type" - ], - "type" : "object", - "properties" : { - "coordinates" : { - "type" : "array", - "items" : { - "type" : "number" - } - }, - "type" : { - "type" : "string" - } - }, - "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." }, - { - "required" : [ - "coordinateDbIds", - "type" - ], - "type" : "object", - "properties" : { - "coordinates" : { - "type" : "array", - "items" : { - "type" : "array", - "items" : { - "type" : "array", - "items" : { - "type" : "number" - } - } - } - }, - "type" : { - "type" : "string" - } - }, - "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." + "startDate" : { + "type" : "string", + "description" : "The beginning of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", + "format" : "date-time", + "nullable" : true } - ] + }, + "description" : "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" }, - "GeoJSONSearchArea" : { + "EventParameter" : { "type" : "object", "properties" : { - "geometry" : { - "$ref" : "#/components/schemas/GeoJSONGeometry" + "code" : { + "type" : "string", + "description" : "The shortened code name of an event parameter\n
ICASA \"Code_Display\"", + "nullable" : true }, - "germplasmOrigin" : { - "$ref" : "#/components/schemas/GermplasmOrigin" + "description" : { + "type" : "string", + "description" : "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter.", + "nullable" : true }, - "imageDbId" : { + "eventDbId" : { "type" : "string" }, - "imageName" : { - "type" : "string" + "name" : { + "type" : "string", + "description" : "The full name of an event parameter\n
ICASA \"Variable_Name\"", + "nullable" : true }, - "observationDbId" : { - "type" : "string" + "units" : { + "type" : "string", + "description" : "The units or data type of the 'value'. \n
If the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'. \n
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. \n
If the value IS a number, then 'unit' should specify the units used eg. 'ml', 'cm', etc\n
ICASA \"Unit_or_type\"", + "nullable" : true }, - "observationUnit" : { - "$ref" : "#/components/schemas/ObservationUnitPosition" + "value" : { + "type" : "string", + "description" : "The single value of this event parameter. This single value is accurate for all the dates in the date range. If 'value' is populated then 'valuesByDate' should NOT be populated.", + "nullable" : true }, - "type" : { - "type" : "string" + "valueDescription" : { + "type" : "string", + "description" : "If the event parameter 'unit' field is 'code', then use 'valueDescription' to add a human readable description to the value.", + "nullable" : true + }, + "valuesByDate" : { + "type" : "array", + "description" : "An array of values corresponding to each timestamp in the 'discreteDates' array of this event. The 'valuesByDate' array should exactly match the size of the 'discreteDates' array. If 'valuesByDate' is populated then 'value' should NOT be populated.", + "nullable" : true, + "items" : { + "type" : "string" + } } - } + }, + "description" : "Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event." }, - "Germplasm" : { - "required" : [ - "commonCropName", - "germplasmDbId", - "germplasmName", - "germplasmPUI" - ], + "EventRequest" : { "type" : "object", "properties" : { - "accessionNumber" : { - "type" : "string" + "dateRangeEnd" : { + "type" : "string", + "description" : "Filter based on an Event start date.", + "format" : "date-time" }, - "acquisitionDate" : { - "type" : "string" + "dateRangeStart" : { + "type" : "string", + "description" : "Filter based on an Event start date.", + "format" : "date-time" }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "eventDbIds" : { + "type" : "array", + "description" : "Filter based on an Event DbId.", + "items" : { + "type" : "string" + } }, - "biologicalStatusOfAccessionCode" : { - "type" : "string", - "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", - "enum" : [ - "100", - "110", - "120", - "130", - "200", - "300", - "400", - "410", - "411", - "412", - "413", - "414", - "415", - "416", - "420", - "421", - "422", - "423", - "500", - "600", - "999" - ] - }, - "biologicalStatusOfAccessionDescription" : { - "type" : "string" - }, - "breedingMethodDbId" : { - "type" : "string" - }, - "breedingMethodName" : { - "type" : "string" - }, - "collection" : { - "type" : "string" - }, - "commonCropName" : { - "type" : "string" - }, - "countryOfOriginCode" : { - "type" : "string" - }, - "defaultDisplayName" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "genus" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "germplasmPreprocessing" : { - "type" : "string" - }, - "instituteCode" : { - "type" : "string" - }, - "instituteName" : { - "type" : "string" - }, - "pedigree" : { - "type" : "string" + "eventTypes" : { + "type" : "array", + "description" : "Filter based on an Event Type", + "items" : { + "type" : "string" + } }, - "sampleDbIds" : { + "observationUnitDbIds" : { "type" : "array", + "description" : "The ID which uniquely identifies an observation unit.", "items" : { "type" : "string" } }, - "seedSource" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "seedSourceDescription" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + } + } + }, + "ExperimentalDesign" : { + "type" : "object", + "properties" : { + "PUI" : { + "type" : "string", + "description" : "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology.", + "nullable" : true }, - "species" : { - "type" : "string" + "description" : { + "type" : "string", + "description" : "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'.", + "nullable" : true }, - "speciesAuthority" : { + "studyDbId" : { "type" : "string" }, - "subtaxa" : { + "studyName" : { "type" : "string" }, - "subtaxaAuthority" : { + "studyPUI" : { "type" : "string" } }, - "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." + "description" : "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology" }, - "GermplasmAttribute" : { + "ExternalReference" : { + "type" : "object", + "properties" : { + "referenceId" : { + "type" : "string", + "description" : "The external reference ID. Could be a simple string or a URI.", + "nullable" : true + }, + "referenceSource" : { + "type" : "string", + "description" : "An identifier for the source system or database of this reference", + "nullable" : true + } + } + }, + "FileFormat" : { + "type" : "string", + "description" : "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response.", + "enum" : [ + "text/csv", + "text/tsv", + "application/excel", + "application/zip", + "application/json" + ] + }, + "GenomeMap" : { "required" : [ - "attributeDbId", - "attributeName", - "methodDbId", - "methodName", - "scaleDbId", - "scaleName", - "traitName" + "commonCropName", + "mapDbId", + "mapName", + "type" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "attributeCategory" : { - "type" : "string" - }, - "attributeDescription" : { - "type" : "string" - }, - "attributeName" : { - "type" : "string" - }, - "attributePUI" : { - "type" : "string" - }, - "attributeValueDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } + "comments" : { + "type" : "string", + "description" : "Additional comments about a `GenomeMap`", + "nullable" : true }, "commonCropName" : { - "type" : "string" - }, - "defaultValue" : { - "type" : "string" + "type" : "string", + "description" : "The common name of the `Crop`" }, "documentationURL" : { - "type" : "string" - }, - "growthStage" : { - "type" : "string" - }, - "institution" : { - "type" : "string" - }, - "language" : { - "type" : "string" - }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" - }, - "ontologyReferenceDbId" : { - "type" : "string" + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true }, - "scaleDbId" : { - "type" : "string" + "linkageGroupCount" : { + "type" : "integer", + "description" : "The number of linkage groups present in a `GenomeMap`", + "format" : "int32", + "nullable" : true }, - "scaleName" : { - "type" : "string" + "mapDbId" : { + "type" : "string", + "description" : "The unique identifier for a `GenomeMap`" }, - "scalePUI" : { - "type" : "string" + "mapName" : { + "type" : "string", + "description" : "The human readable identifier for a `GenomeMap`" }, - "scientist" : { - "type" : "string" + "mapPUI" : { + "type" : "string", + "description" : "The DOI or other permanent identifier for a `GenomeMap`", + "nullable" : true }, - "status" : { - "type" : "string" + "markerCount" : { + "type" : "integer", + "description" : "The number of markers present in a `GenomeMap`", + "format" : "int32", + "nullable" : true }, - "submissionTimestamp" : { - "type" : "string" + "publishedDate" : { + "type" : "string", + "description" : "The date this `GenomeMap` was published", + "format" : "date-time", + "nullable" : true }, - "traitDbId" : { - "type" : "string" + "scientificName" : { + "type" : "string", + "description" : "Full scientific binomial format name. This includes Genus, Species, and Sub-species", + "nullable" : true }, - "traitName" : { - "type" : "string" + "type" : { + "type" : "string", + "description" : "The type of map this represents, usually \"Genetic\" or \"Physical\"" }, - "traitPUI" : { - "type" : "string" + "unit" : { + "type" : "string", + "description" : "The units used to describe the data in a `GenomeMap`", + "nullable" : true } }, - "description" : "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" + "description" : "The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map." }, - "GermplasmAttributeNewRequest" : { - "required" : [ - "attributeDbId", - "attributeName", - "methodDbId", - "methodName", - "scaleDbId", - "scaleName", - "traitName" - ], + "GenomeMapRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "attributeCategory" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "attributeDbId" : { - "type" : "string" + "mapDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a `GenomeMap`", + "items" : { + "type" : "string" + } }, - "attributeDescription" : { - "type" : "string" - }, - "attributeName" : { - "type" : "string" - }, - "attributePUI" : { - "type" : "string" - }, - "attributeValueDbIds" : { + "mapPUIs" : { "type" : "array", + "description" : "The DOI or other permanent identifier for a `GenomeMap`", "items" : { "type" : "string" } }, - "commonCropName" : { - "type" : "string" - }, - "defaultValue" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "growthStage" : { - "type" : "string" - }, - "institution" : { - "type" : "string" - }, - "language" : { - "type" : "string" - }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "ontologyReferenceDbId" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "scaleDbId" : { - "type" : "string" + "scientificName" : { + "type" : "array", + "description" : "Full scientific binomial format name. This includes Genus, Species, and Sub-species", + "items" : { + "type" : "string" + } }, - "scaleName" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "scalePUI" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "scientist" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "status" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } }, - "submissionTimestamp" : { - "type" : "string" + "types" : { + "type" : "array", + "description" : "The type of map, usually \"Genetic\" or \"Physical\"", + "items" : { + "type" : "string" + } + } + } + }, + "GenotypeMetadata" : { + "type" : "object", + "properties" : { + "dataType" : { + "type" : "string", + "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", + "nullable" : true, + "enum" : [ + "string", + "integer", + "float", + "boolean" + ] }, - "traitDbId" : { - "type" : "string" + "fieldAbbreviation" : { + "type" : "string", + "description" : "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard.", + "nullable" : true }, - "traitName" : { - "type" : "string" + "fieldName" : { + "type" : "string", + "description" : "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard.", + "nullable" : true }, - "traitPUI" : { - "type" : "string" + "fieldValue" : { + "type" : "string", + "description" : "The additional metadata value associated with this genotype call", + "nullable" : true } }, - "description" : "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" + "description" : "Genotype Metadata are additional layers of metadata associated with each genotype." }, - "GermplasmAttributeSearchRequest" : { + "GeoJSON" : { "type" : "object", - "properties" : { }, - "description" : "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" + "properties" : { + "geometry" : { + "$ref" : "#/components/schemas/GeoJSONGeometry" + }, + "type" : { + "type" : "string", + "description" : "The literal string \"Feature\"", + "example" : "Feature" + } + }, + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." }, - "GermplasmAttributeValue" : { + "GeoJSONGeometry" : { + "oneOf" : [ + { + "required" : [ + "coordinateDbIds", + "type" + ], + "type" : "object", + "properties" : { + "coordinates" : { + "type" : "array", + "description" : "A single position", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string", + "description" : "The literal string \"Point\"" + } + }, + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." + }, + { + "required" : [ + "coordinateDbIds", + "type" + ], + "type" : "object", + "properties" : { + "coordinates" : { + "type" : "array", + "description" : "An array of linear rings", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string", + "description" : "The literal string \"Polygon\"" + } + }, + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." + } + ] + }, + "GeoJSONPoint" : { "required" : [ - "attributeName", - "attributeValueDbId" + "coordinateDbIds", + "type" ], "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "attributeDbId" : { - "type" : "string" - }, - "attributeName" : { - "type" : "string" - }, - "attributePUI" : { - "type" : "string" - }, - "determinedDate" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" + "coordinates" : { + "type" : "array", + "description" : "A single position", + "items" : { + "type" : "number" + } }, - "value" : { - "type" : "string" + "type" : { + "type" : "string", + "description" : "The literal string \"Point\"" } }, - "description" : "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." }, - "GermplasmAttributeValueNewRequest" : { + "GeoJSONPolygon" : { "required" : [ - "attributeName", - "attributeValueDbId" + "coordinateDbIds", + "type" ], "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "coordinates" : { + "type" : "array", + "description" : "An array of linear rings", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } }, - "attributeDbId" : { - "type" : "string" + "type" : { + "type" : "string", + "description" : "The literal string \"Polygon\"" + } + }, + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." + }, + "GeoJSONSearchArea" : { + "type" : "object", + "properties" : { + "geometry" : { + "$ref" : "#/components/schemas/GeoJSONGeometry" }, - "attributeName" : { - "type" : "string" + "germplasmOrigin" : { + "$ref" : "#/components/schemas/GermplasmOrigin" }, - "attributePUI" : { + "imageDbId" : { "type" : "string" }, - "attributeValueDbId" : { + "imageName" : { "type" : "string" }, - "determinedDate" : { + "observationDbId" : { "type" : "string" }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" + "observationUnit" : { + "$ref" : "#/components/schemas/ObservationUnitPosition" }, - "value" : { - "type" : "string" + "type" : { + "type" : "string", + "description" : "The literal string \"Feature\"", + "example" : "Feature" } - }, - "description" : "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." - }, - "GermplasmAttributeValueSearchRequest" : { - "type" : "object", - "properties" : { }, - "description" : "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." + } }, - "GermplasmChild" : { - "required" : [ - "germplasmDbId", - "germplasmName", - "germplasmPUI", - "parentType" - ], - "type" : "object", - "properties" : { - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" + "Germplasm" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/GermplasmNewRequest" }, - "parentType" : { - "$ref" : "#/components/schemas/ParentType" + { + "required" : [ + "germplasmDbId" + ], + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below." + } + }, + "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." + } + ] + }, + "GermplasmAttribute" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/GermplasmAttributeNewRequest" }, - "pedigreeNodeDbId" : { - "type" : "string" + { + "type" : "object", + "properties" : { + "attributeDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies this attribute within the given database server" + } + }, + "description" : "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" } - }, - "description" : "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes." + ] }, - "GermplasmNewRequest" : { + "GermplasmAttributeNewRequest" : { "required" : [ - "commonCropName", - "germplasmDbId", - "germplasmDbId", - "germplasmName", - "germplasmPUI" + "attributeName", + "methodDbId", + "methodName", + "scaleDbId", + "scaleName", + "traitName" ], "type" : "object", "properties" : { - "accessionNumber" : { - "type" : "string" - }, - "acquisitionDate" : { - "type" : "string" - }, "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "biologicalStatusOfAccessionCode" : { + "attributeCategory" : { "type" : "string", - "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", - "enum" : [ - "100", - "110", - "120", - "130", - "200", - "300", - "400", - "410", - "411", - "412", - "413", - "414", - "415", - "416", - "420", - "421", - "422", - "423", - "500", - "600", - "999" - ] + "description" : "General category for the attribute. very similar to Trait class.", + "example" : "Morphological" }, - "biologicalStatusOfAccessionDescription" : { - "type" : "string" + "attributeDescription" : { + "type" : "string", + "description" : "A human readable description of this attribute", + "example" : "Height of the plant measured in meters by a tape" }, - "breedingMethodDbId" : { - "type" : "string" + "attributeName" : { + "type" : "string", + "description" : "A human readable name for this attribute", + "example" : "Plant Height 1" }, - "breedingMethodName" : { - "type" : "string" + "attributePUI" : { + "type" : "string", + "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", + "example" : "http://my-traits.com/trait/CO_123:0008012" }, - "collection" : { - "type" : "string" + "attributeValueDbIds" : { + "type" : "array", + "description" : "attributeValues", + "nullable" : true, + "items" : { + "type" : "string" + } }, "commonCropName" : { - "type" : "string" + "type" : "string", + "description" : "Crop name (examples: \"Maize\", \"Wheat\")", + "nullable" : true }, - "countryOfOriginCode" : { - "type" : "string" + "contextOfUse" : { + "type" : "array", + "description" : "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "defaultDisplayName" : { - "type" : "string" + "defaultValue" : { + "type" : "string", + "description" : "Variable default value. (examples: \"red\", \"2.3\", etc.)", + "nullable" : true }, "documentationURL" : { - "type" : "string" - }, - "genus" : { - "type" : "string" + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true }, - "germplasmDbId" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "germplasmName" : { - "type" : "string" + "growthStage" : { + "type" : "string", + "description" : "Growth stage at which measurement is made (examples: \"flowering\")", + "nullable" : true }, - "germplasmPUI" : { - "type" : "string" + "institution" : { + "type" : "string", + "description" : "Name of institution submitting the variable", + "nullable" : true }, - "germplasmPreprocessing" : { - "type" : "string" + "language" : { + "type" : "string", + "description" : "2 letter ISO 639-1 code for the language of submission of the variable.", + "nullable" : true }, - "instituteCode" : { + "methodDbId" : { "type" : "string" }, - "instituteName" : { + "methodName" : { "type" : "string" }, - "pedigree" : { + "methodPUI" : { "type" : "string" }, - "sampleDbIds" : { - "type" : "array", - "items" : { - "type" : "string" - } + "ontologyReference" : { + "$ref" : "#/components/schemas/OntologyReference" }, - "seedSource" : { + "scaleDbId" : { "type" : "string" }, - "seedSourceDescription" : { + "scaleName" : { "type" : "string" }, - "species" : { + "scalePUI" : { "type" : "string" }, - "speciesAuthority" : { - "type" : "string" + "scientist" : { + "type" : "string", + "description" : "Name of scientist submitting the variable.", + "nullable" : true }, - "subtaxa" : { - "type" : "string" + "status" : { + "type" : "string", + "description" : "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)", + "nullable" : true }, - "subtaxaAuthority" : { - "type" : "string" - } - }, - "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." - }, - "GermplasmOrigin" : { - "type" : "object", - "properties" : { - "coordinateUncertainty" : { - "type" : "string" + "submissionTimestamp" : { + "type" : "string", + "description" : "Timestamp when the Variable was added (ISO 8601)", + "format" : "date-time", + "nullable" : true }, - "germplasmDbId" : { + "synonyms" : { + "type" : "array", + "description" : "Other variable names", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "traitDbId" : { "type" : "string" }, - "germplasmName" : { + "traitName" : { "type" : "string" }, - "germplasmPUI" : { + "traitPUI" : { "type" : "string" } }, - "description" : "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm." + "description" : "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" }, - "GermplasmParent" : { - "required" : [ - "germplasmDbId", - "germplasmName", - "germplasmPUI", - "parentType" - ], + "GermplasmAttributeRequest" : { "type" : "object", "properties" : { - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" + "attributeCategories" : { + "type" : "array", + "description" : "General category for the attribute. very similar to Trait class.", + "items" : { + "type" : "string" + } }, - "germplasmPUI" : { - "type" : "string" + "attributeDbIds" : { + "type" : "array", + "description" : "List of Germplasm Attribute IDs to search for", + "items" : { + "type" : "string" + } }, - "parentType" : { - "$ref" : "#/components/schemas/ParentType" + "attributeNames" : { + "type" : "array", + "description" : "List of human readable Germplasm Attribute names to search for", + "items" : { + "type" : "string" + } }, - "pedigreeNodeDbId" : { - "type" : "string" - } - }, - "description" : "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes." - }, - "GermplasmSearchRequest" : { - "type" : "object", - "properties" : { }, - "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." - }, - "GrowthFacility" : { - "type" : "object", - "properties" : { - "PUI" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - } - }, - "description" : "Short description of the facility in which the study was carried out." - }, - "Image" : { - "required" : [ - "imageDbId" - ], - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "copyright" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "imageFileName" : { - "type" : "string" - }, - "imageFileSize" : { - "type" : "integer", - "format" : "int32" - }, - "imageHeight" : { - "type" : "integer", - "format" : "int32" + "attributePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", + "items" : { + "type" : "string" + } }, - "imageLocation" : { - "$ref" : "#/components/schemas/GeoJSON" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "imageName" : { - "type" : "string" + "dataTypes" : { + "type" : "array", + "description" : "List of scale data types to filter search results", + "items" : { + "$ref" : "#/components/schemas/TraitDataType" + } }, - "imageTimeStamp" : { - "type" : "string" + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "imageURL" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "imageWidth" : { - "type" : "integer", - "format" : "int32" + "methodDbIds" : { + "type" : "array", + "description" : "List of methods to filter search results", + "items" : { + "type" : "string" + } }, - "mimeType" : { - "type" : "string" + "methodNames" : { + "type" : "array", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "items" : { + "type" : "string" + } }, - "observationDbIds" : { + "methodPUIs" : { "type" : "array", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", "items" : { "type" : "string" } }, - "observationUnitDbId" : { - "type" : "string" + "ontologyDbIds" : { + "type" : "array", + "description" : "List of ontology IDs to search for", + "items" : { + "type" : "string" + } }, - "observationUnitName" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "observationUnitPUI" : { - "type" : "string" - } - }, - "description" : "The metadata for an image file that is connected to some phenotypic observation data." - }, - "ImageNewRequest" : { - "required" : [ - "imageDbId", - "imageDbId" - ], - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "copyright" : { - "type" : "string" + "scaleDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Scale", + "items" : { + "type" : "string" + } }, - "description" : { - "type" : "string" + "scaleNames" : { + "type" : "array", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "items" : { + "type" : "string" + } }, - "imageDbId" : { - "type" : "string" + "scalePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "items" : { + "type" : "string" + } }, - "imageFileName" : { - "type" : "string" + "studyDbId" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "items" : { + "type" : "string" + } }, - "imageFileSize" : { - "type" : "integer", - "format" : "int32" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "imageHeight" : { - "type" : "integer", - "format" : "int32" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "imageLocation" : { - "$ref" : "#/components/schemas/GeoJSON" + "traitAttributePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } }, - "imageName" : { - "type" : "string" + "traitAttributes" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } }, - "imageTimeStamp" : { - "type" : "string" + "traitClasses" : { + "type" : "array", + "description" : "List of trait classes to filter search results", + "items" : { + "type" : "string" + } }, - "imageURL" : { - "type" : "string" + "traitDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Trait", + "items" : { + "type" : "string" + } }, - "imageWidth" : { - "type" : "integer", - "format" : "int32" + "traitEntities" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "items" : { + "type" : "string" + } }, - "mimeType" : { - "type" : "string" + "traitEntityPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "items" : { + "type" : "string" + } }, - "observationDbIds" : { + "traitNames" : { "type" : "array", + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", "items" : { "type" : "string" } }, - "observationUnitDbId" : { - "type" : "string" + "traitPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "items" : { + "type" : "string" + } }, - "observationUnitName" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "observationUnitPUI" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } } - }, - "description" : "The metadata for an image file that is connected to some phenotypic observation data." + } }, - "ImageSearchRequest" : { + "GermplasmAttributeSearchRequest" : { "type" : "object", "properties" : { - "imageFileSizeMax" : { - "type" : "integer", - "format" : "int32" - }, - "imageFileSizeMin" : { + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "methodDbIds" : { + "type" : "array", + "description" : "List of methods to filter search results", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "attributeDbIds" : { + "type" : "array", + "description" : "List of Germplasm Attribute IDs to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + }, + "studyDbId" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "items" : { + "type" : "string" + } + }, + "dataTypes" : { + "type" : "array", + "description" : "List of scale data types to filter search results", + "items" : { + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "attributeNames" : { + "type" : "array", + "description" : "List of human readable Germplasm Attribute names to search for", + "items" : { + "type" : "string" + } + }, + "methodPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "scalePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "traitAttributes" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } + }, + "scaleDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Scale", + "items" : { + "type" : "string" + } + }, + "traitEntityPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "methodNames" : { + "type" : "array", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "items" : { + "type" : "string" + } + }, + "scaleNames" : { + "type" : "array", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "items" : { + "type" : "string" + } + }, + "traitPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "traitClasses" : { + "type" : "array", + "description" : "List of trait classes to filter search results", + "items" : { + "type" : "string" + } + }, + "attributeCategories" : { + "type" : "array", + "description" : "General category for the attribute. very similar to Trait class.", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "ontologyDbIds" : { + "type" : "array", + "description" : "List of ontology IDs to search for", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "traitDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Trait", + "items" : { + "type" : "string" + } + }, + "attributePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "traitNames" : { + "type" : "array", + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "items" : { + "type" : "string" + } + }, + "traitAttributePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } + }, + "traitEntities" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "items" : { + "type" : "string" + } + } + }, + "description" : "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" + }, + "GermplasmAttributeValue" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/GermplasmAttributeValueNewRequest" + }, + { + "type" : "object", + "properties" : { + "attributeValueDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies this attribute value within the given database server" + } + }, + "description" : "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." + } + ] + }, + "GermplasmAttributeValueNewRequest" : { + "required" : [ + "attributeName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "attributeDbId" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "determinedDate" : { + "type" : "string", + "description" : "The date the value of this attribute was determined for a given germplasm", + "format" : "date-time", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "value" : { + "type" : "string", + "description" : "The value of this attribute for a given germplasm", + "nullable" : true + } + }, + "description" : "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." + }, + "GermplasmAttributeValueRequest" : { + "type" : "object", + "properties" : { + "attributeDbIds" : { + "type" : "array", + "description" : "List of Germplasm Attribute IDs to search for", + "items" : { + "type" : "string" + } + }, + "attributeNames" : { + "type" : "array", + "description" : "List of human readable Germplasm Attribute names to search for", + "items" : { + "type" : "string" + } + }, + "attributeValueDbIds" : { + "type" : "array", + "description" : "List of Germplasm Attribute Value IDs to search for", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "dataTypes" : { + "type" : "array", + "description" : "List of scale data types to filter search results", + "items" : { + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "methodDbIds" : { + "type" : "array", + "description" : "List of methods to filter search results", + "items" : { + "type" : "string" + } + }, + "ontologyDbIds" : { + "type" : "array", + "description" : "List of ontology IDs to search for", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "scaleDbIds" : { + "type" : "array", + "description" : "List of scales to filter search results", + "items" : { + "type" : "string" + } + }, + "traitClasses" : { + "type" : "array", + "description" : "List of trait classes to filter search results", + "items" : { + "type" : "string" + } + }, + "traitDbIds" : { + "type" : "array", + "description" : "List of trait unique ID to filter search results", + "items" : { + "type" : "string" + } + } + } + }, + "GermplasmAttributeValueSearchRequest" : { + "type" : "object", + "properties" : { + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "methodDbIds" : { + "type" : "array", + "description" : "List of methods to filter search results", + "items" : { + "type" : "string" + } + }, + "traitClasses" : { + "type" : "array", + "description" : "List of trait classes to filter search results", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "attributeValueDbIds" : { + "type" : "array", + "description" : "List of Germplasm Attribute Value IDs to search for", + "items" : { + "type" : "string" + } + }, + "attributeDbIds" : { + "type" : "array", + "description" : "List of Germplasm Attribute IDs to search for", + "items" : { + "type" : "string" + } + }, + "ontologyDbIds" : { + "type" : "array", + "description" : "List of ontology IDs to search for", + "items" : { + "type" : "string" + } + }, + "dataTypes" : { + "type" : "array", + "description" : "List of scale data types to filter search results", + "items" : { + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "attributeNames" : { + "type" : "array", + "description" : "List of human readable Germplasm Attribute names to search for", + "items" : { + "type" : "string" + } + }, + "traitDbIds" : { + "type" : "array", + "description" : "List of trait unique ID to filter search results", + "items" : { + "type" : "string" + } + }, + "scaleDbIds" : { + "type" : "array", + "description" : "List of scales to filter search results", + "items" : { + "type" : "string" + } + } + }, + "description" : "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit." + }, + "GermplasmChild" : { + "required" : [ + "germplasmDbId", + "germplasmName", + "germplasmPUI", + "parentType" + ], + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "parentType" : { + "$ref" : "#/components/schemas/ParentType" + }, + "pedigreeNodeDbId" : { + "type" : "string" + } + }, + "description" : "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes." + }, + "GermplasmMCPD" : { + "required" : [ + "commonCropName", + "germplasmDbId", + "germplasmName", + "germplasmPUI" + ], + "type" : "object", + "properties" : { + "accessionNames" : { + "type" : "array", + "description" : "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered names or other designations given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase.", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "accessionNumber" : { + "type" : "string", + "description" : "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "nullable" : true, + "example" : "A0000003" + }, + "acquisitionDate" : { + "type" : "string", + "description" : "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "format" : "date", + "nullable" : true + }, + "acquisitionSourceCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)", + "nullable" : true, + "example" : "26", + "enum" : [ + "10", + "11", + "12", + "13", + "14", + "15", + "20", + "21", + "22", + "23", + "24", + "25", + "26", + "27", + "28", + "30", + "40", + "50", + "60", + "61", + "62", + "99" + ] + }, + "alternateIDs" : { + "type" : "array", + "description" : "MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. ", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "ancestralData" : { + "type" : "string", + "description" : "MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", + "nullable" : true, + "example" : "A0000001/A0000002" + }, + "biologicalStatusOfAccessionCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "nullable" : true, + "example" : "421", + "enum" : [ + "100", + "110", + "120", + "130", + "200", + "300", + "400", + "410", + "411", + "412", + "413", + "414", + "415", + "416", + "420", + "421", + "422", + "423", + "500", + "600", + "999" + ] + }, + "breedingInstitutes" : { + "type" : "array", + "description" : "A list of institutes that were involved with breeding a material/germplasm\n
MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard.\n
MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Institute" + } + }, + "collectingInfo" : { + "type" : "object", + "properties" : { + "collectingDate" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "format" : "date", + "nullable" : true + }, + "collectingInstitutes" : { + "type" : "array", + "description" : "Institutes which collected the sample", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Institute" + } + }, + "collectingMissionIdentifier" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\").", + "nullable" : true, + "example" : "CIATFOR_052" + }, + "collectingNumber" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections.", + "nullable" : true, + "example" : "ab109909" + }, + "collectingSite" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string", + "description" : "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown.", + "nullable" : true, + "example" : "20" + }, + "elevation" : { + "type" : "string", + "description" : "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed.", + "nullable" : true, + "example" : "35" + }, + "georeferencingMethod" : { + "type" : "string", + "description" : "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known.", + "nullable" : true, + "example" : "WGS84" + }, + "latitudeDecimal" : { + "type" : "string", + "description" : "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975).", + "nullable" : true, + "example" : "+42.445295" + }, + "latitudeDegrees" : { + "type" : "string", + "description" : "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10", + "nullable" : true, + "example" : "42 26 43.1 N" + }, + "locationDescription" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville).", + "nullable" : true, + "example" : "South east hill near institute buildings" + }, + "longitudeDecimal" : { + "type" : "string", + "description" : "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123).", + "nullable" : true, + "example" : "-076.471934" + }, + "longitudeDegrees" : { + "type" : "string", + "description" : "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076", + "nullable" : true, + "example" : "76 28 19.0 W" + }, + "spatialReferenceSystem" : { + "type" : "string", + "description" : "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum.", + "nullable" : true, + "example" : "WGS84" + } + }, + "description" : "Information about the location where the sample was collected", + "nullable" : true + } + }, + "description" : "Information about the collection of a germplasm" + }, + "commonCropName" : { + "type" : "string", + "description" : "MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\". ", + "nullable" : true, + "example" : "malting barley" + }, + "countryOfOrigin" : { + "type" : "string", + "description" : "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers\" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", + "nullable" : true, + "example" : "Peru" + }, + "donorInfo" : { + "type" : "object", + "properties" : { + "donorAccessionNumber" : { + "type" : "string", + "description" : "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", + "nullable" : true, + "example" : "A0090204" + }, + "donorAccessionPui" : { + "type" : "string", + "description" : "PUI (DOI mostly) of the accession in the donor system.", + "nullable" : true, + "example" : "http://pui.per/accession/A0010025" + }, + "donorInstitute" : { + "$ref" : "#/components/schemas/Institute" + } + }, + "description" : "Information about an accession donor" + }, + "genus" : { + "type" : "string", + "description" : "MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.", + "nullable" : true, + "example" : "Aspergillus" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "instituteCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "nullable" : true, + "example" : "PER001" + }, + "mlsStatus" : { + "type" : "string", + "description" : "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")", + "nullable" : true, + "example" : "0", + "enum" : [ + "", + "0", + "1", + "99" + ] + }, + "remarks" : { + "type" : "string", + "description" : "MCPD (v2.1) (REMARKS) 28. The remarks field is used to add notes or to elaborate on descriptors with value 99 or 999 (= Other). Prefix remarks with the field name they refer to and a colon (:) without space (e.g. COLLSRC:riverside). Distinct remarks referring to different fields are separated by semi-colons without space.", + "nullable" : true, + "example" : "This is an example remark to demonstrate that any notable information can be put here" + }, + "safetyDuplicateInstitutes" : { + "type" : "array", + "description" : "safetyDuplicateInstitutes: SafetyDuplicateInstitutes", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Institute" + } + }, + "species" : { + "type" : "string", + "description" : "MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" ", + "nullable" : true, + "example" : "fructus" + }, + "speciesAuthority" : { + "type" : "string", + "description" : "MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", + "nullable" : true, + "example" : "Smith, 1822" + }, + "storageTypeCodes" : { + "type" : "array", + "description" : "MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) 10) Seed collection 11) Short term 12) Medium term 13) Long term 20) Field collection 30) In vitro collection 40) Cryo-preserved collection 50) DNA collection 99) Other (elaborate in REMARKS field)", + "nullable" : true, + "items" : { + "type" : "string", + "enum" : [ + "10", + "11", + "12", + "13", + "20", + "30", + "40", + "50", + "99" + ] + } + }, + "subtaxon" : { + "type" : "string", + "description" : "MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").", + "nullable" : true, + "example" : "Aspergillus fructus A" + }, + "subtaxonAuthority" : { + "type" : "string", + "description" : "MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", + "nullable" : true, + "example" : "Smith, 1822" + } + }, + "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." + }, + "GermplasmNewRequest" : { + "required" : [ + "commonCropName", + "germplasmName", + "germplasmPUI" + ], + "type" : "object", + "properties" : { + "accessionNumber" : { + "type" : "string", + "description" : "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "nullable" : true + }, + "acquisitionDate" : { + "type" : "string", + "description" : "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "nullable" : true + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "biologicalStatusOfAccessionCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "nullable" : true, + "enum" : [ + "100", + "110", + "120", + "130", + "200", + "300", + "400", + "410", + "411", + "412", + "413", + "414", + "415", + "416", + "420", + "421", + "422", + "423", + "500", + "600", + "999" + ] + }, + "biologicalStatusOfAccessionDescription" : { + "type" : "string", + "description" : "Supplemental text description for 'biologicalStatusOfAccessionCode'", + "nullable" : true + }, + "breedingMethodDbId" : { + "type" : "string" + }, + "breedingMethodName" : { + "type" : "string" + }, + "collection" : { + "type" : "string", + "description" : "A specific panel/collection/population name this germplasm belongs to.", + "nullable" : true + }, + "commonCropName" : { + "type" : "string", + "description" : "Common name for the crop \n\nMCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\"." + }, + "countryOfOriginCode" : { + "type" : "string", + "description" : "3-letter ISO 3166-1 code of the country in which the sample was originally collected \n\nMCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", + "nullable" : true + }, + "defaultDisplayName" : { + "type" : "string", + "description" : "Human readable name used for display purposes", + "nullable" : true + }, + "documentationURL" : { + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true + }, + "donors" : { + "type" : "array", + "description" : "List of donor institutes", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Donor" + } + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "genus" : { + "type" : "string", + "description" : "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature.", + "nullable" : true + }, + "germplasmName" : { + "type" : "string", + "description" : "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space." + }, + "germplasmOrigin" : { + "type" : "array", + "description" : "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/GermplasmOrigin" + } + }, + "germplasmPUI" : { + "type" : "string", + "description" : "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties." + }, + "germplasmPreprocessing" : { + "type" : "string", + "description" : "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary.", + "nullable" : true + }, + "instituteCode" : { + "type" : "string", + "description" : "The code for the institute that maintains the material. \n\nMCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "nullable" : true + }, + "instituteName" : { + "type" : "string", + "description" : "The name of the institute that maintains the material", + "nullable" : true + }, + "pedigree" : { + "type" : "string", + "description" : "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", + "nullable" : true + }, + "sampleDbIds" : { + "type" : "array", + "description" : "samples", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "seedSource" : { + "type" : "string", + "description" : "An identifier for the source of the biological material\n
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: \"mother_accession X father_accession\", or, if father is unknown, as \"mother_accession X UNKNOWN\". For in situ material, the region of provenance may be used when an accession is not available.", + "nullable" : true + }, + "seedSourceDescription" : { + "type" : "string", + "description" : "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source", + "nullable" : true + }, + "species" : { + "type" : "string", + "description" : "Specific epithet portion of the scientific name in lowercase letters.\n\nMCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" \n\nMIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature.", + "nullable" : true + }, + "speciesAuthority" : { + "type" : "string", + "description" : "The authority organization responsible for tracking and maintaining the species name \n\nMCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", + "nullable" : true + }, + "storageTypes" : { + "type" : "array", + "description" : "The type of storage this germplasm is kept in at a genebank.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/StorageType" + } + }, + "subtaxa" : { + "type" : "string", + "description" : "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group).", + "nullable" : true + }, + "subtaxaAuthority" : { + "type" : "string", + "description" : "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", + "nullable" : true + }, + "synonyms" : { + "type" : "array", + "description" : "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Synonym" + } + }, + "taxonIds" : { + "type" : "array", + "description" : "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species.\n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/TaxonId" + } + } + }, + "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." + }, + "GermplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string", + "description" : "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.", + "nullable" : true + }, + "coordinates" : { + "type" : "array", + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + }, + "description" : "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm." + }, + "GermplasmParameters" : { + "type" : "object", + "properties" : { + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + } + } + }, + "GermplasmParent" : { + "required" : [ + "germplasmDbId", + "germplasmName", + "germplasmPUI", + "parentType" + ], + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "parentType" : { + "$ref" : "#/components/schemas/ParentType" + }, + "pedigreeNodeDbId" : { + "type" : "string" + } + }, + "description" : "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes." + }, + "GermplasmRequest" : { + "type" : "object", + "properties" : { + "accessionNumbers" : { + "type" : "array", + "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "items" : { + "type" : "string" + } + }, + "binomialNames" : { + "type" : "array", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "items" : { + "type" : "string" + } + }, + "collections" : { + "type" : "array", + "description" : "A specific panel/collection/population name this germplasm belongs to.", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "familyCodes" : { + "type" : "array", + "description" : "A familyCode representing the family this germplasm belongs to.", + "items" : { + "type" : "string" + } + }, + "genus" : { + "type" : "array", + "description" : "List of Genus names to identify germplasm", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmPUIs" : { + "type" : "array", + "description" : "List of Permanent Unique Identifiers to identify germplasm", + "items" : { + "type" : "string" + } + }, + "instituteCodes" : { + "type" : "array", + "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "items" : { + "type" : "string" + } + }, + "parentDbIds" : { + "type" : "array", + "description" : "Search for Germplasm with these parents", + "items" : { + "type" : "string" + } + }, + "progenyDbIds" : { + "type" : "array", + "description" : "Search for Germplasm with these children", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "species" : { + "type" : "array", + "description" : "List of Species names to identify germplasm", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "synonyms" : { + "type" : "array", + "description" : "List of alternative names or IDs used to reference this germplasm", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + } + } + }, + "GermplasmSearchRequest" : { + "type" : "object", + "properties" : { + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "accessionNumbers" : { + "type" : "array", + "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "synonyms" : { + "type" : "array", + "description" : "List of alternative names or IDs used to reference this germplasm", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "germplasmPUIs" : { + "type" : "array", + "description" : "List of Permanent Unique Identifiers to identify germplasm", + "items" : { + "type" : "string" + } + }, + "parentDbIds" : { + "type" : "array", + "description" : "Search for Germplasm with these parents", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + }, + "familyCodes" : { + "type" : "array", + "description" : "A familyCode representing the family this germplasm belongs to.", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "collections" : { + "type" : "array", + "description" : "A specific panel/collection/population name this germplasm belongs to.", + "items" : { + "type" : "string" + } + }, + "genus" : { + "type" : "array", + "description" : "List of Genus names to identify germplasm", + "items" : { + "type" : "string" + } + }, + "species" : { + "type" : "array", + "description" : "List of Species names to identify germplasm", + "items" : { + "type" : "string" + } + }, + "binomialNames" : { + "type" : "array", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "items" : { + "type" : "string" + } + }, + "instituteCodes" : { + "type" : "array", + "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "items" : { + "type" : "string" + } + }, + "progenyDbIds" : { + "type" : "array", + "description" : "Search for Germplasm with these children", + "items" : { + "type" : "string" + } + } + }, + "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." + }, + "GrowthFacility" : { + "type" : "object", + "properties" : { + "PUI" : { + "type" : "string", + "description" : "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology.", + "nullable" : true + }, + "description" : { + "type" : "string", + "description" : "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out.", + "nullable" : true + } + }, + "description" : "Short description of the facility in which the study was carried out." + }, + "Image" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/ImageNewRequest" + }, + { + "required" : [ + "imageDbId" + ], + "type" : "object", + "properties" : { + "imageDbId" : { + "type" : "string", + "description" : "The unique identifier of an image" + } + }, + "description" : "The metadata for an image file that is connected to some phenotypic observation data." + } + ] + }, + "ImageNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "copyright" : { + "type" : "string", + "description" : "The copyright information of this image. Example 'Copyright 2018 Bob Robertson'", + "nullable" : true + }, + "description" : { + "type" : "string", + "description" : "The human readable description of an image.", + "nullable" : true + }, + "descriptiveOntologyTerms" : { + "type" : "array", + "description" : "A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "imageContent" : { + "type" : "string", + "description" : "The content of the image", + "format" : "binary" + }, + "imageFileName" : { + "type" : "string", + "description" : "The name of the image file. Might be the same as 'imageName', but could be different.", + "nullable" : true + }, + "imageFileSize" : { + "type" : "integer", + "description" : "The size of the image in Bytes.", + "format" : "int32", + "nullable" : true + }, + "imageHeight" : { + "type" : "integer", + "description" : "The height of the image in Pixels.", + "format" : "int32", + "nullable" : true + }, + "imageLocation" : { + "$ref" : "#/components/schemas/GeoJSON" + }, + "imageName" : { + "type" : "string", + "description" : "The human readable name of an image. Might be the same as 'imageFileName', but could be different.", + "nullable" : true + }, + "imageTimeStamp" : { + "type" : "string", + "description" : "The date and time the image was taken", + "format" : "date-time", + "nullable" : true + }, + "imageURL" : { + "type" : "string", + "description" : "The complete, absolute URI path to the image file. Images might be stored on a different host or path than the BrAPI web server.", + "nullable" : true + }, + "imageWidth" : { + "type" : "integer", + "description" : "The width of the image in Pixels.", + "format" : "int32", + "nullable" : true + }, + "mimeType" : { + "type" : "string", + "description" : "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc", + "nullable" : true + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + } + }, + "description" : "The metadata for an image file that is connected to some phenotypic observation data." + }, + "ImageRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "descriptiveOntologyTerms" : { + "type" : "array", + "description" : "A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", + "items" : { + "type" : "string" + } + }, + "imageDbIds" : { + "type" : "array", + "description" : "A list of image Ids to search for", + "items" : { + "type" : "string" + } + }, + "imageFileNames" : { + "type" : "array", + "description" : "Image file names to search for.", + "items" : { + "type" : "string" + } + }, + "imageFileSizeMax" : { + "type" : "integer", + "description" : "A maximum image file size to search for.", + "format" : "int32", + "example" : 20000000 + }, + "imageFileSizeMin" : { + "type" : "integer", + "description" : "A minimum image file size to search for.", + "format" : "int32", + "example" : 1000 + }, + "imageHeightMax" : { + "type" : "integer", + "description" : "A maximum image height to search for.", + "format" : "int32", + "example" : 1080 + }, + "imageHeightMin" : { + "type" : "integer", + "description" : "A minimum image height to search for.", + "format" : "int32", + "example" : 720 + }, + "imageLocation" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + }, + "imageNames" : { + "type" : "array", + "description" : "Human readable names to search for.", + "items" : { + "type" : "string" + } + }, + "imageTimeStampRangeEnd" : { + "type" : "string", + "description" : "The latest timestamp to search for.", + "format" : "date-time" + }, + "imageTimeStampRangeStart" : { + "type" : "string", + "description" : "The earliest timestamp to search for.", + "format" : "date-time" + }, + "imageWidthMax" : { + "type" : "integer", + "description" : "A maximum image width to search for.", + "format" : "int32", + "example" : 1920 + }, + "imageWidthMin" : { + "type" : "integer", + "description" : "A minimum image width to search for.", + "format" : "int32", + "example" : 1280 + }, + "mimeTypes" : { + "type" : "array", + "description" : "A set of image file types to search for.", + "items" : { + "type" : "string" + } + }, + "observationDbIds" : { + "type" : "array", + "description" : "A list of observation Ids this image is associated with to search for", + "items" : { + "type" : "string" + } + }, + "observationUnitDbIds" : { + "type" : "array", + "description" : "A set of observation unit identifiers to search for.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + } + } + }, + "ImageSearchRequest" : { + "type" : "object", + "properties" : { + "imageFileSizeMax" : { + "type" : "integer", + "description" : "A maximum image file size to search for.", + "format" : "int32", + "example" : 20000000 + }, + "imageFileNames" : { + "type" : "array", + "description" : "Image file names to search for.", + "items" : { + "type" : "string" + } + }, + "imageTimeStampRangeStart" : { + "type" : "string", + "description" : "The earliest timestamp to search for.", + "format" : "date-time" + }, + "imageDbIds" : { + "type" : "array", + "description" : "A list of image Ids to search for", + "items" : { + "type" : "string" + } + }, + "observationUnitDbIds" : { + "type" : "array", + "description" : "A set of observation unit identifiers to search for.", + "items" : { + "type" : "string" + } + }, + "imageNames" : { + "type" : "array", + "description" : "Human readable names to search for.", + "items" : { + "type" : "string" + } + }, + "imageWidthMin" : { + "type" : "integer", + "description" : "A minimum image width to search for.", + "format" : "int32", + "example" : 1280 + }, + "imageHeightMax" : { + "type" : "integer", + "description" : "A maximum image height to search for.", + "format" : "int32", + "example" : 1080 + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "descriptiveOntologyTerms" : { + "type" : "array", + "description" : "A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", + "items" : { + "type" : "string" + } + }, + "imageLocation" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + }, + "imageTimeStampRangeEnd" : { + "type" : "string", + "description" : "The latest timestamp to search for.", + "format" : "date-time" + }, + "mimeTypes" : { + "type" : "array", + "description" : "A set of image file types to search for.", + "items" : { + "type" : "string" + } + }, + "observationDbIds" : { + "type" : "array", + "description" : "A list of observation Ids this image is associated with to search for", + "items" : { + "type" : "string" + } + }, + "imageHeightMin" : { + "type" : "integer", + "description" : "A minimum image height to search for.", + "format" : "int32", + "example" : 720 + }, + "imageFileSizeMin" : { + "type" : "integer", + "description" : "A minimum image file size to search for.", + "format" : "int32", + "example" : 1000 + }, + "imageWidthMax" : { + "type" : "integer", + "description" : "A maximum image width to search for.", + "format" : "int32", + "example" : 1920 + } + }, + "description" : "The metadata for an image file that is connected to some phenotypic observation data." + }, + "Institute" : { + "type" : "object", + "properties" : { + "instituteAddress" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "nullable" : true, + "example" : "123 Main Street, Lima, Peru, 5555" + }, + "instituteCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space.", + "nullable" : true, + "example" : "PER001" + }, + "instituteName" : { + "type" : "string", + "description" : "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "nullable" : true, + "example" : "The BrAPI Institute" + } + }, + "description" : "The details of an Institute or other simular entity." + }, + "LastUpdate" : { + "required" : [ + "lastUpdateDbId" + ], + "type" : "object", + "properties" : { + "lastUpdateDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a LastUpdate within the given database server" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "timestamp" : { + "type" : "string", + "description" : "The timestamp of the update.", + "format" : "date-time", + "nullable" : true + }, + "version" : { + "type" : "string", + "description" : "The version of the update.", + "nullable" : true + } + }, + "description" : "The date and time when this study was last modified" + }, + "LinkageGroup" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "linkageGroupName" : { + "type" : "string", + "description" : "The Uniquely Identifiable name of a `LinkageGroup`
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable.", + "nullable" : true, + "example" : "Chromosome 3" + }, + "markerCount" : { + "type" : "integer", + "description" : "The number of markers associated with a `LinkageGroup`.", + "format" : "int32", + "nullable" : true, + "example" : 150 + }, + "maxPosition" : { + "type" : "integer", + "description" : "The maximum position of a marker within a `LinkageGroup`.", + "format" : "int32", + "nullable" : true, + "example" : 2500 + } + }, + "description" : "a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group." + }, + "List" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/ListNewRequest" + }, + { + "required" : [ + "listDbId" + ], + "type" : "object", + "properties" : { + "listDbId" : { + "type" : "string", + "description" : "The unique identifier for a List" + } + }, + "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." + } + ] + }, + "ListNewRequest" : { + "required" : [ + "listName", + "listType" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "data" : { + "type" : "array", + "description" : "The array of DbIds of the BrAPI objects contained in a List", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "dateCreated" : { + "type" : "string", + "description" : "Timestamp when the entity was first created", + "format" : "date-time", + "nullable" : true + }, + "dateModified" : { + "type" : "string", + "description" : "Timestamp when the entity was last updated", + "format" : "date-time", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "listDescription" : { + "type" : "string", + "description" : "Description of a List", + "nullable" : true + }, + "listName" : { + "type" : "string", + "description" : "Human readable name of a List" + }, + "listOwnerName" : { + "type" : "string", + "description" : "Human readable name of a List Owner. (usually a user or person)", + "nullable" : true + }, + "listSize" : { + "type" : "integer", + "description" : "The number of elements in a List", + "format" : "int32", + "nullable" : true + }, + "listSource" : { + "type" : "string", + "description" : "The description of where a List originated from", + "nullable" : true + }, + "listType" : { + "$ref" : "#/components/schemas/ListType" + }, + "personDbId" : { + "type" : "string" + } + }, + "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." + }, + "ListRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "dateCreatedRangeEnd" : { + "type" : "string", + "description" : "Define the end for an interval of time and only include Lists that are created within this interval.", + "format" : "date-time" + }, + "dateCreatedRangeStart" : { + "type" : "string", + "description" : "Define the beginning for an interval of time and only include Lists that are created within this interval.", + "format" : "date-time" + }, + "dateModifiedRangeEnd" : { + "type" : "string", + "description" : "Define the end for an interval of time and only include Lists that are modified within this interval.", + "format" : "date-time" + }, + "dateModifiedRangeStart" : { + "type" : "string", + "description" : "Define the beginning for an interval of time and only include Lists that are modified within this interval.", + "format" : "date-time" + }, + "listDbIds" : { + "type" : "array", + "description" : "An array of primary database identifiers to identify a set of Lists", + "items" : { + "type" : "string" + } + }, + "listNames" : { + "type" : "array", + "description" : "An array of human readable names to identify a set of Lists", + "items" : { + "type" : "string" + } + }, + "listOwnerNames" : { + "type" : "array", + "description" : "An array of names for the people or entities who are responsible for a set of Lists", + "items" : { + "type" : "string" + } + }, + "listOwnerPersonDbIds" : { + "type" : "array", + "description" : "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", + "items" : { + "type" : "string" + } + }, + "listSources" : { + "type" : "array", + "description" : "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", + "items" : { + "type" : "string" + } + }, + "listType" : { + "$ref" : "#/components/schemas/ListType" + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + } + } + }, + "ListSearchRequest" : { + "type" : "object", + "properties" : { + "dateCreatedRangeStart" : { + "type" : "string", + "description" : "Define the beginning for an interval of time and only include Lists that are created within this interval.", + "format" : "date-time" + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "dateModifiedRangeEnd" : { + "type" : "string", + "description" : "Define the end for an interval of time and only include Lists that are modified within this interval.", + "format" : "date-time" + }, + "listSources" : { + "type" : "array", + "description" : "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", + "items" : { + "type" : "string" + } + }, + "listType" : { + "$ref" : "#/components/schemas/ListType" + }, + "dateCreatedRangeEnd" : { + "type" : "string", + "description" : "Define the end for an interval of time and only include Lists that are created within this interval.", + "format" : "date-time" + }, + "listDbIds" : { + "type" : "array", + "description" : "An array of primary database identifiers to identify a set of Lists", + "items" : { + "type" : "string" + } + }, + "listNames" : { + "type" : "array", + "description" : "An array of human readable names to identify a set of Lists", + "items" : { + "type" : "string" + } + }, + "listOwnerPersonDbIds" : { + "type" : "array", + "description" : "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", + "items" : { + "type" : "string" + } + }, + "dateModifiedRangeStart" : { + "type" : "string", + "description" : "Define the beginning for an interval of time and only include Lists that are modified within this interval.", + "format" : "date-time" + }, + "listOwnerNames" : { + "type" : "array", + "description" : "An array of names for the people or entities who are responsible for a set of Lists", + "items" : { + "type" : "string" + } + } + }, + "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." + }, + "ListType" : { + "type" : "string", + "description" : "The type of objects that are referenced in a List", + "enum" : [ + "germplasm", + "markers", + "variants", + "programs", + "trials", + "studies", + "observationUnits", + "observations", + "observationVariables", + "samples" + ] + }, + "Location" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/LocationNewRequest" + }, + { + "required" : [ + "locationDbId" + ], + "type" : "object", + "properties" : { + "locationDbId" : { + "type" : "string", + "description" : "The unique identifier for a Location" + } + }, + "description" : "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." + } + ] + }, + "LocationNewRequest" : { + "required" : [ + "locationName" + ], + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string", + "description" : "A shortened version of the human readable name for a Location", + "nullable" : true + }, + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "childLocationDbIds" : { + "type" : "array", + "description" : "The child locations that belong to this Location. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "coordinateDescription" : { + "type" : "string", + "description" : "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)", + "nullable" : true + }, + "coordinateUncertainty" : { + "type" : "string", + "description" : "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.", + "nullable" : true + }, + "coordinates" : { + "$ref" : "#/components/schemas/GeoJSON" + }, + "countryCode" : { + "type" : "string", + "description" : "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec\n
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.'", + "nullable" : true + }, + "countryName" : { + "type" : "string", + "description" : "The full name of the country where a Location is located\n
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.", + "nullable" : true + }, + "documentationURL" : { + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true + }, + "environmentType" : { + "type" : "string", + "description" : "Describes the general type of environment of a Location. (ex. forest, field, nursery, etc)", + "nullable" : true + }, + "exposure" : { + "type" : "string", + "description" : "Describes the level of protection/exposure for things like sun light and wind at a particular Location", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "instituteAddress" : { + "type" : "string", + "description" : "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.", + "nullable" : true + }, + "instituteName" : { + "type" : "string", + "description" : "The full name of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.", + "nullable" : true + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "locationType" : { + "type" : "string", + "description" : "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)", + "nullable" : true + }, + "siteStatus" : { + "type" : "string", + "description" : "Description of the accessibility of the location (ex. Public, Private)", + "nullable" : true + }, + "slope" : { + "type" : "string", + "description" : "Describes the approximate slope (height/distance) of a Location.", + "nullable" : true + }, + "topography" : { + "type" : "string", + "description" : "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)", + "nullable" : true + } + }, + "description" : "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." + }, + "LocationParameters" : { + "type" : "object", + "properties" : { + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } + } + } + }, + "LocationRequest" : { + "type" : "object", + "properties" : { + "abbreviations" : { + "type" : "array", + "description" : "A list of shortened human readable names for a set of Locations", + "items" : { + "type" : "string" + } + }, + "altitudeMax" : { + "type" : "number", + "description" : "The maximum altitude to search for", + "example" : 200 + }, + "altitudeMin" : { + "type" : "number", + "description" : "The minimum altitude to search for", + "example" : 20 + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "coordinates" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + }, + "countryCodes" : { + "type" : "array", + "description" : "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec", + "items" : { + "type" : "string" + } + }, + "countryNames" : { + "type" : "array", + "description" : "The full name of the country to search for", + "items" : { + "type" : "string" + } + }, + "instituteAddresses" : { + "type" : "array", + "description" : "The street address of the institute to search for", + "items" : { + "type" : "string" + } + }, + "instituteNames" : { + "type" : "array", + "description" : "The name of the institute to search for", + "items" : { + "type" : "string" + } + }, + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } + }, + "locationTypes" : { + "type" : "array", + "description" : "The type of location this represents (ex. Breeding Location, Storage Location, etc)", + "items" : { + "type" : "string" + } + }, + "parentLocationDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "items" : { + "type" : "string" + } + }, + "parentLocationNames" : { + "type" : "array", + "description" : "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + } + } + }, + "LocationSearchRequest" : { + "type" : "object", + "properties" : { + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } + }, + "countryNames" : { + "type" : "array", + "description" : "The full name of the country to search for", + "items" : { + "type" : "string" + } + }, + "coordinates" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "altitudeMax" : { + "type" : "number", + "description" : "The maximum altitude to search for", + "example" : 200 + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "instituteNames" : { + "type" : "array", + "description" : "The name of the institute to search for", + "items" : { + "type" : "string" + } + }, + "countryCodes" : { + "type" : "array", + "description" : "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec", + "items" : { + "type" : "string" + } + }, + "parentLocationNames" : { + "type" : "array", + "description" : "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "items" : { + "type" : "string" + } + }, + "locationTypes" : { + "type" : "array", + "description" : "The type of location this represents (ex. Breeding Location, Storage Location, etc)", + "items" : { + "type" : "string" + } + }, + "parentLocationDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "items" : { + "type" : "string" + } + }, + "instituteAddresses" : { + "type" : "array", + "description" : "The street address of the institute to search for", + "items" : { + "type" : "string" + } + }, + "altitudeMin" : { + "type" : "number", + "description" : "The minimum altitude to search for", + "example" : 20 + }, + "abbreviations" : { + "type" : "array", + "description" : "A list of shortened human readable names for a set of Locations", + "items" : { + "type" : "string" + } + } + }, + "description" : "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." + }, + "MarkerPosition" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "linkageGroupName" : { + "type" : "string", + "description" : "The Uniquely Identifiable name of a `LinkageGroup`\n
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable.", + "nullable" : true + }, + "mapDbId" : { + "type" : "string" + }, + "mapName" : { + "type" : "string" + }, + "mapPUI" : { + "type" : "string" + }, + "position" : { + "type" : "integer", + "description" : "The position of a marker or variant within a `LinkageGroup`", + "format" : "int32", + "nullable" : true + }, + "variantDbId" : { + "type" : "string" + } + }, + "description" : "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." + }, + "MarkerPositionRequest" : { + "type" : "object", + "properties" : { + "linkageGroupNames" : { + "type" : "array", + "description" : "A list of Uniquely Identifiable linkage group names", + "items" : { + "type" : "string" + } + }, + "mapDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `GenomeMaps` within the given database server", + "items" : { + "type" : "string" + } + }, + "maxPosition" : { + "type" : "integer", + "description" : "The maximum position of markers in a given map", + "format" : "int32", + "example" : 4000 + }, + "minPosition" : { + "type" : "integer", + "description" : "The minimum position of markers in a given map", + "format" : "int32", + "example" : 250 + }, + "variantDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "items" : { + "type" : "string" + } + } + } + }, + "MarkerPositionSearchRequest" : { + "type" : "object", + "properties" : { + "linkageGroupNames" : { + "type" : "array", + "description" : "A list of Uniquely Identifiable linkage group names", + "items" : { + "type" : "string" + } + }, + "variantDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "items" : { + "type" : "string" + } + }, + "mapDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `GenomeMaps` within the given database server", + "items" : { + "type" : "string" + } + }, + "maxPosition" : { + "type" : "integer", + "description" : "The maximum position of markers in a given map", + "format" : "int32", + "example" : 4000 + }, + "minPosition" : { + "type" : "integer", + "description" : "The minimum position of markers in a given map", + "format" : "int32", + "example" : 250 + } + }, + "description" : "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." + }, + "MetadataField" : { + "type" : "object", + "properties" : { + "dataType" : { + "type" : "string", + "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", + "nullable" : true, + "enum" : [ + "string", + "integer", + "float", + "boolean" + ] + }, + "fieldAbbreviation" : { + "type" : "string", + "description" : "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"", + "nullable" : true + }, + "fieldName" : { + "type" : "string", + "description" : "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"", + "nullable" : true + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + }, + "description" : "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard " + }, + "Method" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/MethodNewRequest" + }, + { + "required" : [ + "methodDbId" + ], + "type" : "object", + "properties" : { + "methodDbId" : { + "type" : "string", + "description" : "Method unique identifier", + "nullable" : true + } + }, + "description" : "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". " + } + ] + }, + "MethodNewRequest" : { + "required" : [ + "methodName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "bibliographicalReference" : { + "type" : "string", + "description" : "Bibliographical reference describing the method.\n
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method.", + "nullable" : true + }, + "description" : { + "type" : "string", + "description" : "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "formula" : { + "type" : "string", + "description" : "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation", + "nullable" : true + }, + "methodClass" : { + "type" : "string", + "description" : "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)", + "nullable" : true + }, + "methodName" : { + "type" : "string", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation" + }, + "methodPUI" : { + "type" : "string", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "nullable" : true + }, + "ontologyReference" : { + "$ref" : "#/components/schemas/OntologyReference" + } + }, + "description" : "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". " + }, + "MethodRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "methodDbIds" : { + "type" : "array", + "description" : "The unique identifier for a method.", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "description" : "The unique identifier for an observation variable.", + "items" : { + "type" : "string" + } + }, + "ontologyDbIds" : { + "type" : "array", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + } + } + }, + "MlsStatus" : { + "type" : "string", + "description" : "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")", + "enum" : [ + "", + "0", + "1", + "99" + ] + }, + "Observation" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/ObservationNewRequest" + }, + { + "required" : [ + "observationDbId" + ], + "type" : "object", + "properties" : { + "observationDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies an observation" + } + }, + "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." + } + ] + }, + "ObservationNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "collector" : { + "type" : "string", + "description" : "The name or identifier of the entity which collected the observation", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "geoCoordinates" : { + "$ref" : "#/components/schemas/GeoJSON" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationTimeStamp" : { + "type" : "string", + "description" : "The date and time when this observation was made", + "format" : "date-time", + "nullable" : true + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "observationVariableDbId" : { + "type" : "string" + }, + "observationVariableName" : { + "type" : "string" + }, + "observationVariablePUI" : { + "type" : "string" + }, + "seasonDbId" : { + "type" : "string" + }, + "seasonName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "uploadedBy" : { + "type" : "string", + "description" : "The name or id of the user who uploaded the observation to the database system", + "nullable" : true + }, + "value" : { + "type" : "string", + "description" : "The value of the data collected as an observation", + "nullable" : true + } + }, + "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." + }, + "ObservationRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } + }, + "observationDbIds" : { + "type" : "array", + "description" : "The unique id of an Observation", + "items" : { + "type" : "string" + } + }, + "observationLevelRelationships" : { + "type" : "array", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationLevels" : { + "type" : "array", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevel" + } + }, + "observationTimeStampRangeEnd" : { + "type" : "string", + "description" : "Timestamp range end", + "format" : "date-time" + }, + "observationTimeStampRangeStart" : { + "type" : "string", + "description" : "Timestamp range start", + "format" : "date-time" + }, + "observationUnitDbIds" : { + "type" : "array", + "description" : "The unique id of an Observation Unit", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelCodes" : { + "type" : "array", + "description" : "The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelNames" : { + "type" : "array", + "description" : "The Observation Unit Level. Returns only the observation unit of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelOrders" : { + "type" : "array", + "description" : "The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelRelationshipCodes" : { + "type" : "array", + "description" : "The Observation Unit Level Code. \n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelRelationshipDbIds" : { + "type" : "array", + "description" : "The observationUnitDbId associated with a particular level and code.\n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelRelationshipNames" : { + "type" : "array", + "description" : "The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. \n
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. \n
Use this parameter to identify groups of observation units that share a relationship level. \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelRelationshipOrders" : { + "type" : "array", + "description" : "The Observation Unit Level Order Number. \n
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "description" : "The DbIds of Variables to search for", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "description" : "The names of Variables to search for", + "items" : { + "type" : "string" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "seasonDbIds" : { + "type" : "array", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + } + } + }, + "ObservationSearchRequest" : { + "type" : "object", + "properties" : { + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "observationUnitDbIds" : { + "type" : "array", + "description" : "The unique id of an Observation Unit", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "seasonDbIds" : { + "type" : "array", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "observationLevelRelationships" : { + "type" : "array", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationLevels" : { + "type" : "array", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevel" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "description" : "The names of Variables to search for", + "items" : { + "type" : "string" + } + }, + "observationDbIds" : { + "type" : "array", + "description" : "The unique id of an Observation", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "description" : "The DbIds of Variables to search for", + "items" : { + "type" : "string" + } + }, + "observationTimeStampRangeStart" : { + "type" : "string", + "description" : "Timestamp range start", + "format" : "date-time" + }, + "observationTimeStampRangeEnd" : { + "type" : "string", + "description" : "Timestamp range end", + "format" : "date-time" + } + }, + "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." + }, + "ObservationTreatment" : { + "type" : "object", + "properties" : { + "factor" : { + "type" : "string", + "description" : "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.", + "nullable" : true, + "example" : "test-factor:dia2020-2-nv.fertilizer" + }, + "modality" : { + "type" : "string", + "description" : "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. ", + "nullable" : true, + "example" : "test-factor:dia2020-2-nv.lf" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + } + }, + "description" : "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor." + }, + "ObservationUnit" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/ObservationUnitNewRequest" + }, + { + "required" : [ + "observationUnitDbId" + ], + "type" : "object", + "properties" : { + "observationUnitDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies an observation unit\n\nMIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. " + } + }, + "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + } + ] + }, + "ObservationUnitHierarchyLevel" : { + "type" : "object", + "properties" : { + "levelName" : { + "type" : "string", + "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "nullable" : true + }, + "levelOrder" : { + "type" : "integer", + "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "format" : "int32", + "nullable" : true + } + }, + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" " + }, + "ObservationUnitLevel" : { + "type" : "object", + "properties" : { + "levelCode" : { + "type" : "string", + "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", + "nullable" : true + }, + "levelName" : { + "type" : "string", + "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "nullable" : true + }, + "levelOrder" : { + "type" : "integer", + "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "format" : "int32", + "nullable" : true + } + }, + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" " + }, + "ObservationUnitLevelRelationship" : { + "type" : "object", + "properties" : { + "levelCode" : { + "type" : "string", + "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", + "nullable" : true + }, + "levelName" : { + "type" : "string", + "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "nullable" : true + }, + "levelOrder" : { + "type" : "integer", + "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "format" : "int32", + "nullable" : true + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + } + }, + "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** " + }, + "ObservationUnitNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string", + "description" : "A human readable name for an observation unit", + "nullable" : true + }, + "observationUnitPUI" : { + "type" : "string", + "description" : "A Permanent Unique Identifier for an observation unit\n\nMIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible.", + "nullable" : true + }, + "observationUnitPosition" : { + "type" : "array", + "description" : "All positional and layout information related to this Observation Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) \nor level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. \nLevels of observation must be consistent with those listed in the Study section.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ObservationUnitPosition" + } + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "treatments" : { + "type" : "array", + "description" : "List of treatments applied to an observation unit.\n\nMIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ObservationTreatment" + } + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + }, + "ObservationUnitPosition" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "nullable" : true, + "enum" : [ + "CHECK", + "TEST", + "FILLER" + ] + }, + "geoCoordinates" : { + "type" : "array", + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "$ref" : "#/components/schemas/ObservationUnitLevel" + }, + "observationLevelRelationships" : { + "type" : "array", + "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string", + "description" : "The X position coordinate for an observation unit. Different systems may use different coordinate systems.", + "nullable" : true + }, + "positionCoordinateXType" : { + "$ref" : "#/components/schemas/PositionCoordinateType" + }, + "positionCoordinateY" : { + "type" : "string", + "description" : "The Y position coordinate for an observation unit. Different systems may use different coordinate systems.", + "nullable" : true + }, + "positionCoordinateYType" : { + "$ref" : "#/components/schemas/PositionCoordinateType" + } + }, + "description" : "All positional and layout information related to this Observation Unit" + }, + "ObservationUnitRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "includeObservations" : { + "type" : "boolean", + "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", + "example" : false + }, + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } + }, + "observationLevelRelationships" : { + "type" : "array", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationLevels" : { + "type" : "array", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevel" + } + }, + "observationUnitDbIds" : { + "type" : "array", + "description" : "The unique id of an observation unit", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelCodes" : { + "type" : "array", + "description" : "The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelNames" : { + "type" : "array", + "description" : "The Observation Unit Level. Returns only the observation unit of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelOrders" : { + "type" : "array", + "description" : "The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelRelationshipCodes" : { + "type" : "array", + "description" : "The Observation Unit Level Code. \n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelRelationshipDbIds" : { + "type" : "array", + "description" : "The observationUnitDbId associated with a particular level and code.\n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelRelationshipNames" : { + "type" : "array", + "description" : "The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. \n
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. \n
Use this parameter to identify groups of observation units that share a relationship level. \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitLevelRelationshipOrders" : { + "type" : "array", + "description" : "The Observation Unit Level Order Number. \n
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitNames" : { + "type" : "array", + "description" : "The human readable identifier for an Observation Unit", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "description" : "The DbIds of Variables to search for", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "description" : "The names of Variables to search for", + "items" : { + "type" : "string" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "seasonDbIds" : { + "type" : "array", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + } + } + }, + "ObservationUnitSearchRequest" : { + "type" : "object", + "properties" : { + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "observationUnitNames" : { + "type" : "array", + "description" : "The human readable identifier for an Observation Unit", + "items" : { + "type" : "string" + } + }, + "observationUnitDbIds" : { + "type" : "array", + "description" : "The unique id of an observation unit", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "seasonDbIds" : { + "type" : "array", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "observationLevelRelationships" : { + "type" : "array", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationLevels" : { + "type" : "array", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "items" : { + "$ref" : "#/components/schemas/ObservationUnitLevel" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "includeObservations" : { + "type" : "boolean", + "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", + "example" : false + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "description" : "The names of Variables to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "description" : "The DbIds of Variables to search for", + "items" : { + "type" : "string" + } + } + }, + "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + }, + "ObservationVariable" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/ObservationVariableNewRequest" + }, + { + "required" : [ + "observationVariableDbId" + ], + "type" : "object", + "properties" : { + "observationVariableDbId" : { + "type" : "string", + "description" : "Variable unique identifier\n\nMIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation." + } + } + } + ] + }, + "ObservationVariableNewRequest" : { + "required" : [ + "methodDbId", + "methodName", + "observationVariableName", + "scaleDbId", + "scaleName", + "traitName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "commonCropName" : { + "type" : "string", + "description" : "Crop name (examples: \"Maize\", \"Wheat\")", + "nullable" : true + }, + "contextOfUse" : { + "type" : "array", + "description" : "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "defaultValue" : { + "type" : "string", + "description" : "Variable default value. (examples: \"red\", \"2.3\", etc.)", + "nullable" : true + }, + "documentationURL" : { + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "growthStage" : { + "type" : "string", + "description" : "Growth stage at which measurement is made (examples: \"flowering\")", + "nullable" : true + }, + "institution" : { + "type" : "string", + "description" : "Name of institution submitting the variable", + "nullable" : true + }, + "language" : { + "type" : "string", + "description" : "2 letter ISO 639-1 code for the language of submission of the variable.", + "nullable" : true + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "observationVariableName" : { + "type" : "string", + "description" : "Variable name (usually a short name)\n\nMIAPPE V1.1 (DM-84) Variable name - Name of the variable." + }, + "observationVariablePUI" : { + "type" : "string", + "description" : "The Permanent Unique Identifier of a Observation Variable, usually in the form of a URI", + "nullable" : true + }, + "ontologyReference" : { + "$ref" : "#/components/schemas/OntologyReference" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string", + "description" : "Name of scientist submitting the variable.", + "nullable" : true + }, + "status" : { + "type" : "string", + "description" : "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)", + "nullable" : true + }, + "submissionTimestamp" : { + "type" : "string", + "description" : "Timestamp when the Variable was added (ISO 8601)", + "format" : "date-time", + "nullable" : true + }, + "synonyms" : { + "type" : "array", + "description" : "Other variable names", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + } + }, + "ObservationVariableParameters" : { + "type" : "object", + "properties" : { + "observationVariableDbIds" : { + "type" : "array", + "description" : "The DbIds of Variables to search for", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "description" : "The names of Variables to search for", + "items" : { + "type" : "string" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "items" : { + "type" : "string" + } + } + } + }, + "ObservationVariableRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "dataTypes" : { + "type" : "array", + "description" : "List of scale data types to filter search results", + "items" : { + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "methodDbIds" : { + "type" : "array", + "description" : "List of methods to filter search results", + "items" : { + "type" : "string" + } + }, + "methodNames" : { + "type" : "array", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "items" : { + "type" : "string" + } + }, + "methodPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "description" : "The DbIds of Variables to search for", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "description" : "The names of Variables to search for", + "items" : { + "type" : "string" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "ontologyDbIds" : { + "type" : "array", + "description" : "List of ontology IDs to search for", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "scaleDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Scale", + "items" : { + "type" : "string" + } + }, + "scaleNames" : { + "type" : "array", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "items" : { + "type" : "string" + } + }, + "scalePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "studyDbId" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "traitAttributePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } + }, + "traitAttributes" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } + }, + "traitClasses" : { + "type" : "array", + "description" : "List of trait classes to filter search results", + "items" : { + "type" : "string" + } + }, + "traitDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Trait", + "items" : { + "type" : "string" + } + }, + "traitEntities" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "items" : { + "type" : "string" + } + }, + "traitEntityPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "items" : { + "type" : "string" + } + }, + "traitNames" : { + "type" : "array", + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "items" : { + "type" : "string" + } + }, + "traitPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + } + } + }, + "ObservationVariableSearchRequest" : { + "type" : "object", + "properties" : { + "methodDbIds" : { + "type" : "array", + "description" : "List of methods to filter search results", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + }, + "studyDbId" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "items" : { + "type" : "string" + } + }, + "dataTypes" : { + "type" : "array", + "description" : "List of scale data types to filter search results", + "items" : { + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "methodPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "scalePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "traitAttributes" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } + }, + "scaleDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Scale", + "items" : { + "type" : "string" + } + }, + "traitEntityPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "items" : { + "type" : "string" + } + }, + "methodNames" : { + "type" : "array", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "items" : { + "type" : "string" + } + }, + "scaleNames" : { + "type" : "array", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "items" : { + "type" : "string" + } + }, + "traitPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "traitClasses" : { + "type" : "array", + "description" : "List of trait classes to filter search results", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "ontologyDbIds" : { + "type" : "array", + "description" : "List of ontology IDs to search for", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "description" : "The names of Variables to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "traitDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Trait", + "items" : { + "type" : "string" + } + }, + "traitNames" : { + "type" : "array", + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "description" : "The DbIds of Variables to search for", + "items" : { + "type" : "string" + } + }, + "traitAttributePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } + }, + "traitEntities" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "items" : { + "type" : "string" + } + } + } + }, + "Ontology" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/OntologyNewRequest" + }, + { + "required" : [ + "ontologyDbId" + ], + "type" : "object", + "properties" : { + "ontologyDbId" : { + "type" : "string", + "description" : "Ontology database unique identifier" + } + }, + "description" : "The identifier and metadata needed to reference an external controlled vocabulary" + } + ] + }, + "OntologyNewRequest" : { + "required" : [ + "ontologyName" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "authors" : { + "type" : "string", + "description" : "Ontology's list of authors (no specific format)", + "nullable" : true + }, + "copyright" : { + "type" : "string", + "description" : "Ontology copyright", + "nullable" : true + }, + "description" : { + "type" : "string", + "description" : "Human readable description of Ontology", + "nullable" : true + }, + "documentationURL" : { + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true + }, + "licence" : { + "type" : "string", + "description" : "Ontology licence", + "nullable" : true + }, + "ontologyName" : { + "type" : "string", + "description" : "Ontology name" + }, + "version" : { + "type" : "string", + "description" : "Ontology version (no specific format)", + "nullable" : true + } + }, + "description" : "The identifier and metadata needed to reference an external controlled vocabulary" + }, + "OntologyParameters" : { + "type" : "object", + "properties" : { + "ontologyDbIds" : { + "type" : "array", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "items" : { + "type" : "string" + } + } + } + }, + "OntologyReference" : { + "required" : [ + "ontologyDbId", + "ontologyName" + ], + "type" : "object", + "properties" : { + "documentationLinks" : { + "type" : "array", + "description" : "links to various ontology documentation", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/DocumentationLink" + } + }, + "ontologyDbId" : { + "type" : "string" + }, + "ontologyName" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a ontology reference", + "nullable" : true + }, + "version" : { + "type" : "string", + "description" : "Ontology version (no specific format)", + "nullable" : true + } + }, + "description" : "MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)." + }, + "OntologyRequest" : { + "type" : "object", + "properties" : { + "ontologyDbIds" : { + "type" : "array", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "items" : { + "type" : "string" + } + }, + "ontologyNames" : { + "type" : "array", + "description" : "The human readable identifier for an ontology definition.", + "items" : { + "type" : "string" + } + } + } + }, + "OntologyTerm" : { + "type" : "object", + "properties" : { + "term" : { + "type" : "string", + "description" : "Ontology term - the label of the ontology term the termId is pointing to.", + "nullable" : true + }, + "termURI" : { + "type" : "string", + "description" : "Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation.", + "nullable" : true + } + }, + "description" : "A pointer to an ontology used by a genomic reference" + }, + "Pagination" : { + "type" : "object", + "properties" : { + "dimension" : { + "type" : "string", + "description" : "The dimension of the matrix being paginated", + "nullable" : true, + "enum" : [ + "CALLSETS", + "VARIANTS" + ] + }, + "page" : { "type" : "integer", - "format" : "int32" + "description" : "the requested page number (zero indexed)", + "format" : "int32", + "nullable" : true }, - "imageHeightMax" : { + "pageSize" : { "type" : "integer", - "format" : "int32" + "description" : "the maximum number of elements per page in this dimension of the matrix", + "format" : "int32", + "nullable" : true + }, + "totalCount" : { + "type" : "integer", + "description" : "The total number of elements that are available on the server and match the requested query parameters.", + "format" : "int32", + "nullable" : true + }, + "totalPages" : { + "type" : "integer", + "description" : "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)", + "format" : "int32", + "nullable" : true + } + }, + "description" : "Pagination info for the matrix" + }, + "ParentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ + "MALE", + "FEMALE", + "SELF", + "POPULATION", + "CLONAL" + ] + }, + "PedigreeNode" : { + "required" : [ + "germplasmDbId", + "germplasmName", + "germplasmPUI", + "pedigreeNodeDbId" + ], + "type" : "object", + "properties" : { + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" + }, + "breedingMethodDbId" : { + "type" : "string" + }, + "breedingMethodName" : { + "type" : "string" + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "crossingYear" : { + "type" : "integer", + "description" : "The year the parents were originally crossed", + "format" : "int32", + "nullable" : true + }, + "defaultDisplayName" : { + "type" : "string", + "description" : "Human readable name used for display purposes", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "familyCode" : { + "type" : "string", + "description" : "The code representing the family of this germplasm", + "nullable" : true + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "parents" : { + "type" : "array", + "description" : "A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. \n
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/GermplasmParent" + } + }, + "pedigreeNodeDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a pedigree node", + "nullable" : true + }, + "pedigreeString" : { + "type" : "string", + "description" : "The string representation of the pedigree for this germplasm in PURDY notation", + "nullable" : true + }, + "progeny" : { + "type" : "array", + "description" : "A list of germplasm references that are direct children of this germplasm. These represent edges in the tree, connecting to other nodes.\n
The given germplasm could have a large number of progeny, across a number of different breeding methods. The 'parentType' shows \n the type of parent this germplasm is to each of the child germplasm references.\n
If the parameter 'includeProgeny' is set to false, then this array should be empty, null, or not present in the response.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/GermplasmChild" + } + }, + "siblingDbIds" : { + "type" : "array", + "description" : "A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Siblings share at least one parent with the given germplasm. \n
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response.", + "nullable" : true, + "items" : { + "type" : "string" + } + } + }, + "description" : "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances." + }, + "PedigreeNodeRequest" : { + "type" : "object", + "properties" : { + "accessionNumbers" : { + "type" : "array", + "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "items" : { + "type" : "string" + } + }, + "binomialNames" : { + "type" : "array", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "items" : { + "type" : "string" + } + }, + "collections" : { + "type" : "array", + "description" : "A specific panel/collection/population name this germplasm belongs to.", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "familyCodes" : { + "type" : "array", + "description" : "A familyCode representing the family this germplasm belongs to.", + "items" : { + "type" : "string" + } + }, + "genus" : { + "type" : "array", + "description" : "List of Genus names to identify germplasm", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmPUIs" : { + "type" : "array", + "description" : "List of Permanent Unique Identifiers to identify germplasm", + "items" : { + "type" : "string" + } + }, + "includeFullTree" : { + "type" : "boolean", + "description" : "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", + "example" : true }, - "imageHeightMin" : { - "type" : "integer", - "format" : "int32" + "includeParents" : { + "type" : "boolean", + "description" : "If this parameter is true, include the array of parents in the response", + "example" : true }, - "imageLocation" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" + "includeProgeny" : { + "type" : "boolean", + "description" : "If this parameter is true, include the array of progeny in the response", + "example" : true }, - "imageTimeStampRangeEnd" : { - "type" : "string" + "includeSiblings" : { + "type" : "boolean", + "description" : "If this parameter is true, include the array of siblings in the response", + "example" : true }, - "imageTimeStampRangeStart" : { - "type" : "string" + "instituteCodes" : { + "type" : "array", + "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "items" : { + "type" : "string" + } }, - "imageWidthMax" : { + "pedigreeDepth" : { "type" : "integer", - "format" : "int32" + "description" : "Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc)", + "format" : "int32", + "example" : 3 }, - "imageWidthMin" : { + "progenyDepth" : { "type" : "integer", - "format" : "int32" - } - }, - "description" : "The metadata for an image file that is connected to some phenotypic observation data." - }, - "LastUpdate" : { - "required" : [ - "lastUpdateDbId" - ], - "type" : "object", - "properties" : { - "lastUpdateDbId" : { - "type" : "string" + "description" : "Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc)", + "format" : "int32", + "example" : 3 }, - "studyDbId" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "studyName" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "studyPUI" : { - "type" : "string" + "species" : { + "type" : "array", + "description" : "List of Species names to identify germplasm", + "items" : { + "type" : "string" + } }, - "timestamp" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "version" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "synonyms" : { + "type" : "array", + "description" : "List of alternative names or IDs used to reference this germplasm", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } } - }, - "description" : "The date and time when this study was last modified" + } }, - "List" : { - "required" : [ - "listDbId", - "listName", - "listType" - ], + "PedigreeNodeSearchRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "dateCreated" : { - "type" : "string" + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "dateModified" : { - "type" : "string" + "accessionNumbers" : { + "type" : "array", + "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "items" : { + "type" : "string" + } }, - "listDescription" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "listName" : { - "type" : "string" + "includeParents" : { + "type" : "boolean", + "description" : "If this parameter is true, include the array of parents in the response", + "example" : true }, - "listOwnerName" : { - "type" : "string" + "synonyms" : { + "type" : "array", + "description" : "List of alternative names or IDs used to reference this germplasm", + "items" : { + "type" : "string" + } }, - "listSize" : { - "type" : "integer", - "format" : "int32" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "listSource" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "listType" : { - "$ref" : "#/components/schemas/ListType" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "personDbId" : { - "type" : "string" - } - }, - "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." - }, - "ListNewRequest" : { - "required" : [ - "listDbId", - "listDbId", - "listName", - "listType" - ], - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "dateCreated" : { - "type" : "string" + "germplasmPUIs" : { + "type" : "array", + "description" : "List of Permanent Unique Identifiers to identify germplasm", + "items" : { + "type" : "string" + } }, - "dateModified" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "listDbId" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } }, - "listDescription" : { - "type" : "string" + "progenyDepth" : { + "type" : "integer", + "description" : "Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc)", + "format" : "int32", + "example" : 3 }, - "listName" : { - "type" : "string" + "familyCodes" : { + "type" : "array", + "description" : "A familyCode representing the family this germplasm belongs to.", + "items" : { + "type" : "string" + } }, - "listOwnerName" : { - "type" : "string" + "includeProgeny" : { + "type" : "boolean", + "description" : "If this parameter is true, include the array of progeny in the response", + "example" : true }, - "listSize" : { - "type" : "integer", - "format" : "int32" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "listSource" : { - "type" : "string" + "collections" : { + "type" : "array", + "description" : "A specific panel/collection/population name this germplasm belongs to.", + "items" : { + "type" : "string" + } }, - "listType" : { - "$ref" : "#/components/schemas/ListType" + "genus" : { + "type" : "array", + "description" : "List of Genus names to identify germplasm", + "items" : { + "type" : "string" + } }, - "personDbId" : { - "type" : "string" - } - }, - "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." - }, - "ListSearchRequest" : { - "type" : "object", - "properties" : { - "dateCreatedRangeEnd" : { - "type" : "string" + "includeSiblings" : { + "type" : "boolean", + "description" : "If this parameter is true, include the array of siblings in the response", + "example" : true }, - "dateCreatedRangeStart" : { - "type" : "string" + "species" : { + "type" : "array", + "description" : "List of Species names to identify germplasm", + "items" : { + "type" : "string" + } }, - "dateModifiedRangeEnd" : { - "type" : "string" + "pedigreeDepth" : { + "type" : "integer", + "description" : "Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc)", + "format" : "int32", + "example" : 3 }, - "dateModifiedRangeStart" : { - "type" : "string" + "binomialNames" : { + "type" : "array", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "items" : { + "type" : "string" + } }, - "listType" : { - "$ref" : "#/components/schemas/ListType" + "includeFullTree" : { + "type" : "boolean", + "description" : "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", + "example" : true + }, + "instituteCodes" : { + "type" : "array", + "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "items" : { + "type" : "string" + } } }, - "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." + "description" : "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances." }, - "ListType" : { - "type" : "string", - "description" : "The type of objects that are referenced in a List", - "enum" : [ - "germplasm", - "markers", - "variants", - "programs", - "trials", - "studies", - "observationUnits", - "observations", - "observationVariables", - "samples" + "Person" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/PersonNewRequest" + }, + { + "required" : [ + "personDbId" + ], + "type" : "object", + "properties" : { + "personDbId" : { + "type" : "string", + "description" : "Unique ID for a person" + } + }, + "description" : "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." + } ] }, - "Location" : { - "required" : [ - "locationDbId", - "locationName" - ], + "PersonNewRequest" : { "type" : "object", "properties" : { - "abbreviation" : { - "type" : "string" - }, "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "childLocationDbIds" : { + "description" : { + "type" : "string", + "description" : "description of this person", + "nullable" : true + }, + "emailAddress" : { + "type" : "string", + "description" : "email address for this person", + "nullable" : true + }, + "externalReferences" : { "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, "items" : { - "type" : "string" + "$ref" : "#/components/schemas/ExternalReference" } }, - "coordinateDescription" : { - "type" : "string" - }, - "coordinateUncertainty" : { - "type" : "string" - }, - "coordinates" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "countryCode" : { - "type" : "string" - }, - "countryName" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "environmentType" : { - "type" : "string" - }, - "exposure" : { - "type" : "string" - }, - "instituteAddress" : { - "type" : "string" - }, - "instituteName" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" + "firstName" : { + "type" : "string", + "description" : "Persons first name", + "nullable" : true }, - "locationName" : { - "type" : "string" + "lastName" : { + "type" : "string", + "description" : "Persons last name", + "nullable" : true }, - "locationType" : { - "type" : "string" + "mailingAddress" : { + "type" : "string", + "description" : "physical address of this person", + "nullable" : true }, - "siteStatus" : { - "type" : "string" + "middleName" : { + "type" : "string", + "description" : "Persons middle name", + "nullable" : true }, - "slope" : { - "type" : "string" + "phoneNumber" : { + "type" : "string", + "description" : "phone number of this person", + "nullable" : true }, - "topography" : { - "type" : "string" + "userID" : { + "type" : "string", + "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", + "nullable" : true } }, - "description" : "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." + "description" : "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." }, - "LocationNewRequest" : { - "required" : [ - "locationDbId", - "locationDbId", - "locationName" - ], + "PersonRequest" : { "type" : "object", "properties" : { - "abbreviation" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "emailAddresses" : { + "type" : "array", + "description" : "email address for this person", + "items" : { + "type" : "string" + } }, - "childLocationDbIds" : { + "firstNames" : { "type" : "array", + "description" : "Persons first name", "items" : { "type" : "string" } }, - "coordinateDescription" : { - "type" : "string" + "lastNames" : { + "type" : "array", + "description" : "Persons last name", + "items" : { + "type" : "string" + } }, - "coordinateUncertainty" : { - "type" : "string" + "mailingAddresses" : { + "type" : "array", + "description" : "physical address of this person", + "items" : { + "type" : "string" + } }, - "coordinates" : { - "$ref" : "#/components/schemas/GeoJSON" + "middleNames" : { + "type" : "array", + "description" : "Persons middle name", + "items" : { + "type" : "string" + } }, - "countryCode" : { - "type" : "string" + "personDbIds" : { + "type" : "array", + "description" : "Unique ID for this person", + "items" : { + "type" : "string" + } }, - "countryName" : { - "type" : "string" + "phoneNumbers" : { + "type" : "array", + "description" : "phone number of this person", + "items" : { + "type" : "string" + } }, - "documentationURL" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "environmentType" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "exposure" : { - "type" : "string" + "userIDs" : { + "type" : "array", + "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", + "items" : { + "type" : "string" + } + } + } + }, + "PersonSearchRequest" : { + "type" : "object", + "properties" : { + "middleNames" : { + "type" : "array", + "description" : "Persons middle name", + "items" : { + "type" : "string" + } }, - "instituteAddress" : { - "type" : "string" + "emailAddresses" : { + "type" : "array", + "description" : "email address for this person", + "items" : { + "type" : "string" + } }, - "instituteName" : { - "type" : "string" + "userIDs" : { + "type" : "array", + "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", + "items" : { + "type" : "string" + } }, - "locationDbId" : { - "type" : "string" + "personDbIds" : { + "type" : "array", + "description" : "Unique ID for this person", + "items" : { + "type" : "string" + } }, - "locationName" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "locationType" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "siteStatus" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "slope" : { - "type" : "string" + "firstNames" : { + "type" : "array", + "description" : "Persons first name", + "items" : { + "type" : "string" + } }, - "topography" : { - "type" : "string" - } - }, - "description" : "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." - }, - "LocationSearchRequest" : { - "type" : "object", - "properties" : { - "altitudeMax" : { - "type" : "number" + "lastNames" : { + "type" : "array", + "description" : "Persons last name", + "items" : { + "type" : "string" + } }, - "altitudeMin" : { - "type" : "number" + "mailingAddresses" : { + "type" : "array", + "description" : "physical address of this person", + "items" : { + "type" : "string" + } }, - "coordinates" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" + "phoneNumbers" : { + "type" : "array", + "description" : "phone number of this person", + "items" : { + "type" : "string" + } } }, - "description" : "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc." + "description" : "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." }, - "MarkerPosition" : { + "PlannedCross" : { + "required" : [ + "plannedCrossDbId" + ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "linkageGroupName" : { - "type" : "string" + "crossType" : { + "$ref" : "#/components/schemas/CrossType" }, - "mapDbId" : { + "crossingProjectDbId" : { "type" : "string" }, - "mapName" : { + "crossingProjectName" : { "type" : "string" }, - "mapPUI" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "position" : { - "type" : "integer", - "format" : "int32" + "parent1" : { + "$ref" : "#/components/schemas/CrossParent" }, - "variantDbId" : { - "type" : "string" - } - }, - "description" : "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." - }, - "MarkerPositionSearchRequest" : { - "type" : "object", - "properties" : { - "maxPosition" : { - "type" : "integer", - "format" : "int32" + "parent2" : { + "$ref" : "#/components/schemas/CrossParent" }, - "minPosition" : { - "type" : "integer", - "format" : "int32" - } - }, - "description" : "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." - }, - "MetadataField" : { - "type" : "object", - "properties" : { - "dataType" : { + "plannedCrossDbId" : { "type" : "string", - "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", - "enum" : [ - "string", - "integer", - "float", - "boolean" - ] - }, - "fieldAbbreviation" : { - "type" : "string" + "description" : "the unique identifier for a planned cross" }, - "fieldName" : { - "type" : "string" - }, - "variantSetDbId" : { - "type" : "string" + "plannedCrossName" : { + "type" : "string", + "description" : "the human readable name for a planned cross", + "nullable" : true }, - "variantSetName" : { - "type" : "string" + "status" : { + "type" : "string", + "description" : "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", + "nullable" : true, + "enum" : [ + "TODO", + "DONE", + "SKIPPED" + ] } }, - "description" : "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard " + "description" : "Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field." }, - "Method" : { - "required" : [ - "methodDbId", - "methodName" - ], + "PlannedCrossRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "bibliographicalReference" : { - "type" : "string" + "crossingProjectDbIds" : { + "type" : "array", + "description" : "Search for Crossing Projects with this unique id", + "items" : { + "type" : "string" + } }, - "description" : { - "type" : "string" + "crossingProjectNames" : { + "type" : "array", + "description" : "The human readable name for a crossing project", + "items" : { + "type" : "string" + } }, - "formula" : { - "type" : "string" + "plannedCrossDbIds" : { + "type" : "array", + "description" : "Search for Planned Cross with this unique id", + "items" : { + "type" : "string" + } }, - "methodClass" : { - "type" : "string" + "plannedCrossNames" : { + "type" : "array", + "description" : "Search for Planned Cross with this human readable name", + "items" : { + "type" : "string" + } }, - "methodName" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "methodPUI" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "ontologyReferenceDbId" : { - "type" : "string" + "statuses" : { + "type" : "array", + "description" : "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", + "items" : { + "type" : "string", + "enum" : [ + "TODO", + "DONE", + "SKIPPED" + ] + } } - }, - "description" : "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". " + } }, - "MethodNewRequest" : { + "PlannedCrossStatus" : { + "type" : "string", + "description" : "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", + "enum" : [ + "TODO", + "DONE", + "SKIPPED" + ] + }, + "Plate" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/PlateNewRequest" + }, + { + "type" : "object", + "properties" : { + "plateDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a `Plate`" + } + }, + "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." + } + ] + }, + "PlateFormat" : { + "type" : "string", + "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", + "enum" : [ + "PLATE_96", + "TUBES" + ] + }, + "PlateNewRequest" : { "required" : [ - "methodDbId", - "methodDbId", - "methodName" + "plateName" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "bibliographicalReference" : { + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "plateBarcode" : { + "type" : "string", + "description" : "A unique identifier physically attached to a `Plate`", + "nullable" : true + }, + "plateFormat" : { + "type" : "string", + "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", + "nullable" : true, + "enum" : [ + "PLATE_96", + "TUBES" + ] + }, + "plateName" : { + "type" : "string", + "description" : "A human readable name for a `Plate`" + }, + "programDbId" : { "type" : "string" }, - "description" : { + "programName" : { "type" : "string" }, - "formula" : { + "sampleType" : { + "type" : "string", + "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", + "nullable" : true, + "enum" : [ + "DNA", + "RNA", + "TISSUE", + "MIXED" + ] + }, + "studyDbId" : { "type" : "string" }, - "methodClass" : { + "studyName" : { "type" : "string" }, - "methodDbId" : { + "studyPUI" : { "type" : "string" }, - "methodName" : { + "trialDbId" : { "type" : "string" }, - "methodPUI" : { + "trialName" : { "type" : "string" }, - "ontologyReferenceDbId" : { + "trialPUI" : { "type" : "string" } }, - "description" : "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". " + "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." }, - "Observation" : { - "required" : [ - "observationDbId" - ], + "PlateRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "collector" : { - "type" : "string" + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "geoCoordinates" : { - "$ref" : "#/components/schemas/GeoJSON" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "germplasmDbId" : { - "type" : "string" + "observationUnitDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies an observation unit", + "items" : { + "type" : "string" + } }, - "germplasmName" : { - "type" : "string" + "plateBarcodes" : { + "type" : "array", + "description" : "A unique identifier physically attached to the plate", + "items" : { + "type" : "string" + } }, - "germplasmPUI" : { - "type" : "string" + "plateDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a plate of samples", + "items" : { + "type" : "string" + } }, - "observationTimeStamp" : { - "type" : "string" + "plateNames" : { + "type" : "array", + "description" : "The human readable name of a plate of samples", + "items" : { + "type" : "string" + } }, - "observationUnitDbId" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "observationUnitName" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "observationUnitPUI" : { - "type" : "string" + "sampleDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a sample", + "items" : { + "type" : "string" + } }, - "observationVariableDbId" : { - "type" : "string" + "sampleGroupDbIds" : { + "type" : "array", + "description" : "The unique identifier for a group of related Samples", + "items" : { + "type" : "string" + } }, - "observationVariableName" : { - "type" : "string" + "sampleNames" : { + "type" : "array", + "description" : "The human readable name of the sample", + "items" : { + "type" : "string" + } }, - "observationVariablePUI" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "seasonDbId" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "seasonName" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "studyDbId" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + } + } + }, + "PlateSearchRequest" : { + "type" : "object", + "properties" : { + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "studyName" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "studyPUI" : { - "type" : "string" + "observationUnitDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies an observation unit", + "items" : { + "type" : "string" + } }, - "uploadedBy" : { + "plateBarcodes" : { + "type" : "array", + "description" : "A unique identifier physically attached to the plate", + "items" : { + "type" : "string" + } + }, + "plateNames" : { + "type" : "array", + "description" : "The human readable name of a plate of samples", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "sampleDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a sample", + "items" : { + "type" : "string" + } + }, + "plateDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a plate of samples", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + }, + "sampleGroupDbIds" : { + "type" : "array", + "description" : "The unique identifier for a group of related Samples", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "sampleNames" : { + "type" : "array", + "description" : "The human readable name of the sample", + "items" : { + "type" : "string" + } + } + }, + "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." + }, + "PollinationEvent" : { + "type" : "object", + "properties" : { + "crossDbId" : { "type" : "string" }, - "value" : { + "crossName" : { "type" : "string" + }, + "pollinationNumber" : { + "type" : "string", + "description" : "The unique identifier for this pollination event", + "nullable" : true + }, + "pollinationSuccessful" : { + "type" : "boolean", + "description" : "True if the pollination was successful", + "nullable" : true + }, + "pollinationTimeStamp" : { + "type" : "string", + "description" : "The timestamp when the pollination took place", + "format" : "date-time", + "nullable" : true } }, - "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." + "description" : "A Pollination Event that was used or attempted for a Cross." }, - "ObservationNewRequest" : { + "PositionCoordinateType" : { + "type" : "string", + "description" : "The type of positional coordinate. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ + "LONGITUDE", + "LATITUDE", + "PLANTED_ROW", + "PLANTED_INDIVIDUAL", + "GRID_ROW", + "GRID_COL", + "MEASURED_ROW", + "MEASURED_COL" + ] + }, + "Program" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/ProgramNewRequest" + }, + { + "required" : [ + "programDbId" + ], + "type" : "object", + "properties" : { + "programDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies the program" + } + }, + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." + } + ] + }, + "ProgramNewRequest" : { "required" : [ - "observationDbId", - "observationDbId" + "programName" ], "type" : "object", "properties" : { + "abbreviation" : { + "type" : "string", + "description" : "A shortened version of the human readable name for a Program", + "nullable" : true + }, "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "collector" : { - "type" : "string" - }, - "geoCoordinates" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" + "commonCropName" : { + "type" : "string", + "description" : "Common name for the crop which this program is for", + "nullable" : true }, - "observationDbId" : { - "type" : "string" + "documentationURL" : { + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true }, - "observationTimeStamp" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "observationUnitDbId" : { - "type" : "string" + "fundingInformation" : { + "type" : "string", + "description" : "Information describing the grant or funding source for this program", + "nullable" : true }, - "observationUnitName" : { - "type" : "string" + "objective" : { + "type" : "string", + "description" : "The primary objective of the program", + "nullable" : true }, - "observationUnitPUI" : { + "personDbId" : { "type" : "string" }, - "observationVariableDbId" : { - "type" : "string" + "programName" : { + "type" : "string", + "description" : "Human readable name of the program" }, - "observationVariableName" : { - "type" : "string" + "programType" : { + "type" : "string", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "nullable" : true, + "enum" : [ + "STANDARD", + "PROJECT" + ] + } + }, + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." + }, + "ProgramParameters" : { + "type" : "object", + "properties" : { + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "observationVariablePUI" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + } + } + }, + "ProgramRequest" : { + "type" : "object", + "properties" : { + "abbreviations" : { + "type" : "array", + "description" : "A list of shortened human readable names for a set of Programs", + "items" : { + "type" : "string" + } }, - "seasonDbId" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "seasonName" : { - "type" : "string" + "leadPersonDbIds" : { + "type" : "array", + "description" : "The person DbIds of the program leader to search for", + "items" : { + "type" : "string" + } }, - "studyDbId" : { - "type" : "string" + "leadPersonNames" : { + "type" : "array", + "description" : "The names of the program leader to search for", + "items" : { + "type" : "string" + } }, - "studyName" : { - "type" : "string" + "objectives" : { + "type" : "array", + "description" : "A program objective to search for", + "items" : { + "type" : "string" + } }, - "studyPUI" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "uploadedBy" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "value" : { - "type" : "string" + "programTypes" : { + "type" : "array", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "items" : { + "type" : "string", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding.", + "enum" : [ + "STANDARD", + "PROJECT" + ] + } } - }, - "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." + } }, - "ObservationSearchRequest" : { + "ProgramSearchRequest" : { "type" : "object", "properties" : { - "observationTimeStampRangeEnd" : { - "type" : "string" + "leadPersonNames" : { + "type" : "array", + "description" : "The names of the program leader to search for", + "items" : { + "type" : "string" + } }, - "observationTimeStampRangeStart" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "objectives" : { + "type" : "array", + "description" : "A program objective to search for", + "items" : { + "type" : "string" + } + }, + "leadPersonDbIds" : { + "type" : "array", + "description" : "The person DbIds of the program leader to search for", + "items" : { + "type" : "string" + } + }, + "programTypes" : { + "type" : "array", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "items" : { + "type" : "string", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding.", + "enum" : [ + "STANDARD", + "PROJECT" + ] + } + }, + "abbreviations" : { + "type" : "array", + "description" : "A list of shortened human readable names for a set of Programs", + "items" : { + "type" : "string" + } } }, - "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." }, - "ObservationTreatment" : { + "ProgramType" : { + "type" : "string", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "enum" : [ + "STANDARD", + "PROJECT" + ] + }, + "Publication" : { "type" : "object", "properties" : { - "factor" : { - "type" : "string" + "publicationPUI" : { + "type" : "string", + "description" : "The permanent unique identifier of the publication.", + "nullable" : true }, - "modality" : { - "type" : "string" + "publicationReference" : { + "type" : "string", + "description" : "The publication reference.", + "nullable" : true }, - "observationUnitDbId" : { + "trialDbId" : { "type" : "string" }, - "observationUnitName" : { + "trialName" : { "type" : "string" }, - "observationUnitPUI" : { + "trialPUI" : { "type" : "string" } }, - "description" : "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor." + "description" : "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended." }, - "ObservationUnit" : { + "Reference" : { "required" : [ - "observationUnitDbId" + "referenceDbId", + "referenceName" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "crossDbId" : { - "type" : "string" - }, - "crossName" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" + "commonCropName" : { + "type" : "string", + "description" : "Common name for the crop", + "nullable" : true }, - "locationDbId" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "locationName" : { - "type" : "string" + "isDerived" : { + "type" : "boolean", + "description" : "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", + "nullable" : true }, - "observationUnitName" : { - "type" : "string" + "length" : { + "type" : "integer", + "description" : "The length of this `Reference` sequence.", + "format" : "int32", + "nullable" : true }, - "observationUnitPUI" : { - "type" : "string" + "md5checksum" : { + "type" : "string", + "description" : "The MD5 checksum uniquely representing this `Reference` as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM).", + "nullable" : true }, - "programDbId" : { - "type" : "string" + "referenceDbId" : { + "type" : "string", + "description" : "The unique identifier for a `Reference`" }, - "programName" : { - "type" : "string" + "referenceName" : { + "type" : "string", + "description" : "The human readable name of a `Reference` within a `ReferenceSet`." }, - "seedLotDbId" : { + "referenceSetDbId" : { "type" : "string" }, - "seedLotName" : { + "referenceSetName" : { "type" : "string" }, - "studyDbId" : { - "type" : "string" + "sourceAccessions" : { + "type" : "array", + "description" : "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`.", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "studyName" : { - "type" : "string" + "sourceDivergence" : { + "type" : "number", + "description" : "The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from.", + "nullable" : true }, - "studyPUI" : { - "type" : "string" + "sourceGermplasmDbIds" : { + "type" : "array", + "description" : "All known corresponding Germplasm", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "trialDbId" : { - "type" : "string" + "sourceURI" : { + "type" : "string", + "description" : "The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the `getReferenceBases()` method to obtain sequence bases for a `Reference` instead of attempting to retrieve this URI.", + "nullable" : true }, - "trialName" : { - "type" : "string" + "species" : { + "$ref" : "#/components/schemas/OntologyTerm" }, - "trialPUI" : { - "type" : "string" + "variantDbIds" : { + "type" : "array", + "description" : "variants", + "nullable" : true, + "items" : { + "type" : "string" + } } }, - "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + "description" : "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." }, - "ObservationUnitHierarchyLevel" : { + "ReferenceBases" : { "type" : "object", "properties" : { - "levelName" : { - "type" : "string" + "nextPageToken" : { + "type" : "string", + "description" : "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there are not any additional results.", + "nullable" : true, + "example" : "3a3d658a" }, - "levelOrder" : { + "offset" : { "type" : "integer", - "format" : "int32" + "description" : "The offset position (0-based) of the given sequence from the start of this `Reference`. This value will differ for each page in a request.", + "format" : "int32", + "nullable" : true, + "example" : 20000 + }, + "sequence" : { + "type" : "string", + "description" : "A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`.", + "nullable" : true, + "example" : "TAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATATTAGGATTGAGCTCTATAT" } }, - "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" " + "description" : "A string representation of the `Reference` base alleles." }, - "ObservationUnitLevel" : { + "ReferenceBasesRequest" : { "type" : "object", "properties" : { - "levelCode" : { - "type" : "string" - }, - "levelName" : { - "type" : "string" - }, - "levelOrder" : { + "end" : { "type" : "integer", + "description" : "The end position (0-based, exclusive) of this query. Defaults to the length of this `Reference`.", "format" : "int32" - } - }, - "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" " - }, - "ObservationUnitLevelRelationship" : { - "type" : "object", - "properties" : { - "levelCode" : { - "type" : "string" }, - "levelName" : { - "type" : "string" + "pageToken" : { + "type" : "string", + "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response." }, - "levelOrder" : { + "start" : { "type" : "integer", + "description" : "The start position (0-based) of this query. Defaults to 0.\nGenomic positions are non-negative integers less than reference length.\nRequests spanning the join of circular genomes are represented as\ntwo requests one on each side of the join (position 0).", "format" : "int32" - }, - "observationUnit" : { - "$ref" : "#/components/schemas/ObservationUnit" } - }, - "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** " + } }, - "ObservationUnitNewRequest" : { - "required" : [ - "observationUnitDbId", - "observationUnitDbId" - ], + "ReferenceRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "accessions" : { + "type" : "array", + "description" : "If specified, return the references for which the `accession` matches this string (case-sensitive, exact match).", + "items" : { + "type" : "string" + } }, - "crossDbId" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "crossName" : { - "type" : "string" + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "germplasmDbId" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "germplasmName" : { - "type" : "string" + "isDerived" : { + "type" : "boolean", + "description" : "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", + "format" : "boolean" }, - "germplasmPUI" : { - "type" : "string" + "maxLength" : { + "type" : "integer", + "description" : "The minimum length of this `References` sequence.", + "format" : "int32", + "example" : 90000 }, - "locationDbId" : { - "type" : "string" + "md5checksums" : { + "type" : "array", + "description" : "If specified, return the references for which the `md5checksum` matches this string (case-sensitive, exact match).", + "items" : { + "type" : "string" + } }, - "locationName" : { - "type" : "string" + "minLength" : { + "type" : "integer", + "description" : "The minimum length of this `References` sequence.", + "format" : "int32", + "example" : 4000 }, - "observationUnitDbId" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "observationUnitName" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "observationUnitPUI" : { - "type" : "string" + "referenceDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `References` within the given database server", + "items" : { + "type" : "string" + } }, - "programDbId" : { - "type" : "string" + "referenceSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `ReferenceSets` within the given database server", + "items" : { + "type" : "string" + } }, - "programName" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "seedLotDbId" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "seedLotName" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "studyDbId" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + } + } + }, + "ReferenceSearchRequest" : { + "type" : "object", + "properties" : { + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "studyName" : { - "type" : "string" + "isDerived" : { + "type" : "boolean", + "description" : "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", + "format" : "boolean" }, - "studyPUI" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "minLength" : { + "type" : "integer", + "description" : "The minimum length of this `References` sequence.", + "format" : "int32", + "example" : 4000 + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "trialDbId" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "trialName" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "trialPUI" : { - "type" : "string" - } - }, - "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." - }, - "ObservationUnitPosition" : { - "type" : "object", - "properties" : { - "entryType" : { - "type" : "string", - "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", - "enum" : [ - "CHECK", - "TEST", - "FILLER" - ] + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "observationLevel" : { - "$ref" : "#/components/schemas/ObservationUnitLevel" + "referenceSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `ReferenceSets` within the given database server", + "items" : { + "type" : "string" + } }, - "observationUnitDbId" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "observationUnitName" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } }, - "observationUnitPUI" : { - "type" : "string" + "md5checksums" : { + "type" : "array", + "description" : "If specified, return the references for which the `md5checksum` matches this string (case-sensitive, exact match).", + "items" : { + "type" : "string" + } }, - "positionCoordinateX" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "positionCoordinateXType" : { - "$ref" : "#/components/schemas/PositionCoordinateType" + "referenceDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `References` within the given database server", + "items" : { + "type" : "string" + } }, - "positionCoordinateY" : { - "type" : "string" + "accessions" : { + "type" : "array", + "description" : "If specified, return the references for which the `accession` matches this string (case-sensitive, exact match).", + "items" : { + "type" : "string" + } }, - "positionCoordinateYType" : { - "$ref" : "#/components/schemas/PositionCoordinateType" + "maxLength" : { + "type" : "integer", + "description" : "The minimum length of this `References` sequence.", + "format" : "int32", + "example" : 90000 } }, - "description" : "All positional and layout information related to this Observation Unit" + "description" : "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." }, - "ObservationUnitSearchRequest" : { - "type" : "object", - "properties" : { - "includeObservations" : { - "type" : "boolean" + "ReferenceSet" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/ReferenceSetNewRequest" + }, + { + "required" : [ + "referenceSetDbId" + ], + "type" : "object", + "properties" : { + "referenceSetDbId" : { + "type" : "string", + "description" : "The unique identifier for a ReferenceSet" + } + }, + "description" : "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." } - }, - "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + ] }, - "ObservationVariable" : { + "ReferenceSetNewRequest" : { "required" : [ - "methodDbId", - "methodName", - "observationVariableDbId", - "observationVariableName", - "scaleDbId", - "scaleName", - "traitName" + "referenceSetName" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "commonCropName" : { - "type" : "string" - }, - "defaultValue" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "growthStage" : { - "type" : "string" - }, - "institution" : { - "type" : "string" - }, - "language" : { - "type" : "string" - }, - "methodDbId" : { - "type" : "string" + "assemblyPUI" : { + "type" : "string", + "description" : "The remaining information is about the source of the sequences Public id of this reference set, such as `GRCH_37`.", + "nullable" : true }, - "methodName" : { - "type" : "string" + "commonCropName" : { + "type" : "string", + "description" : "Common name for the crop", + "nullable" : true }, - "methodPUI" : { - "type" : "string" + "description" : { + "type" : "string", + "description" : "Optional free text description of this reference set.", + "nullable" : true }, - "observationVariableName" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "observationVariablePUI" : { - "type" : "string" + "isDerived" : { + "type" : "boolean", + "description" : "A reference set may be derived from a source if it contains additional sequences, or some of the sequences within it are derived (see the definition of `isDerived` in `Reference`).", + "nullable" : true }, - "ontologyReferenceDbId" : { - "type" : "string" + "md5checksum" : { + "type" : "string", + "description" : "Order-independent MD5 checksum which identifies this `ReferenceSet`.\n\nTo compute this checksum, make a list of `Reference.md5checksum` for all\n`Reference` s in this set. Then sort that list, and take the MD5 hash of\nall the strings concatenated together. Express the hash as a lower-case\nhexadecimal string.", + "nullable" : true }, - "scaleDbId" : { + "referenceDbId" : { "type" : "string" }, - "scaleName" : { + "referenceName" : { "type" : "string" }, - "scalePUI" : { - "type" : "string" + "referenceSetName" : { + "type" : "string", + "description" : "The human readable name of a ReferenceSet" }, - "scientist" : { - "type" : "string" + "sourceAccessions" : { + "type" : "array", + "description" : "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`.", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "status" : { - "type" : "string" + "sourceGermplasmDbIds" : { + "type" : "array", + "description" : "All known corresponding Germplasm", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "submissionTimestamp" : { - "type" : "string" + "sourceURI" : { + "type" : "string", + "description" : "Specifies a FASTA format file/string.", + "nullable" : true }, - "traitDbId" : { - "type" : "string" + "species" : { + "$ref" : "#/components/schemas/OntologyTerm" }, - "traitName" : { - "type" : "string" + "variantDbIds" : { + "type" : "array", + "description" : "variants", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "traitPUI" : { - "type" : "string" + "variantSetDbIds" : { + "type" : "array", + "description" : "variantSets", + "nullable" : true, + "items" : { + "type" : "string" + } } - } + }, + "description" : "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." }, - "ObservationVariableNewRequest" : { - "required" : [ - "methodDbId", - "methodName", - "observationVariableDbId", - "observationVariableDbId", - "observationVariableName", - "scaleDbId", - "scaleName", - "traitName" - ], + "ReferenceSetRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "accessions" : { + "type" : "array", + "description" : "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match).", + "items" : { + "type" : "string" + } }, - "commonCropName" : { - "type" : "string" + "assemblyPUIs" : { + "type" : "array", + "description" : "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match).", + "items" : { + "type" : "string" + } }, - "defaultValue" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "documentationURL" : { - "type" : "string" + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "md5checksums" : { + "type" : "array", + "description" : "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match).", + "items" : { + "type" : "string" + } }, - "growthStage" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "institution" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "language" : { - "type" : "string" + "referenceSetDbIds" : { + "type" : "array", + "description" : "The `ReferenceSets` to search.", + "items" : { + "type" : "string" + } }, - "methodDbId" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "methodName" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "methodPUI" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "observationVariableDbId" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + } + } + }, + "ReferenceSetSearchRequest" : { + "type" : "object", + "properties" : { + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "observationVariableName" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "observationVariablePUI" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "ontologyReferenceDbId" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "scaleDbId" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "scaleName" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "scalePUI" : { - "type" : "string" + "referenceSetDbIds" : { + "type" : "array", + "description" : "The `ReferenceSets` to search.", + "items" : { + "type" : "string" + } }, - "scientist" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "status" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } }, - "submissionTimestamp" : { - "type" : "string" + "md5checksums" : { + "type" : "array", + "description" : "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match).", + "items" : { + "type" : "string" + } }, - "traitDbId" : { - "type" : "string" + "assemblyPUIs" : { + "type" : "array", + "description" : "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match).", + "items" : { + "type" : "string" + } }, - "traitName" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "traitPUI" : { - "type" : "string" + "accessions" : { + "type" : "array", + "description" : "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match).", + "items" : { + "type" : "string" + } } - } + }, + "description" : "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." }, - "ObservationVariableSearchRequest" : { - "type" : "object", - "properties" : { } + "Sample" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/SampleNewRequest" + }, + { + "type" : "object", + "properties" : { + "sampleDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a `Sample`\n
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample.", + "nullable" : true + } + }, + "description" : "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." + } + ] }, - "Ontology" : { + "SampleNewRequest" : { "required" : [ - "ontologyDbId", - "ontologyName" + "sampleName" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "authors" : { - "type" : "string" + "callSetDbIds" : { + "type" : "array", + "description" : "", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "copyright" : { - "type" : "string" + "column" : { + "type" : "integer", + "description" : "The Column identifier for this `Sample` location in the `Plate`", + "format" : "int32", + "nullable" : true }, - "description" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "documentationURL" : { + "germplasmDbId" : { "type" : "string" }, - "licence" : { + "germplasmName" : { "type" : "string" }, - "ontologyName" : { + "germplasmPUI" : { "type" : "string" }, - "version" : { + "observationUnitDbId" : { "type" : "string" - } - }, - "description" : "The identifier and metadata needed to reference an external controlled vocabulary" - }, - "OntologyNewRequest" : { - "required" : [ - "ontologyDbId", - "ontologyDbId", - "ontologyName" - ], - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" }, - "authors" : { + "observationUnitName" : { "type" : "string" }, - "copyright" : { + "observationUnitPUI" : { "type" : "string" }, - "description" : { + "plateDbId" : { "type" : "string" }, - "documentationURL" : { + "plateName" : { "type" : "string" }, - "licence" : { + "programDbId" : { "type" : "string" }, - "ontologyDbId" : { + "programName" : { "type" : "string" }, - "ontologyName" : { - "type" : "string" + "row" : { + "type" : "string", + "description" : "The Row identifier for this `Sample` location in the `Plate`", + "nullable" : true }, - "version" : { - "type" : "string" - } - }, - "description" : "The identifier and metadata needed to reference an external controlled vocabulary" - }, - "OntologyReference" : { - "required" : [ - "ontology" - ], - "type" : "object", - "properties" : { - "ontology" : { - "$ref" : "#/components/schemas/Ontology" + "sampleBarcode" : { + "type" : "string", + "description" : "A unique identifier physically attached to the `Sample`", + "nullable" : true + }, + "sampleDescription" : { + "type" : "string", + "description" : "Description of a `Sample`\n
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing.", + "nullable" : true + }, + "sampleGroupId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a group of `Samples`", + "nullable" : true + }, + "sampleName" : { + "type" : "string", + "description" : "The human readable name of the `Sample`" + }, + "samplePUI" : { + "type" : "string", + "description" : "A permanent unique identifier for the `Sample` (DOI, URL, UUID, etc)\n
MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible. ", + "nullable" : true + }, + "sampleTimestamp" : { + "type" : "string", + "description" : "The date and time a `Sample` was collected from the field\n
MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested", + "format" : "date-time", + "nullable" : true + }, + "sampleType" : { + "type" : "string", + "description" : "The type of `Sample` taken. ex. 'DNA', 'RNA', 'Tissue', etc", + "nullable" : true }, - "ontologyReferenceDbId" : { + "studyDbId" : { "type" : "string" }, - "version" : { - "type" : "string" - } - }, - "description" : "MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)." - }, - "OntologyTerm" : { - "type" : "object", - "properties" : { - "term" : { + "studyName" : { "type" : "string" }, - "termURI" : { + "studyPUI" : { "type" : "string" - } - }, - "description" : "A pointer to an ontology used by a genomic reference" - }, - "Pagination" : { - "type" : "object", - "properties" : { - "alleleMatrix" : { - "$ref" : "#/components/schemas/AlleleMatrix" }, - "dimension" : { + "takenBy" : { "type" : "string", - "description" : "The dimension of the matrix being paginated", - "enum" : [ - "CALLSETS", - "VARIANTS" - ] + "description" : "The name or identifier of the entity which took the `Sample` from the field", + "nullable" : true }, - "page" : { - "type" : "integer", - "format" : "int32" + "tissueType" : { + "type" : "string", + "description" : "The type of tissue sampled. ex. 'Leaf', 'Root', etc.\n
MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology).", + "nullable" : true }, - "pageSize" : { - "type" : "integer", - "format" : "int32" + "trialDbId" : { + "type" : "string" }, - "totalCount" : { - "type" : "integer", - "format" : "int32" + "trialName" : { + "type" : "string" }, - "totalPages" : { - "type" : "integer", - "format" : "int32" + "trialPUI" : { + "type" : "string" + }, + "well" : { + "type" : "string", + "description" : "The Well identifier for this `Sample` location in the `Plate`. Usually a concatenation of Row and Column, or just a number if the `Samples` are not part of an ordered `Plate`.", + "nullable" : true } }, - "description" : "Pagination info for the matrix" - }, - "ParentType" : { - "type" : "string", - "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", - "enum" : [ - "MALE", - "FEMALE", - "SELF", - "POPULATION", - "CLONAL" - ] + "description" : "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." }, - "PedigreeNode" : { - "required" : [ - "germplasmDbId", - "germplasmName", - "germplasmPUI" - ], + "SampleRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "breedingMethodDbId" : { - "type" : "string" + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "breedingMethodName" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "crossingProjectDbId" : { - "type" : "string" + "observationUnitDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies an `ObservationUnit`", + "items" : { + "type" : "string" + } }, - "crossingProjectName" : { - "type" : "string" + "plateDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a `Plate` of `Samples`", + "items" : { + "type" : "string" + } }, - "crossingYear" : { - "type" : "integer", - "format" : "int32" + "plateNames" : { + "type" : "array", + "description" : "The human readable name of a `Plate` of `Samples`", + "items" : { + "type" : "string" + } }, - "defaultDisplayName" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "familyCode" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "germplasmDbId" : { - "type" : "string" + "sampleDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a `Sample`", + "items" : { + "type" : "string" + } }, - "germplasmName" : { - "type" : "string" + "sampleGroupDbIds" : { + "type" : "array", + "description" : "The unique identifier for a group of related `Samples`", + "items" : { + "type" : "string" + } }, - "germplasmPUI" : { - "type" : "string" + "sampleNames" : { + "type" : "array", + "description" : "The human readable name of the `Sample`", + "items" : { + "type" : "string" + } }, - "pedigreeNodeDbId" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "pedigreeString" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "siblingDbIds" : { + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { "type" : "array", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } } - }, - "description" : "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances." + } }, - "PedigreeNodeSearchRequest" : { + "SampleSearchRequest" : { "type" : "object", "properties" : { - "includeFullTree" : { - "type" : "boolean" + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "includeParents" : { - "type" : "boolean" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "includeProgeny" : { - "type" : "boolean" + "observationUnitDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies an `ObservationUnit`", + "items" : { + "type" : "string" + } }, - "includeSiblings" : { - "type" : "boolean" + "plateNames" : { + "type" : "array", + "description" : "The human readable name of a `Plate` of `Samples`", + "items" : { + "type" : "string" + } }, - "pedigreeDepth" : { - "type" : "integer", - "format" : "int32" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "progenyDepth" : { - "type" : "integer", - "format" : "int32" - } - }, - "description" : "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances." - }, - "Person" : { - "required" : [ - "personDbId" - ], - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "description" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "emailAddress" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "firstName" : { - "type" : "string" + "sampleDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a `Sample`", + "items" : { + "type" : "string" + } + }, + "plateDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a `Plate` of `Samples`", + "items" : { + "type" : "string" + } }, - "lastName" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "mailingAddress" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } }, - "middleName" : { - "type" : "string" + "sampleGroupDbIds" : { + "type" : "array", + "description" : "The unique identifier for a group of related `Samples`", + "items" : { + "type" : "string" + } }, - "phoneNumber" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "userID" : { - "type" : "string" + "sampleNames" : { + "type" : "array", + "description" : "The human readable name of the `Sample`", + "items" : { + "type" : "string" + } } }, - "description" : "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." + "description" : "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." }, - "PersonNewRequest" : { + "SampleType" : { + "type" : "string", + "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", + "enum" : [ + "DNA", + "RNA", + "TISSUE", + "MIXED" + ] + }, + "Scale" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/ScaleNewRequest" + }, + { + "required" : [ + "scaleDbId" + ], + "type" : "object", + "properties" : { + "scaleDbId" : { + "type" : "string", + "description" : "Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID." + } + }, + "description" : "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"." + } + ] + }, + "ScaleNewRequest" : { "required" : [ - "personDbId", - "personDbId" + "scaleName" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "description" : { - "type" : "string" - }, - "emailAddress" : { - "type" : "string" + "dataType" : { + "type" : "string", + "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", + "nullable" : true, + "enum" : [ + "Code", + "Date", + "Duration", + "Nominal", + "Numerical", + "Ordinal", + "Text" + ] }, - "firstName" : { - "type" : "string" + "decimalPlaces" : { + "type" : "integer", + "description" : "For numerical, number of decimal places to be reported", + "format" : "int32", + "nullable" : true }, - "lastName" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "mailingAddress" : { - "type" : "string" + "ontologyReference" : { + "$ref" : "#/components/schemas/OntologyReference" }, - "middleName" : { - "type" : "string" + "scaleName" : { + "type" : "string", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable" }, - "personDbId" : { - "type" : "string" + "scalePUI" : { + "type" : "string", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "nullable" : true }, - "phoneNumber" : { - "type" : "string" + "units" : { + "type" : "string", + "description" : "This field can be used to describe the units used for this scale. This should be the abbreviated \nform of the units, intended to be displayed with every value using this scale. Usually this only \napplies when `dataType` is Numeric, but could also be included for other dataTypes when applicable.", + "nullable" : true }, - "userID" : { - "type" : "string" + "validValues" : { + "$ref" : "#/components/schemas/ValidValues" } }, - "description" : "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." - }, - "PersonSearchRequest" : { - "type" : "object", - "properties" : { }, - "description" : "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." + "description" : "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"." }, - "PlannedCross" : { - "required" : [ - "plannedCrossDbId" - ], + "ScaleRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "crossType" : { - "$ref" : "#/components/schemas/CrossType" - }, - "crossingProjectDbId" : { - "type" : "string" - }, - "crossingProjectName" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "parent1" : { - "$ref" : "#/components/schemas/CrossParent" + "observationVariableDbIds" : { + "type" : "array", + "description" : "The unique identifier for an observation variable.", + "items" : { + "type" : "string" + } }, - "parent2" : { - "$ref" : "#/components/schemas/CrossParent" + "ontologyDbIds" : { + "type" : "array", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "items" : { + "type" : "string" + } }, - "plannedCrossDbId" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "plannedCrossName" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "status" : { - "type" : "string", - "description" : "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", - "enum" : [ - "TODO", - "DONE", - "SKIPPED" - ] + "scaleDbIds" : { + "type" : "array", + "description" : "The unique identifier for a scale.", + "items" : { + "type" : "string" + } } - }, - "description" : "Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field." + } }, - "Plate" : { + "Season" : { "required" : [ - "plateDbId", - "plateName" + "seasonDbId" ], "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "plateBarcode" : { - "type" : "string" - }, - "plateFormat" : { + "seasonDbId" : { "type" : "string", - "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", - "enum" : [ - "PLATE_96", - "TUBES" - ] - }, - "plateName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" + "description" : "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'" }, - "programName" : { - "type" : "string" - }, - "sampleType" : { + "seasonName" : { "type" : "string", - "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", - "enum" : [ - "DNA", - "RNA", - "TISSUE", - "MIXED" - ] + "description" : "Name of the season. ex. 'Spring', 'Q2', 'Season A', etc.", + "nullable" : true }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" + "year" : { + "type" : "integer", + "description" : "The 4 digit year of the season.", + "format" : "int32", + "nullable" : true + } + }, + "description" : "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"." + }, + "SeasonRequest" : { + "type" : "object", + "properties" : { + "seasonDbIds" : { + "type" : "array", + "description" : "The unique identifier for a season. For backward compatibility it can be a string like '2012', '1957-2004'.", + "items" : { + "type" : "string" + } }, - "studyPUI" : { - "type" : "string" + "seasonNames" : { + "type" : "array", + "description" : "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\".", + "items" : { + "type" : "string" + } }, - "trialDbId" : { - "type" : "string" + "seasons" : { + "type" : "array", + "description" : "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\".", + "items" : { + "type" : "string" + } }, - "trialName" : { - "type" : "string" + "years" : { + "type" : "array", + "description" : "The 4 digit year of a season. Example \"2017\"", + "items" : { + "type" : "string" + } + } + } + }, + "SeedLot" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/SeedLotNewRequest" }, - "trialPUI" : { - "type" : "string" + { + "required" : [ + "seedLotDbId" + ], + "type" : "object", + "properties" : { + "seedLotDbId" : { + "type" : "string", + "description" : "Unique DbId for the Seed Lot" + } + }, + "description" : "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program." } - }, - "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." + ] }, - "PlateNewRequest" : { + "SeedLotNewRequest" : { "required" : [ - "plateDbId", - "plateName" + "seedLotName" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "plateBarcode" : { - "type" : "string" + "amount" : { + "type" : "number", + "description" : "The current balance of the amount of material in a SeedLot. Could be a count (seeds, bulbs, etc) or a weight (kg of seed).", + "nullable" : true }, - "plateDbId" : { - "type" : "string" + "contentMixture" : { + "type" : "array", + "description" : "The mixture of germplasm present in the seed lot.\n
\nIf this seed lot only contains a single germplasm, the response should contain the name \nand DbId of that germplasm with a mixturePercentage value of 100\n
\nIf the seed lot contains a mixture of different germplasm, the response should contain \nthe name and DbId every germplasm present. The mixturePercentage field should contain \nthe ratio of each germplasm in the total mixture. All of the mixturePercentage values \nin this array should sum to equal 100.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ContentMixture" + } }, - "plateFormat" : { + "createdDate" : { "type" : "string", - "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", - "enum" : [ - "PLATE_96", - "TUBES" - ] + "description" : "The time stamp for when this seed lot was created", + "format" : "date-time", + "nullable" : true }, - "plateName" : { + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "lastUpdated" : { + "type" : "string", + "description" : "The timestamp for the last update to this Seed Lot (including transactions)", + "format" : "date-time", + "nullable" : true + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { "type" : "string" }, "programDbId" : { @@ -12837,801 +20240,1025 @@ "programName" : { "type" : "string" }, - "sampleType" : { + "seedLotDescription" : { "type" : "string", - "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", - "enum" : [ - "DNA", - "RNA", - "TISSUE", - "MIXED" - ] - }, - "studyDbId" : { - "type" : "string" + "description" : "A general description of this Seed Lot", + "nullable" : true }, - "studyName" : { - "type" : "string" + "seedLotName" : { + "type" : "string", + "description" : "A human readable name for this Seed Lot" }, - "studyPUI" : { - "type" : "string" + "sourceCollection" : { + "type" : "string", + "description" : "The description of the source where this material was originally collected (wild, nursery, etc)", + "nullable" : true }, - "trialDbId" : { - "type" : "string" + "storageLocation" : { + "type" : "string", + "description" : "Description the storage location", + "nullable" : true }, - "trialName" : { - "type" : "string" + "transactions" : { + "type" : "array", + "description" : "The complete history of transactions for this seed lot. This includes seed increases, seed usage (planting), and trading with other breeding programs.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/SeedLotTransaction" + } }, - "trialPUI" : { - "type" : "string" + "units" : { + "type" : "string", + "description" : "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)", + "nullable" : true } }, - "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." + "description" : "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program." }, - "PlateSearchRequest" : { + "SeedLotRequest" : { "type" : "object", - "properties" : { }, - "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." + "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "crossDbIds" : { + "type" : "array", + "description" : "Search for Cross with this unique id", + "items" : { + "type" : "string" + } + }, + "crossNames" : { + "type" : "array", + "description" : "Search for Cross with this human readable name", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "seedLotDbIds" : { + "type" : "array", + "description" : "Unique id for a seed lot on this server", + "items" : { + "type" : "string" + } + } + } }, - "PollinationEvent" : { + "SeedLotTransaction" : { + "required" : [ + "transactionDbId" + ], "type" : "object", "properties" : { - "crossDbId" : { - "type" : "string" + "additionalInfo" : { + "$ref" : "#/components/schemas/AdditionalInfo" }, - "crossName" : { + "amount" : { + "type" : "number", + "description" : "The number of units being transferred between SeedLots. Could be a count (seeds, bulbs, etc) or a weight (kg of seed).", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "seedLotDbId" : { "type" : "string" }, - "pollinationNumber" : { + "seedLotName" : { "type" : "string" }, - "pollinationSuccessful" : { - "type" : "boolean" + "transactionDbId" : { + "type" : "string", + "description" : "Unique DbId for the Seed Lot Transaction" }, - "pollinationTimeStamp" : { - "type" : "string" + "transactionDescription" : { + "type" : "string", + "description" : "A general description of this Seed Lot Transaction", + "nullable" : true + }, + "transactionTimestamp" : { + "type" : "string", + "description" : "The time stamp for when the transaction occurred", + "format" : "date-time", + "nullable" : true + }, + "units" : { + "type" : "string", + "description" : "A description of the things being transferred between SeedLots in a transaction (seeds, bulbs, kg, etc)", + "nullable" : true } }, - "description" : "A Pollination Event that was used or attempted for a Cross." + "description" : "The record of an event where material was moved in or out of a particular SeedLot" }, - "PositionCoordinateType" : { + "SortBy" : { "type" : "string", - "description" : "The type of positional coordinate. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "description" : "Name of the field to sort by.", "enum" : [ - "LONGITUDE", - "LATITUDE", - "PLANTED_ROW", - "PLANTED_INDIVIDUAL", - "GRID_ROW", - "GRID_COL", - "MEASURED_ROW", - "MEASURED_COL" - ] - }, - "Program" : { - "required" : [ + "studyDbId", + "trialDbId", "programDbId", + "locationDbId", + "seasonDbId", + "studyType", + "studyName", + "studyLocation", "programName" - ], + ] + }, + "SortOrder" : { + "type" : "string", + "description" : "Sort order direction. Ascending/Descending.", + "enum" : [ + "asc", + "ASC", + "desc", + "DESC" + ] + }, + "StorageType" : { "type" : "object", "properties" : { - "abbreviation" : { - "type" : "string" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" + "code" : { + "type" : "string", + "description" : "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", + "nullable" : true, + "enum" : [ + "10", + "11", + "12", + "13", + "20", + "30", + "40", + "50", + "99" + ] }, - "fundingInformation" : { - "type" : "string" + "description" : { + "type" : "string", + "description" : "A supplemental text description of the storage type", + "nullable" : true }, - "objective" : { + "germplasmDbId" : { "type" : "string" }, - "personDbId" : { + "germplasmName" : { "type" : "string" }, - "programName" : { + "germplasmPUI" : { "type" : "string" + } + }, + "description" : "The type of storage this germplasm is kept in at a genebank." + }, + "StorageTypeCode" : { + "type" : "string", + "description" : "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", + "enum" : [ + "10", + "11", + "12", + "13", + "20", + "30", + "40", + "50", + "99" + ] + }, + "Study" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/StudyNewRequest" }, - "programType" : { - "type" : "string", - "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", - "enum" : [ - "STANDARD", - "PROJECT" - ] + { + "required" : [ + "studyDbId" + ], + "type" : "object", + "properties" : { + "studyDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a study within the given database server\n\nMIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution." + } + }, + "description" : "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." } - }, - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." + ] }, - "ProgramNewRequest" : { + "StudyNewRequest" : { "required" : [ - "programDbId", - "programDbId", - "programName" + "studyName" ], "type" : "object", "properties" : { - "abbreviation" : { - "type" : "string" + "active" : { + "type" : "boolean", + "description" : "A flag to indicate if a Study is currently active and ongoing", + "nullable" : true }, "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, "commonCropName" : { - "type" : "string" + "type" : "string", + "description" : "Common name for the crop associated with this study", + "nullable" : true + }, + "culturalPractices" : { + "type" : "string", + "description" : "MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study.", + "nullable" : true + }, + "dataLinks" : { + "type" : "array", + "description" : "List of links to extra data files associated with this study. Extra data could include notes, images, and reference data.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/DataLink" + } }, "documentationURL" : { - "type" : "string" + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true }, - "fundingInformation" : { - "type" : "string" + "endDate" : { + "type" : "string", + "description" : "The date the study ends\n\nMIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended", + "format" : "date-time", + "nullable" : true }, - "objective" : { - "type" : "string" + "environmentParameters" : { + "type" : "array", + "description" : "Environmental parameters that were kept constant throughout the study and did not change between observation units.\n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below).", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/EnvironmentParameter" + } }, - "personDbId" : { - "type" : "string" + "experimentalDesign" : { + "$ref" : "#/components/schemas/ExperimentalDesign" }, - "programDbId" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "programName" : { - "type" : "string" + "growthFacility" : { + "$ref" : "#/components/schemas/GrowthFacility" }, - "programType" : { + "lastUpdate" : { + "$ref" : "#/components/schemas/LastUpdate" + }, + "license" : { "type" : "string", - "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", - "enum" : [ - "STANDARD", - "PROJECT" - ] - } - }, - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." - }, - "ProgramSearchRequest" : { - "type" : "object", - "properties" : { }, - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." - }, - "Publication" : { - "type" : "object", - "properties" : { - "publicationPUI" : { - "type" : "string" + "description" : "The usage license associated with the study data", + "nullable" : true }, - "publicationReference" : { + "locationDbId" : { "type" : "string" }, - "trialDbId" : { + "locationName" : { "type" : "string" }, - "trialName" : { - "type" : "string" + "observationLevels" : { + "type" : "array", + "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ObservationUnitHierarchyLevel" + } }, - "trialPUI" : { - "type" : "string" - } - }, - "description" : "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended." - }, - "Reference" : { - "required" : [ - "referenceDbId", - "referenceName" - ], - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "observationUnitsDescription" : { + "type" : "string", + "description" : "MIAPPE V1.1 (DM-25) Observation unit description - General description of the observation units in the study.", + "nullable" : true }, - "commonCropName" : { - "type" : "string" + "seasons" : { + "type" : "array", + "description" : "List of seasons over which this study was performed.", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "isDerived" : { - "type" : "boolean" + "startDate" : { + "type" : "string", + "description" : "The date this study started\n\nMIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started", + "format" : "date-time", + "nullable" : true }, - "length" : { - "type" : "integer", - "format" : "int32" + "studyCode" : { + "type" : "string", + "description" : "A short human readable code for a study", + "nullable" : true }, - "md5checksum" : { - "type" : "string" + "studyDescription" : { + "type" : "string", + "description" : "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study", + "nullable" : true }, - "referenceDbId" : { - "type" : "string" + "studyName" : { + "type" : "string", + "description" : "The human readable name for a study\n\nMIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study" }, - "referenceName" : { - "type" : "string" + "studyPUI" : { + "type" : "string", + "description" : "A permanent unique identifier associated with this study data. For example, a URI or DOI", + "nullable" : true }, - "referenceSetDbId" : { - "type" : "string" + "studyType" : { + "type" : "string", + "description" : "The type of study being performed. ex. \"Yield Trial\", etc", + "nullable" : true }, - "referenceSetName" : { + "trialDbId" : { "type" : "string" }, - "sourceDivergence" : { - "type" : "number" + "trialName" : { + "type" : "string" }, - "sourceGermplasmDbIds" : { + "trialPUI" : { + "type" : "string" + } + }, + "description" : "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." + }, + "StudyParameters" : { + "type" : "object", + "properties" : { + "studyDbIds" : { "type" : "array", + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } }, - "sourceURI" : { - "type" : "string" - }, - "species" : { - "$ref" : "#/components/schemas/OntologyTerm" - }, - "variantDbIds" : { + "studyNames" : { "type" : "array", + "description" : "List of study names to filter search results", "items" : { "type" : "string" } } - }, - "description" : "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." + } }, - "ReferenceSearchRequest" : { + "StudyRequest" : { "type" : "object", "properties" : { - "isDerived" : { - "type" : "boolean" + "active" : { + "type" : "boolean", + "description" : "A flag to indicate if a Study is currently active and ongoing", + "example" : true }, - "maxLength" : { - "type" : "integer", - "format" : "int32" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "minLength" : { - "type" : "integer", - "format" : "int32" - } - }, - "description" : "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." - }, - "ReferenceSet" : { - "required" : [ - "referenceSetDbId", - "referenceSetName" - ], - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "assemblyPUI" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "commonCropName" : { - "type" : "string" + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } }, - "description" : { - "type" : "string" + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } }, - "isDerived" : { - "type" : "boolean" + "observationVariableDbIds" : { + "type" : "array", + "description" : "The DbIds of Variables to search for", + "items" : { + "type" : "string" + } }, - "md5checksum" : { - "type" : "string" + "observationVariableNames" : { + "type" : "array", + "description" : "The names of Variables to search for", + "items" : { + "type" : "string" + } }, - "referenceDbId" : { - "type" : "string" + "observationVariablePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "items" : { + "type" : "string" + } }, - "referenceName" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "referenceSetName" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "sourceGermplasmDbIds" : { + "seasonDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a season", + "items" : { + "type" : "string" + } + }, + "sortBy" : { + "type" : "string", + "description" : "Name of the field to sort by.", + "enum" : [ + "studyDbId", + "trialDbId", + "programDbId", + "locationDbId", + "seasonDbId", + "studyType", + "studyName", + "studyLocation", + "programName" + ] + }, + "sortOrder" : { + "type" : "string", + "description" : "Sort order direction. Ascending/Descending.", + "enum" : [ + "asc", + "ASC", + "desc", + "DESC" + ] + }, + "studyCodes" : { "type" : "array", + "description" : "A short human readable code for a study", "items" : { "type" : "string" } }, - "sourceURI" : { - "type" : "string" - }, - "species" : { - "$ref" : "#/components/schemas/OntologyTerm" - }, - "variantDbIds" : { + "studyDbIds" : { "type" : "array", + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } }, - "variantSetDbIds" : { + "studyNames" : { "type" : "array", + "description" : "List of study names to filter search results", "items" : { "type" : "string" } - } - }, - "description" : "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." - }, - "ReferenceSetNewRequest" : { - "required" : [ - "referenceSetDbId", - "referenceSetDbId", - "referenceSetName" - ], - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "assemblyPUI" : { - "type" : "string" - }, - "commonCropName" : { - "type" : "string" - }, - "description" : { - "type" : "string" - }, - "isDerived" : { - "type" : "boolean" - }, - "md5checksum" : { - "type" : "string" - }, - "referenceDbId" : { - "type" : "string" - }, - "referenceName" : { - "type" : "string" - }, - "referenceSetDbId" : { - "type" : "string" - }, - "referenceSetName" : { - "type" : "string" }, - "sourceGermplasmDbIds" : { + "studyPUIs" : { "type" : "array", + "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", "items" : { "type" : "string" } }, - "sourceURI" : { - "type" : "string" - }, - "species" : { - "$ref" : "#/components/schemas/OntologyTerm" - }, - "variantDbIds" : { + "studyTypes" : { "type" : "array", + "description" : "The type of study being performed. ex. \"Yield Trial\", etc", "items" : { "type" : "string" } }, - "variantSetDbIds" : { + "trialDbIds" : { "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } - } - }, - "description" : "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." - }, - "ReferenceSetSearchRequest" : { - "type" : "object", - "properties" : { }, - "description" : "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data." - }, - "Sample" : { - "required" : [ - "sampleDbId", - "sampleName" - ], - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" }, - "callSetDbIds" : { + "trialNames" : { "type" : "array", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } - }, - "column" : { - "type" : "integer", - "format" : "int32" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, - "plateDbId" : { - "type" : "string" - }, - "plateName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" - }, - "programName" : { - "type" : "string" - }, - "row" : { - "type" : "string" - }, - "sampleBarcode" : { - "type" : "string" - }, - "sampleDescription" : { - "type" : "string" - }, - "sampleGroupId" : { - "type" : "string" - }, - "sampleName" : { - "type" : "string" - }, - "samplePUI" : { - "type" : "string" - }, - "sampleTimestamp" : { - "type" : "string" - }, - "sampleType" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "takenBy" : { - "type" : "string" - }, - "tissueType" : { - "type" : "string" - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - }, - "well" : { - "type" : "string" } - }, - "description" : "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." + } }, - "SampleNewRequest" : { - "required" : [ - "sampleDbId", - "sampleName" - ], + "StudySearchRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "callSetDbIds" : { + "germplasmDbIds" : { "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", "items" : { "type" : "string" } }, - "column" : { - "type" : "integer", - "format" : "int32" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } }, - "observationUnitPUI" : { - "type" : "string" + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } }, - "plateDbId" : { - "type" : "string" + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "items" : { + "type" : "string" + } }, - "plateName" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "programDbId" : { - "type" : "string" + "seasonDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a season", + "items" : { + "type" : "string" + } }, - "programName" : { - "type" : "string" + "active" : { + "type" : "boolean", + "description" : "A flag to indicate if a Study is currently active and ongoing", + "example" : true }, - "row" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "sampleBarcode" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "sampleDbId" : { - "type" : "string" + "studyCodes" : { + "type" : "array", + "description" : "A short human readable code for a study", + "items" : { + "type" : "string" + } }, - "sampleDescription" : { - "type" : "string" + "studyPUIs" : { + "type" : "array", + "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", + "items" : { + "type" : "string" + } }, - "sampleGroupId" : { - "type" : "string" + "observationVariablePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "items" : { + "type" : "string" + } }, - "sampleName" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "samplePUI" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "sampleTimestamp" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } }, - "sampleType" : { - "type" : "string" + "observationVariableNames" : { + "type" : "array", + "description" : "The names of Variables to search for", + "items" : { + "type" : "string" + } }, - "studyDbId" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "studyName" : { - "type" : "string" + "observationVariableDbIds" : { + "type" : "array", + "description" : "The DbIds of Variables to search for", + "items" : { + "type" : "string" + } }, - "studyPUI" : { - "type" : "string" + "sortOrder" : { + "type" : "string", + "description" : "Sort order direction. Ascending/Descending.", + "enum" : [ + "asc", + "ASC", + "desc", + "DESC" + ] }, - "takenBy" : { - "type" : "string" + "sortBy" : { + "type" : "string", + "description" : "Name of the field to sort by.", + "enum" : [ + "studyDbId", + "trialDbId", + "programDbId", + "locationDbId", + "seasonDbId", + "studyType", + "studyName", + "studyLocation", + "programName" + ] }, - "tissueType" : { + "studyTypes" : { + "type" : "array", + "description" : "The type of study being performed. ex. \"Yield Trial\", etc", + "items" : { + "type" : "string" + } + } + }, + "description" : "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." + }, + "Synonym" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { "type" : "string" }, - "trialDbId" : { + "germplasmName" : { "type" : "string" }, - "trialName" : { + "germplasmPUI" : { "type" : "string" }, - "trialPUI" : { - "type" : "string" + "synonym" : { + "type" : "string", + "description" : "Alternative name or ID used to reference this germplasm", + "nullable" : true }, - "well" : { - "type" : "string" + "type" : { + "type" : "string", + "description" : "A descriptive classification for this synonym", + "nullable" : true } }, - "description" : "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." - }, - "SampleSearchRequest" : { - "type" : "object", - "properties" : { }, - "description" : "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)." + "description" : "Alternative names or IDs used to reference this germplasm" }, - "Scale" : { + "TaxonId" : { "required" : [ - "scaleDbId", - "scaleName" + "sourceName", + "taxonId" ], "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "dataType" : { - "type" : "string", - "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", - "enum" : [ - "Code", - "Date", - "Duration", - "Nominal", - "Numerical", - "Ordinal", - "Text" - ] - }, - "decimalPlaces" : { - "type" : "integer", - "format" : "int32" - }, - "ontologyReferenceDbId" : { + "germplasmDbId" : { "type" : "string" }, - "scaleName" : { + "germplasmName" : { "type" : "string" }, - "scalePUI" : { + "germplasmPUI" : { "type" : "string" }, - "units" : { - "type" : "string" + "sourceName" : { + "type" : "string", + "description" : "The human readable name of the taxonomy provider" }, - "validValues" : { - "$ref" : "#/components/schemas/ValidValues" + "taxonId" : { + "type" : "string", + "description" : "The identifier (name, ID, URI) of a particular taxonomy within the source provider" } }, - "description" : "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"." + "description" : "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended." }, - "ScaleNewRequest" : { + "Trait" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/TraitNewRequest" + }, + { + "type" : "object", + "properties" : { + "traitDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a trait", + "nullable" : true + } + }, + "description" : "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". " + } + ] + }, + "TraitDataType" : { + "type" : "string", + "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", + "enum" : [ + "Code", + "Date", + "Duration", + "Nominal", + "Numerical", + "Ordinal", + "Text" + ] + }, + "TraitNewRequest" : { "required" : [ - "scaleDbId", - "scaleDbId", - "scaleName" + "traitName" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "dataType" : { + "alternativeAbbreviations" : { + "type" : "array", + "description" : "A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention.", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "attribute" : { "type" : "string", - "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", - "enum" : [ - "Code", - "Date", - "Duration", - "Nominal", - "Numerical", - "Ordinal", - "Text" - ] + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "nullable" : true }, - "decimalPlaces" : { - "type" : "integer", - "format" : "int32" + "attributePUI" : { + "type" : "string", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "nullable" : true }, - "ontologyReferenceDbId" : { - "type" : "string" + "entity" : { + "type" : "string", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "nullable" : true }, - "scaleDbId" : { - "type" : "string" + "entityPUI" : { + "type" : "string", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A Trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the Entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "nullable" : true }, - "scaleName" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "scalePUI" : { - "type" : "string" + "mainAbbreviation" : { + "type" : "string", + "description" : "A shortened version of the human readable name for a Trait", + "nullable" : true }, - "units" : { - "type" : "string" + "ontologyReference" : { + "$ref" : "#/components/schemas/OntologyReference" }, - "validValues" : { - "$ref" : "#/components/schemas/ValidValues" - } - }, - "description" : "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"." - }, - "Season" : { - "required" : [ - "seasonDbId" - ], - "type" : "object", - "properties" : { - "seasonDbId" : { - "type" : "string" + "status" : { + "type" : "string", + "description" : "Trait status (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)", + "nullable" : true }, - "seasonName" : { - "type" : "string" + "synonyms" : { + "type" : "array", + "description" : "Other trait names", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "year" : { - "type" : "integer", - "format" : "int32" + "traitClass" : { + "type" : "string", + "description" : "A classification to describe the type of trait and the context it should be considered in.\n
examples- \"morphological\", \"phenological\", \"agronomical\", \"physiological\", \"abiotic stress\", \"biotic stress\", \"biochemical\", \"quality traits\", \"fertility\", etc.", + "nullable" : true + }, + "traitDescription" : { + "type" : "string", + "description" : "The description of a trait", + "nullable" : true + }, + "traitName" : { + "type" : "string", + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation" + }, + "traitPUI" : { + "type" : "string", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "nullable" : true } }, - "description" : "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"." + "description" : "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". " }, - "SeedLot" : { - "required" : [ - "seedLotDbId", - "seedLotName" - ], + "TraitRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "amount" : { - "type" : "number" - }, - "createdDate" : { - "type" : "string" - }, - "lastUpdated" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" - }, - "locationName" : { - "type" : "string" - }, - "programDbId" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "programName" : { - "type" : "string" + "observationVariableDbIds" : { + "type" : "array", + "description" : "The unique identifier for an observation variable.", + "items" : { + "type" : "string" + } }, - "seedLotDescription" : { - "type" : "string" + "ontologyDbIds" : { + "type" : "array", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "items" : { + "type" : "string" + } }, - "seedLotName" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "sourceCollection" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "storageLocation" : { - "type" : "string" + "traitDbIds" : { + "type" : "array", + "description" : "The unique identifier for a trait.", + "items" : { + "type" : "string" + } + } + } + }, + "Trial" : { + "allOf" : [ + { + "$ref" : "#/components/schemas/TrialNewRequest" }, - "units" : { - "type" : "string" + { + "required" : [ + "trialDbId" + ], + "type" : "object", + "properties" : { + "trialDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a trial\n\nMIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution." + } + }, + "description" : "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." } - }, - "description" : "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program." + ] }, - "SeedLotNewRequest" : { + "TrialNewRequest" : { "required" : [ - "seedLotDbId", - "seedLotDbId", - "seedLotName" + "trialName" ], "type" : "object", "properties" : { + "active" : { + "type" : "boolean", + "description" : "A flag to indicate if a Trial is currently active and ongoing", + "nullable" : true + }, "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "amount" : { - "type" : "number" + "commonCropName" : { + "type" : "string", + "description" : "Common name for the crop associated with this trial", + "nullable" : true }, - "createdDate" : { - "type" : "string" + "contacts" : { + "type" : "array", + "description" : "List of contact entities associated with this trial", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Contact" + } }, - "lastUpdated" : { - "type" : "string" + "datasetAuthorships" : { + "type" : "array", + "description" : "License and citation information for the data in this trial", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/DatasetAuthorships" + } }, - "locationDbId" : { - "type" : "string" + "documentationURL" : { + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true }, - "locationName" : { - "type" : "string" + "endDate" : { + "type" : "string", + "description" : "The date this trial ends", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, "programDbId" : { "type" : "string" @@ -13639,343 +21266,401 @@ "programName" : { "type" : "string" }, - "seedLotDbId" : { - "type" : "string" + "publications" : { + "type" : "array", + "description" : "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Publication" + } }, - "seedLotDescription" : { - "type" : "string" + "startDate" : { + "type" : "string", + "description" : "The date this trial started", + "nullable" : true }, - "seedLotName" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "sourceCollection" : { - "type" : "string" + "trialDescription" : { + "type" : "string", + "description" : "The human readable description of a trial\n\nMIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail.", + "nullable" : true }, - "storageLocation" : { - "type" : "string" + "trialName" : { + "type" : "string", + "description" : "The human readable name of a trial\n\nMIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation." }, - "units" : { - "type" : "string" + "trialPUI" : { + "type" : "string", + "description" : "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", + "nullable" : true } }, - "description" : "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program." + "description" : "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." }, - "SeedLotTransaction" : { - "required" : [ - "transactionDbId" - ], + "TrialParameters" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "amount" : { - "type" : "number" - }, - "seedLotDbId" : { - "type" : "string" - }, - "seedLotName" : { - "type" : "string" - }, - "transactionDbId" : { - "type" : "string" - }, - "transactionDescription" : { - "type" : "string" - }, - "transactionTimestamp" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "units" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } } - }, - "description" : "The record of an event where material was moved in or out of a particular SeedLot" + } }, - "StorageType" : { + "TrialRequest" : { "type" : "object", "properties" : { - "code" : { - "type" : "string", - "description" : "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", - "enum" : [ - "10", - "11", - "12", - "13", - "20", - "30", - "40", - "50", - "99" - ] - }, - "description" : { - "type" : "string" - }, - "germplasmDbId" : { - "type" : "string" + "active" : { + "type" : "boolean", + "description" : "A flag to indicate if a Trial is currently active and ongoing", + "example" : true }, - "germplasmName" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "germplasmPUI" : { - "type" : "string" - } - }, - "description" : "The type of storage this germplasm is kept in at a genebank." - }, - "Study" : { - "required" : [ - "studyDbId", - "studyName" - ], - "type" : "object", - "properties" : { - "active" : { - "type" : "boolean" + "contactDbIds" : { + "type" : "array", + "description" : "List of contact entities associated with this trial", + "items" : { + "type" : "string" + } }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } }, - "commonCropName" : { - "type" : "string" + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } }, - "contactDbIds" : { + "observationVariableDbIds" : { "type" : "array", + "description" : "The DbIds of Variables to search for", "items" : { "type" : "string" } }, - "culturalPractices" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" - }, - "endDate" : { - "type" : "string" - }, - "experimentalDesign" : { - "$ref" : "#/components/schemas/ExperimentalDesign" - }, - "growthFacility" : { - "$ref" : "#/components/schemas/GrowthFacility" - }, - "lastUpdateDbId" : { - "type" : "string" - }, - "license" : { - "type" : "string" - }, - "locationDbId" : { - "type" : "string" - }, - "locationName" : { - "type" : "string" + "observationVariableNames" : { + "type" : "array", + "description" : "The names of Variables to search for", + "items" : { + "type" : "string" + } }, - "observationLevelDbIds" : { + "observationVariablePUIs" : { "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", "items" : { "type" : "string" } }, - "observationUnitsDescription" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "observationVariableDbIds" : { + "programNames" : { "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "startDate" : { - "type" : "string" + "searchDateRangeEnd" : { + "type" : "string", + "description" : "The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "format" : "date" }, - "studyCode" : { - "type" : "string" + "searchDateRangeStart" : { + "type" : "string", + "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "format" : "date" }, - "studyDescription" : { - "type" : "string" + "sortBy" : { + "type" : "string", + "description" : "Name of the field to sort by.", + "enum" : [ + "trialDbId", + "trialName", + "programDbId", + "programName", + "locationDbId", + "startDate", + "endDate" + ] }, - "studyName" : { - "type" : "string" + "sortOrder" : { + "type" : "string", + "description" : "Sort order direction. Ascending/Descending.", + "enum" : [ + "asc", + "ASC", + "desc", + "DESC" + ] }, - "studyPUI" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "studyType" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "trialDbId" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "trialName" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } }, - "trialPUI" : { - "type" : "string" + "trialPUIs" : { + "type" : "array", + "description" : "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", + "items" : { + "type" : "string" + } } - }, - "description" : "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." + } }, - "StudyNewRequest" : { - "required" : [ - "studyDbId", - "studyDbId", - "studyName" - ], + "TrialSearchRequest" : { "type" : "object", "properties" : { - "active" : { - "type" : "boolean" + "locationDbIds" : { + "type" : "array", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", + "items" : { + "type" : "string" + } }, - "commonCropName" : { - "type" : "string" + "searchDateRangeEnd" : { + "type" : "string", + "description" : "The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "format" : "date" }, - "contactDbIds" : { + "programNames" : { "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "culturalPractices" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" + "active" : { + "type" : "boolean", + "description" : "A flag to indicate if a Trial is currently active and ongoing", + "example" : true }, - "endDate" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "experimentalDesign" : { - "$ref" : "#/components/schemas/ExperimentalDesign" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "growthFacility" : { - "$ref" : "#/components/schemas/GrowthFacility" + "observationVariablePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "items" : { + "type" : "string" + } }, - "lastUpdateDbId" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "license" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "locationDbId" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } }, - "locationName" : { - "type" : "string" + "trialPUIs" : { + "type" : "array", + "description" : "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", + "items" : { + "type" : "string" + } }, - "observationLevelDbIds" : { + "observationVariableNames" : { "type" : "array", + "description" : "The names of Variables to search for", "items" : { "type" : "string" } }, - "observationUnitsDescription" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, "observationVariableDbIds" : { "type" : "array", + "description" : "The DbIds of Variables to search for", "items" : { "type" : "string" } }, - "startDate" : { - "type" : "string" - }, - "studyCode" : { - "type" : "string" - }, - "studyDbId" : { - "type" : "string" - }, - "studyDescription" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, - "studyType" : { - "type" : "string" + "sortOrder" : { + "type" : "string", + "description" : "Sort order direction. Ascending/Descending.", + "enum" : [ + "asc", + "ASC", + "desc", + "DESC" + ] }, - "trialDbId" : { - "type" : "string" + "sortBy" : { + "type" : "string", + "description" : "Name of the field to sort by.", + "enum" : [ + "trialDbId", + "trialName", + "programDbId", + "programName", + "locationDbId", + "startDate", + "endDate" + ] }, - "trialName" : { - "type" : "string" + "contactDbIds" : { + "type" : "array", + "description" : "List of contact entities associated with this trial", + "items" : { + "type" : "string" + } }, - "trialPUI" : { - "type" : "string" - } - }, - "description" : "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." - }, - "StudySearchRequest" : { - "type" : "object", - "properties" : { - "active" : { - "type" : "boolean" + "searchDateRangeStart" : { + "type" : "string", + "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "format" : "date" } }, - "description" : "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." + "description" : "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." }, - "Synonym" : { + "ValidValues" : { "type" : "object", "properties" : { - "germplasmDbId" : { - "type" : "string" + "categories" : { + "type" : "array", + "description" : "List of possible values with optional labels", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ValidValuesCategory" + } }, - "germplasmName" : { - "type" : "string" + "maximumValue" : { + "type" : "string", + "description" : "Maximum value for numerical, date, and time scales. Typically used for data capture control and QC.", + "nullable" : true }, - "germplasmPUI" : { + "minimumValue" : { + "type" : "string", + "description" : "Minimum value for numerical, date, and time scales. Typically used for data capture control and QC.", + "nullable" : true + }, + "scaleDbId" : { "type" : "string" }, - "synonym" : { + "scaleName" : { "type" : "string" }, - "type" : { + "scalePUI" : { "type" : "string" } }, - "description" : "Alternative names or IDs used to reference this germplasm" + "description" : "Metadata describing the acceptable values for this Scale" }, - "TaxonId" : { - "required" : [ - "sourceName", - "taxonId" - ], + "ValidValuesCategory" : { "type" : "object", "properties" : { - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, - "sourceName" : { - "type" : "string" + "label" : { + "type" : "string", + "description" : "A text label for a category", + "nullable" : true }, - "taxonId" : { - "type" : "string" + "value" : { + "type" : "string", + "description" : "The actual value for a category", + "nullable" : true } }, - "description" : "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended." + "description" : "If the Scale is a categorical type, these objects define the valid options" }, - "Trait" : { + "Variable" : { "required" : [ - "traitDbId", + "methodDbId", + "methodName", + "scaleDbId", + "scaleName", "traitName" ], "type" : "object", @@ -13983,31 +21668,99 @@ "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "attribute" : { + "commonCropName" : { + "type" : "string", + "description" : "Crop name (examples: \"Maize\", \"Wheat\")", + "nullable" : true + }, + "contextOfUse" : { + "type" : "array", + "description" : "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "defaultValue" : { + "type" : "string", + "description" : "Variable default value. (examples: \"red\", \"2.3\", etc.)", + "nullable" : true + }, + "documentationURL" : { + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "format" : "uri", + "nullable" : true + }, + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "growthStage" : { + "type" : "string", + "description" : "Growth stage at which measurement is made (examples: \"flowering\")", + "nullable" : true + }, + "institution" : { + "type" : "string", + "description" : "Name of institution submitting the variable", + "nullable" : true + }, + "language" : { + "type" : "string", + "description" : "2 letter ISO 639-1 code for the language of submission of the variable.", + "nullable" : true + }, + "methodDbId" : { "type" : "string" }, - "attributePUI" : { + "methodName" : { "type" : "string" }, - "entity" : { + "methodPUI" : { "type" : "string" }, - "entityPUI" : { + "ontologyReference" : { + "$ref" : "#/components/schemas/OntologyReference" + }, + "scaleDbId" : { "type" : "string" }, - "mainAbbreviation" : { + "scaleName" : { "type" : "string" }, - "ontologyReferenceDbId" : { + "scalePUI" : { "type" : "string" }, + "scientist" : { + "type" : "string", + "description" : "Name of scientist submitting the variable.", + "nullable" : true + }, "status" : { - "type" : "string" + "type" : "string", + "description" : "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)", + "nullable" : true }, - "traitClass" : { - "type" : "string" + "submissionTimestamp" : { + "type" : "string", + "description" : "Timestamp when the Variable was added (ISO 8601)", + "format" : "date-time", + "nullable" : true }, - "traitDescription" : { + "synonyms" : { + "type" : "array", + "description" : "Other variable names", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "traitDbId" : { "type" : "string" }, "traitName" : { @@ -14017,432 +21770,779 @@ "type" : "string" } }, - "description" : "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". " + "description" : "A unique combination of Trait, Method, and Scale to define a clear context for an Observation." }, - "TraitDataType" : { - "type" : "string", - "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", - "enum" : [ - "Code", - "Date", - "Duration", - "Nominal", - "Numerical", - "Ordinal", - "Text" - ] + "VariableBaseClassParameters" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "dataTypes" : { + "type" : "array", + "description" : "List of scale data types to filter search results", + "items" : { + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "methodDbIds" : { + "type" : "array", + "description" : "List of methods to filter search results", + "items" : { + "type" : "string" + } + }, + "methodNames" : { + "type" : "array", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "items" : { + "type" : "string" + } + }, + "methodPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "ontologyDbIds" : { + "type" : "array", + "description" : "List of ontology IDs to search for", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "scaleDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Scale", + "items" : { + "type" : "string" + } + }, + "scaleNames" : { + "type" : "array", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "items" : { + "type" : "string" + } + }, + "scalePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "studyDbId" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "traitAttributePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } + }, + "traitAttributes" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } + }, + "traitClasses" : { + "type" : "array", + "description" : "List of trait classes to filter search results", + "items" : { + "type" : "string" + } + }, + "traitDbIds" : { + "type" : "array", + "description" : "The unique identifier for a Trait", + "items" : { + "type" : "string" + } + }, + "traitEntities" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "items" : { + "type" : "string" + } + }, + "traitEntityPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "items" : { + "type" : "string" + } + }, + "traitNames" : { + "type" : "array", + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "items" : { + "type" : "string" + } + }, + "traitPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + } + } }, - "TraitNewRequest" : { + "Variant" : { "required" : [ - "traitDbId", - "traitName" + "variantDbId" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "attribute" : { - "type" : "string" + "analysis" : { + "type" : "array", + "description" : "Set of Analysis descriptors for this VariantSet", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "attributePUI" : { - "type" : "string" + "ciend" : { + "type" : "array", + "description" : "Similar to \"cipos\", but for the variant's end position (which is derived from start + svlen).", + "nullable" : true, + "items" : { + "type" : "integer", + "format" : "int32" + } }, - "entity" : { - "type" : "string" + "cipos" : { + "type" : "array", + "description" : "In the case of structural variants, start and end of the variant may not\nbe known with an exact base position. \"cipos\" provides an interval with\nhigh confidence for the start position. The interval is provided by 0 or\n2 signed integers which are added to the start position.\nBased on the use in VCF v4.2", + "nullable" : true, + "items" : { + "type" : "integer", + "format" : "int32" + } }, - "entityPUI" : { - "type" : "string" + "created" : { + "type" : "string", + "description" : "The timestamp when this variant was created.", + "format" : "date-time", + "nullable" : true }, - "mainAbbreviation" : { - "type" : "string" + "end" : { + "type" : "integer", + "description" : "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated \nby `start + referenceBases.length`.", + "format" : "int32", + "nullable" : true }, - "ontologyReferenceDbId" : { - "type" : "string" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "status" : { - "type" : "string" + "filtersApplied" : { + "type" : "boolean", + "description" : "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value.", + "nullable" : true }, - "traitClass" : { - "type" : "string" + "filtersFailed" : { + "type" : "array", + "description" : "Zero or more filters that failed for this variant. VCF column 7 \"FILTER\" shared across all alleles in the same VCF record.", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "traitDbId" : { - "type" : "string" + "filtersPassed" : { + "type" : "boolean", + "description" : "True if all filters for this variant passed. VCF column 7 \"FILTER\" value PASS.", + "nullable" : true }, - "traitDescription" : { - "type" : "string" + "referenceBases" : { + "type" : "string", + "description" : "The reference bases for this variant. They start at the given start position.", + "nullable" : true }, - "traitName" : { + "referenceDbId" : { "type" : "string" }, - "traitPUI" : { + "referenceName" : { "type" : "string" - } - }, - "description" : "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". " - }, - "Trial" : { - "required" : [ - "trialDbId", - "trialName" - ], - "type" : "object", - "properties" : { - "active" : { - "type" : "boolean" - }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" }, - "commonCropName" : { + "referenceSetDbId" : { "type" : "string" }, - "contacts" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/Contact" - } - }, - "documentationURL" : { + "referenceSetName" : { "type" : "string" }, - "endDate" : { - "type" : "string" + "start" : { + "type" : "integer", + "description" : "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The start position at which this variant occurs (0-based). This corresponds to the first base of the string \nof reference bases. Genomic positions are non-negative integers less than reference length. Variants spanning \nthe join of circular genomes are represented as two variants one on each side of the join (position 0).", + "format" : "int32", + "nullable" : true }, - "programDbId" : { - "type" : "string" + "svlen" : { + "type" : "integer", + "description" : "Length of the - if labeled as such in variant_type - structural variation. Based on the use in VCF v4.2", + "format" : "int32", + "nullable" : true }, - "programName" : { - "type" : "string" + "updated" : { + "type" : "string", + "description" : "The time at which this variant was last updated.", + "format" : "date-time", + "nullable" : true }, - "startDate" : { - "type" : "string" + "variantDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a `Variant`" }, - "studyDbIds" : { + "variantNames" : { "type" : "array", + "description" : "A human readable name associated with a `Variant`", + "nullable" : true, "items" : { "type" : "string" } }, - "trialDescription" : { + "variantSetDbId" : { "type" : "string" }, - "trialName" : { + "variantSetName" : { "type" : "string" }, - "trialPUI" : { - "type" : "string" + "variantType" : { + "type" : "string", + "description" : "The \"variant_type\" is used to denote e.g. structural variants.\nExamples:\n DUP : duplication of sequence following \"start\"\n DEL : deletion of sequence following \"start\"", + "nullable" : true } }, - "description" : "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." + "description" : "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF." }, - "TrialNewRequest" : { - "required" : [ - "trialDbId", - "trialDbId", - "trialName" - ], + "VariantRequest" : { "type" : "object", "properties" : { - "active" : { - "type" : "boolean" + "callSetDbIds" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", + "items" : { + "type" : "string" + } }, - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "commonCropName" : { - "type" : "string" + "end" : { + "type" : "integer", + "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", + "format" : "int32", + "example" : 1500 }, - "contacts" : { + "programDbIds" : { "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { - "$ref" : "#/components/schemas/Contact" + "type" : "string" } }, - "documentationURL" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "endDate" : { - "type" : "string" + "referenceDbId" : { + "type" : "string", + "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", + "example" : "120a2d5c" }, - "programDbId" : { - "type" : "string" + "referenceDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a genotype `Reference`", + "items" : { + "type" : "string" + } }, - "programName" : { - "type" : "string" + "referenceSetDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a genotype `ReferenceSet`", + "items" : { + "type" : "string" + } }, - "startDate" : { - "type" : "string" + "start" : { + "type" : "integer", + "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", + "format" : "int32", + "example" : 100 }, "studyDbIds" : { "type" : "array", + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } }, - "trialDbId" : { - "type" : "string" - }, - "trialDescription" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" - } - }, - "description" : "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." - }, - "TrialSearchRequest" : { - "type" : "object", - "properties" : { - "active" : { - "type" : "boolean" - }, - "searchDateRangeEnd" : { - "type" : "string" - }, - "searchDateRangeStart" : { - "type" : "string" - } - }, - "description" : "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." - }, - "ValidValues" : { - "type" : "object", - "properties" : { - "maximumValue" : { - "type" : "string" - }, - "minimumValue" : { - "type" : "string" - }, - "scaleDbId" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "scaleName" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "scalePUI" : { - "type" : "string" - } - }, - "description" : "Metadata describing the acceptable values for this Scale" - }, - "ValidValuesCategory" : { - "type" : "object", - "properties" : { - "label" : { - "type" : "string" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } }, - "validValues" : { - "$ref" : "#/components/schemas/ValidValues" + "variantDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Variants`", + "items" : { + "type" : "string" + } }, - "value" : { - "type" : "string" + "variantSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `VariantSets`", + "items" : { + "type" : "string" + } } - }, - "description" : "If the Scale is a categorical type, these objects define the valid options" + } }, - "Variable" : { - "required" : [ - "method", - "scale", - "trait" - ], + "VariantSearchRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" - }, - "commonCropName" : { - "type" : "string" + "referenceDbId" : { + "type" : "string", + "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", + "example" : "120a2d5c" }, - "contextOfUse" : { + "programNames" : { "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "defaultValue" : { - "type" : "string" - }, - "documentationURL" : { - "type" : "string" + "start" : { + "type" : "integer", + "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", + "format" : "int32", + "example" : 100 }, - "growthStage" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "institution" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "language" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "method" : { - "$ref" : "#/components/schemas/Method" + "referenceSetDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a genotype `ReferenceSet`", + "items" : { + "type" : "string" + } }, - "ontologyReference" : { - "$ref" : "#/components/schemas/OntologyReference" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "scale" : { - "$ref" : "#/components/schemas/Scale" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } }, - "scientist" : { - "type" : "string" + "variantSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `VariantSets`", + "items" : { + "type" : "string" + } }, - "status" : { - "type" : "string" + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } }, - "submissionTimestamp" : { - "type" : "string" + "referenceDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a genotype `Reference`", + "items" : { + "type" : "string" + } }, - "synonyms" : { + "variantDbIds" : { "type" : "array", + "description" : "A list of IDs which uniquely identify `Variants`", "items" : { "type" : "string" } }, - "trait" : { - "$ref" : "#/components/schemas/Trait" + "end" : { + "type" : "integer", + "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", + "format" : "int32", + "example" : 1500 + }, + "callSetDbIds" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", + "items" : { + "type" : "string" + } } }, - "description" : "A unique combination of Trait, Method, and Scale to define a clear context for an Observation." + "description" : "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF." }, - "Variant" : { + "VariantSet" : { "required" : [ - "variantDbId" + "variantSetDbId" ], "type" : "object", "properties" : { "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "created" : { - "type" : "string" + "analysis" : { + "type" : "array", + "description" : "Set of Analysis descriptors for this VariantSet", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Analysis" + } }, - "end" : { + "callSetCount" : { "type" : "integer", - "format" : "int32" + "description" : "The number of CallSets included in this VariantSet", + "format" : "int32", + "nullable" : true }, - "filtersApplied" : { - "type" : "boolean" + "externalReferences" : { + "type" : "array", + "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/ExternalReference" + } }, - "filtersPassed" : { - "type" : "boolean" + "metadataFields" : { + "type" : "array", + "description" : "The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard ", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/MetadataField" + } }, - "referenceBases" : { + "referenceSetDbId" : { "type" : "string" }, - "referenceDbId" : { + "referenceSetName" : { "type" : "string" }, - "referenceName" : { + "studyDbId" : { "type" : "string" }, - "referenceSetDbId" : { + "studyName" : { "type" : "string" }, - "referenceSetName" : { + "studyPUI" : { "type" : "string" }, - "start" : { - "type" : "integer", - "format" : "int32" - }, - "svlen" : { + "variantCount" : { "type" : "integer", - "format" : "int32" - }, - "updated" : { - "type" : "string" - }, - "variantDbId" : { - "type" : "string" + "description" : "The number of Variants included in this VariantSet", + "format" : "int32", + "nullable" : true }, "variantSetDbId" : { - "type" : "string" + "type" : "string", + "description" : "The unique identifier for a VariantSet" }, "variantSetName" : { - "type" : "string" - }, - "variantType" : { - "type" : "string" + "type" : "string", + "description" : "The human readable name for a VariantSet", + "nullable" : true } }, - "description" : "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF." + "description" : "A VariantSet is a collection of variants and variant calls intended to be analyzed together." }, - "VariantSearchRequest" : { + "VariantSetRequest" : { "type" : "object", "properties" : { - "end" : { - "type" : "integer", - "format" : "int32" + "callSetDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a CallSet", + "items" : { + "type" : "string" + } }, - "referenceDbId" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "start" : { - "type" : "integer", - "format" : "int32" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "referenceDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a genotype Reference", + "items" : { + "type" : "string" + } + }, + "referenceSetDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a genotype ReferenceSet", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + }, + "variantDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a Variant", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a VariantSet", + "items" : { + "type" : "string" + } } - }, - "description" : "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF." + } }, - "VariantSet" : { - "required" : [ - "variantSetDbId" - ], + "VariantSetSearchRequest" : { "type" : "object", "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" + "variantSetDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a VariantSet", + "items" : { + "type" : "string" + } }, - "analysiDbIds" : { + "studyNames" : { "type" : "array", + "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "callSetCount" : { - "type" : "integer", - "format" : "int32" + "referenceDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a genotype Reference", + "items" : { + "type" : "string" + } }, - "referenceSetDbId" : { - "type" : "string" + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "referenceSetName" : { - "type" : "string" + "variantDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a Variant", + "items" : { + "type" : "string" + } }, - "studyDbId" : { - "type" : "string" + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } }, - "studyName" : { - "type" : "string" + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "studyPUI" : { - "type" : "string" + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } }, - "variantCount" : { - "type" : "integer", - "format" : "int32" + "callSetDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a CallSet", + "items" : { + "type" : "string" + } }, - "variantSetDbId" : { - "type" : "string" + "referenceSetDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a genotype ReferenceSet", + "items" : { + "type" : "string" + } }, - "variantSetName" : { - "type" : "string" + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } } }, "description" : "A VariantSet is a collection of variants and variant calls intended to be analyzed together." }, - "VariantSetSearchRequest" : { - "type" : "object", - "properties" : { }, - "description" : "A VariantSet is a collection of variants and variant calls intended to be analyzed together." - }, "basePagination" : { "required" : [ "currentPage", @@ -14740,6 +22840,43 @@ } } }, + "StudyStudyTypeListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "StudyStudyTypeListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + } + } + } + } + } + }, "StudySingleResponse" : { "description" : "OK", "content" : { @@ -15255,6 +23392,32 @@ } } }, + "ReferenceBasesSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ReferenceBasesSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ReferenceBases" + } + } + } + } + } + }, "ObservationUnitListResponse" : { "description" : "OK", "content" : { @@ -16073,6 +24236,32 @@ } } }, + "GermplasmMCPDSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "GermplasmMCPDSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/GermplasmMCPD" + } + } + } + } + } + }, "ReferenceSetListResponse" : { "description" : "OK", "content" : { @@ -16299,6 +24488,43 @@ } } }, + "LinkageGroupListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "LinkageGroupListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/LinkageGroup" + } + } + } + } + } + } + } + } + }, "ScaleSingleResponse" : { "description" : "OK", "content" : { @@ -16614,6 +24840,43 @@ } } }, + "GermplasmAttributeAttributeCategoryListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "GermplasmAttributeAttributeCategoryListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + } + } + } + } + } + }, "GermplasmAttributeValueSingleResponse" : { "description" : "OK", "content" : { @@ -16863,6 +25126,19 @@ }, "example" : 1000 }, + "authorizationHeader" : { + "name" : "Authorization", + "in" : "header", + "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", + "required" : false, + "style" : "simple", + "explode" : false, + "schema" : { + "pattern" : "^Bearer .*$", + "type" : "string" + }, + "example" : "Bearer XXXX" + }, "page" : { "name" : "page", "in" : "query", @@ -16887,19 +25163,6 @@ "type" : "string" }, "example" : "33c27874" - }, - "authorizationHeader" : { - "name" : "Authorization", - "in" : "header", - "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", - "required" : false, - "style" : "simple", - "explode" : false, - "schema" : { - "pattern" : "^Bearer .*$", - "type" : "string" - }, - "example" : "Bearer XXXX" } }, "securitySchemes" : { diff --git a/Specification/Generated/brapi_generated.ttl b/Specification/Generated/brapi_generated.ttl index 2342ca0d..d9d17179 100644 --- a/Specification/Generated/brapi_generated.ttl +++ b/Specification/Generated/brapi_generated.ttl @@ -10,13 +10,6 @@ PREFIX xsd: rdfs:label "language"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Specifies a FASTA format file/string."@en; - rdfs:domain ; - rdfs:label "sourceURI"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes."@en; @@ -32,6 +25,13 @@ PREFIX xsd: rdfs:label "sourceName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Specifies a FASTA format file/string."@en; + rdfs:domain ; + rdfs:label "sourceURI"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Describes the approximate slope (height/distance) of a Location."@en; @@ -67,13 +67,6 @@ PREFIX xsd: rdfs:label "scale"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "fromSeedLotTransactions"@en; - rdfs:domain ; - rdfs:label "fromSeedLotTransactions"@en; - rdfs:range . - rdf:type owl:Class; rdfs:comment "Metadata describing the acceptable values for this Scale"@en; @@ -136,7 +129,7 @@ PREFIX xsd: rdfs:range xsd:string . [ rdf:type owl:Class; - owl:oneOf ( ) + owl:oneOf ( ) ] . @@ -233,6 +226,22 @@ PREFIX xsd: rdfs:label "crossName"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) 10) Seed collection 11) Short term 12) Medium term 13) Long term 20) Field collection 30) In vitro collection 40) Cryo-preserved collection 50) DNA collection 99) Other (elaborate in REMARKS field)"@en; + rdfs:domain ; + rdfs:label "storageTypeCodes"@en; + rdfs:range . + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`."@en; + rdfs:domain ; + rdfs:label "sequence"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)"@en; @@ -247,6 +256,9 @@ PREFIX xsd: rdfs:label "samples"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -254,8 +266,12 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . + + rdf:type owl:ObjectProperty; + rdfs:comment "The child germplasm"@en; + rdfs:domain ; + rdfs:label "childGermplasm"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -269,13 +285,6 @@ PREFIX xsd: rdfs:comment "Links to various ontology documentation"@en; rdfs:label "DocumentationLink"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "The child germplasm"@en; - rdfs:domain ; - rdfs:label "childGermplasm"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The name or identifier of the entity which took the `Sample` from the field"@en; @@ -312,6 +321,13 @@ PREFIX xsd: rdfs:comment "The type of documentation, which can be OBO Foundry, an RDF term or a webpage."@en; rdfs:label "DocumentationLinkType"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The version of the update."@en; + rdfs:domain ; + rdfs:label "version"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "A general description of this Seed Lot Transaction"@en; @@ -319,11 +335,11 @@ PREFIX xsd: rdfs:label "transactionDescription"@en; rdfs:range xsd:string . - + rdf:type owl:DatatypeProperty; - rdfs:comment "The version of the update."@en; - rdfs:domain ; - rdfs:label "version"@en; + rdfs:comment "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\"."@en; + rdfs:domain ; + rdfs:label "instituteCode"@en; rdfs:range xsd:string . @@ -341,7 +357,7 @@ PREFIX xsd: rdfs:range . - rdf:type owl:NamedIndividual , . + rdf:type , owl:NamedIndividual , . rdf:type owl:DatatypeProperty; @@ -395,6 +411,13 @@ PREFIX xsd: rdfs:label "pedigreeNodes"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero]."@en; + rdfs:domain ; + rdfs:label "collectingDate"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "Geometry associated with an image"@en; @@ -409,6 +432,13 @@ PREFIX xsd: rdfs:label "familyCode"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The linkage groups present in a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "linkageGroups"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "A list of germplasm references that are direct children of this germplasm. These represent edges in the tree, connecting to other nodes.\n
The given germplasm could have a large number of progeny, across a number of different breeding methods. The 'parentType' shows \n the type of parent this germplasm is to each of the child germplasm references.\n
If the parameter 'includeProgeny' is set to false, then this array should be empty, null, or not present in the response."@en; @@ -456,6 +486,10 @@ PREFIX xsd: rdfs:label "unknownString"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The ID which uniquely identifies a CallSet within the given database server"@en; @@ -534,6 +568,34 @@ PREFIX xsd: rdfs:label "growthStage"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered names or other designations given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase."@en; + rdfs:domain ; + rdfs:label "accessionNames"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Information about the collection of a germplasm"@en; + rdfs:domain ; + rdfs:label "collectingInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\". "@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\")."@en; + rdfs:domain ; + rdfs:label "subtaxon"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The contacts email address\n\nMIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person."@en; @@ -627,7 +689,7 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - rdf:type owl:NamedIndividual , . + rdf:type , owl:NamedIndividual , . rdf:type owl:ObjectProperty; @@ -643,6 +705,9 @@ PREFIX xsd: rdfs:label "observationUnits"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -658,12 +723,12 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A free space containing any additional information related to a particular object."@en; - rdfs:domain ; - rdfs:label "additionalProperties"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "crosses"@en; + rdfs:domain ; + rdfs:label "crosses"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -672,13 +737,6 @@ PREFIX xsd: rdfs:label "availableFormats"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "crosses"@en; - rdfs:domain ; - rdfs:label "crosses"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding "@en; @@ -734,13 +792,6 @@ PREFIX xsd: rdfs:label "crossType"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "the type of cross"@en; - rdfs:domain ; - rdfs:label "crossType"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "variants"@en; @@ -748,6 +799,13 @@ PREFIX xsd: rdfs:label "variants"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "the type of cross"@en; + rdfs:domain ; + rdfs:label "crossType"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . @@ -772,11 +830,23 @@ PREFIX xsd: rdfs:label "traitDbId"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The complete history of transactions for this seed lot. This includes seed increases, seed usage (planting), and trading with other breeding programs."@en; + rdfs:domain ; + rdfs:label "transactions"@en; + rdfs:range . + rdf:type owl:Class; rdfs:comment "The techniques and protocol used to produce a Cross or Germplasm"@en; rdfs:label "BreedingMethod"@en . + + rdf:type owl:Class; + rdfs:comment "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit."@en; + rdfs:label "Observation"@en . + rdf:type owl:ObjectProperty; rdfs:comment "associated pedigreeNode"@en; @@ -784,10 +854,12 @@ PREFIX xsd: rdfs:label "pedigreeNode"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit."@en; - rdfs:label "Observation"@en . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -796,12 +868,12 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975)."@en; + rdfs:domain ; + rdfs:label "latitudeDecimal"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -878,6 +950,13 @@ PREFIX xsd: rdfs:label "publicationReference"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Uniquely Identifiable name of a `LinkageGroup`
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable."@en; + rdfs:domain ; + rdfs:label "linkageGroupName"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "references"@en; @@ -945,7 +1024,10 @@ PREFIX xsd: rdfs:range . - rdf:type owl:NamedIndividual , . + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . rdf:type owl:ObjectProperty; @@ -954,6 +1036,9 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:Class; rdfs:comment "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)"@en; @@ -978,6 +1063,13 @@ PREFIX xsd: rdfs:label "copyright"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero]."@en; + rdfs:domain ; + rdfs:label "acquisitionDate"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable."@en; @@ -1005,6 +1097,11 @@ PREFIX xsd: rdfs:label "ontologyDbId"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "A string representation of the `Reference` base alleles."@en; + rdfs:label "ReferenceBases"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of institution submitting the variable"@en; @@ -1012,13 +1109,6 @@ PREFIX xsd: rdfs:label "institution"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "toSeedLotTransactions"@en; - rdfs:domain ; - rdfs:label "toSeedLotTransactions"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The human readable name of an image. Might be the same as 'imageFileName', but could be different."@en; @@ -1047,6 +1137,13 @@ PREFIX xsd: rdfs:label "instituteName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076"@en; + rdfs:domain ; + rdfs:label "longitudeDegrees"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "License and citation information for the data in this trial"@en; @@ -1057,6 +1154,11 @@ PREFIX xsd: rdfs:comment "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy."@en; rdfs:label "Germplasm"@en . + + rdf:type owl:Class; + rdfs:comment "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy."@en; + rdfs:label "GermplasmMCPD"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "Persons first name"@en; @@ -1071,9 +1173,6 @@ PREFIX xsd: rdfs:label "markerPositions"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard."@en; @@ -1081,6 +1180,16 @@ PREFIX xsd: rdfs:label "donorInstituteCode"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")"@en; + rdfs:domain ; + rdfs:label "mlsStatus"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; @@ -1093,12 +1202,9 @@ PREFIX xsd: rdfs:comment "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances."@en; rdfs:label "PedigreeNode"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology licence"@en; - rdfs:domain ; - rdfs:label "licence"@en; - rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -1107,6 +1213,13 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology licence"@en; + rdfs:domain ; + rdfs:label "licence"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The Y position coordinate for an observation unit. Different systems may use different coordinate systems."@en; @@ -1173,6 +1286,11 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . + + rdf:type owl:Class; + rdfs:comment "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

"@en , "The type of field represented in this data matrix. This is intended to help parse the data out of JSON."@en , "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON."@en; + rdfs:label "DataType"@en . + rdf:type owl:ObjectProperty; rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; @@ -1180,11 +1298,6 @@ PREFIX xsd: rdfs:label "germplasmOrigin"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

"@en , "The type of field represented in this data matrix. This is intended to help parse the data out of JSON."@en , "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON."@en; - rdfs:label "DataType"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "Supplemental text description for 'biologicalStatusOfAccessionCode'"@en; @@ -1235,6 +1348,12 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "associated event"@en; @@ -1251,7 +1370,7 @@ PREFIX xsd: rdf:type owl:DatatypeProperty; - rdfs:comment "The date and time when this study was last modified"@en; + rdfs:comment "The ID which uniquely identifies a LastUpdate within the given database server"@en; rdfs:domain ; rdfs:label "lastUpdateDbId"@en; rdfs:range xsd:string . @@ -1287,11 +1406,6 @@ PREFIX xsd: rdfs:label "traitPUI"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; - rdfs:label "FileFormat"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "Unique DbId for the Seed Lot"@en; @@ -1299,6 +1413,11 @@ PREFIX xsd: rdfs:label "seedLotDbId"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; + rdfs:label "FileFormat"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository."@en; @@ -1323,14 +1442,6 @@ PREFIX xsd: rdfs:label "svlen"@en; rdfs:range xsd:integer . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; @@ -1345,6 +1456,13 @@ PREFIX xsd: rdfs:label "pagination"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\")."@en; + rdfs:domain ; + rdfs:label "collectingMissionIdentifier"@en; + rdfs:range xsd:string . + rdf:type owl:NamedIndividual , . @@ -1362,6 +1480,10 @@ PREFIX xsd: rdfs:label "attributeDescription"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The date the study ends\n\nMIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended"@en; @@ -1376,6 +1498,11 @@ PREFIX xsd: rdfs:label "calls"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "The identifier and metadata needed to reference an external controlled vocabulary"@en; + rdfs:label "Ontology"@en . + rdf:type owl:ObjectProperty; rdfs:comment "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species.\n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended."@en; @@ -1383,10 +1510,9 @@ PREFIX xsd: rdfs:label "taxonIds"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "The identifier and metadata needed to reference an external controlled vocabulary"@en; - rdfs:label "Ontology"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -1471,10 +1597,6 @@ PREFIX xsd: rdfs:comment "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc."@en; rdfs:label "Location"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The string representation of the pedigree for this germplasm in PURDY notation"@en; @@ -1496,10 +1618,6 @@ PREFIX xsd: rdfs:label "crossingProject"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The related observation unit identifier, if relevant."@en; @@ -1533,13 +1651,6 @@ PREFIX xsd: rdfs:label "mapPUI"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; @@ -1547,6 +1658,12 @@ PREFIX xsd: rdfs:label "trait"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc"@en; @@ -1557,13 +1674,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below."@en; - rdfs:domain ; - rdfs:label "germplasmDbId"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -1571,6 +1681,13 @@ PREFIX xsd: rdfs:label "calls"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below."@en; + rdfs:domain ; + rdfs:label "germplasmDbId"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. "@en; @@ -1599,6 +1716,11 @@ PREFIX xsd: rdfs:label "observationVariable"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit"@en; + rdfs:label "GermplasmAttribute"@en . + rdf:type owl:ObjectProperty; rdfs:comment "siblingPedigreeNodes"@en; @@ -1606,11 +1728,6 @@ PREFIX xsd: rdfs:label "siblingPedigreeNodes"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit"@en; - rdfs:label "GermplasmAttribute"@en . - rdf:type owl:ObjectProperty; rdfs:comment "observations"@en; @@ -1715,17 +1832,17 @@ PREFIX xsd: rdfs:label "scale"@en; rdfs:range . - + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; + rdfs:domain ; rdfs:label "additionalInfo"@en; rdfs:range . - + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; + rdfs:domain ; rdfs:label "additionalInfo"@en; rdfs:range . @@ -1736,6 +1853,10 @@ PREFIX xsd: rdfs:label "observationUnits"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The unique identifier for a Location"@en; @@ -1750,12 +1871,7 @@ PREFIX xsd: rdfs:label "mailingAddress"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string."@en; - rdfs:domain ; - rdfs:label "phaseSet"@en; - rdfs:range xsd:string . + rdf:type owl:NamedIndividual , . rdf:type owl:DatatypeProperty; @@ -1764,6 +1880,13 @@ PREFIX xsd: rdfs:label "trialName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string."@en; + rdfs:domain ; + rdfs:label "phaseSet"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard "@en; @@ -1788,13 +1911,6 @@ PREFIX xsd: rdfs:label "crosses"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a separator for unphased allele calls."@en; - rdfs:domain ; - rdfs:label "sepUnphased"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "the description for a crossing project"@en; @@ -1802,6 +1918,13 @@ PREFIX xsd: rdfs:label "crossingProjectDescription"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a separator for unphased allele calls."@en; + rdfs:domain ; + rdfs:label "sepUnphased"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The time stamp for when this seed lot was created"@en; @@ -1826,6 +1949,16 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -1882,10 +2015,24 @@ PREFIX xsd: rdfs:label "value"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "Information about an accession donor"@en; + rdfs:domain ; + rdfs:label "donorInfo"@en; + rdfs:range . + rdf:type owl:Class; rdfs:label "ObservationVariable"@en . + + rdf:type owl:ObjectProperty; + rdfs:comment "donors associated with a germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted."@en; @@ -1959,10 +2106,6 @@ PREFIX xsd: rdfs:comment "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; rdfs:label "SampleType"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The unique identifier for a Reference"@en; @@ -2005,13 +2148,16 @@ PREFIX xsd: rdfs:label "parentPedigreeNodes"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name of a List"@en; - rdfs:domain ; - rdfs:label "listName"@en; + rdfs:comment "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space."@en; + rdfs:domain ; + rdfs:label "instituteAddress"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a trial"@en; @@ -2019,9 +2165,6 @@ PREFIX xsd: rdfs:label "trial"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "The string used as a separator for phased allele calls."@en; @@ -2029,6 +2172,13 @@ PREFIX xsd: rdfs:label "sepPhased"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name of a List"@en; + rdfs:domain ; + rdfs:label "listName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended."@en; @@ -2043,6 +2193,13 @@ PREFIX xsd: rdfs:label "variants"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "bases"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "Ontology version (no specific format)"@en; @@ -2050,6 +2207,13 @@ PREFIX xsd: rdfs:label "version"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" "@en; + rdfs:domain ; + rdfs:label "species"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "Genotype Metadata are additional layers of metadata associated with each genotype."@en; @@ -2090,6 +2254,10 @@ PREFIX xsd: rdfs:label "observationTimeStamp"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -2135,6 +2303,13 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . + + rdf:type owl:ObjectProperty; + rdfs:comment "The mulit-crop passport descriptors (MCPD) for this germplasm"@en; + rdfs:domain ; + rdfs:label "mcpd"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "observations"@en; @@ -2170,6 +2345,13 @@ PREFIX xsd: rdfs:label "publicReleaseDate"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "Information about the location where the sample was collected"@en; + rdfs:domain ; + rdfs:label "collectingSite"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "The identifier for the Seed Lot being transferred out of"@en; @@ -2184,6 +2366,9 @@ PREFIX xsd: rdfs:label "callSets"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "Numerical or categorical value\n\nMIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment."@en; @@ -2198,6 +2383,13 @@ PREFIX xsd: rdfs:label "environmentParametersDbId"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. "@en; + rdfs:domain ; + rdfs:label "alternateIDs"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "General category for the attribute. very similar to Trait class."@en; @@ -2299,8 +2491,12 @@ PREFIX xsd: rdfs:label "dataType"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there are not any additional results."@en; + rdfs:domain ; + rdfs:label "nextPageToken"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -2309,6 +2505,9 @@ PREFIX xsd: rdfs:label "entity"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; @@ -2316,10 +2515,6 @@ PREFIX xsd: rdfs:label "scale"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "crossingProjects"@en; @@ -2327,6 +2522,13 @@ PREFIX xsd: rdfs:label "crossingProjects"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "the unique identifier for a cross"@en; + rdfs:domain ; + rdfs:label "crossDbId"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow."@en; @@ -2353,15 +2555,8 @@ PREFIX xsd: rdfs:label "analysisName"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "the unique identifier for a cross"@en; - rdfs:domain ; - rdfs:label "crossDbId"@en; - rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . + rdf:type , owl:NamedIndividual , . rdf:type owl:ObjectProperty; @@ -2370,13 +2565,6 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "the human readable name of a cross attribute"@en; - rdfs:domain ; - rdfs:label "crossAttributeName"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; @@ -2387,6 +2575,20 @@ PREFIX xsd: rdfs:comment "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; rdfs:label "GeoJSONPoint"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "the human readable name of a cross attribute"@en; + rdfs:domain ; + rdfs:label "crossAttributeName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required."@en; + rdfs:domain ; + rdfs:label "genus"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Persons last name"@en; @@ -2443,6 +2645,10 @@ PREFIX xsd: rdfs:label "trait"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -2476,13 +2682,6 @@ PREFIX xsd: rdfs:label "submissionTimestamp"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; @@ -2490,6 +2689,13 @@ PREFIX xsd: rdfs:label "imageLocation"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -2497,6 +2703,13 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known."@en; + rdfs:domain ; + rdfs:label "georeferencingMethod"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "the requested page number (zero indexed)"@en; @@ -2510,6 +2723,9 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . @@ -2555,6 +2771,13 @@ PREFIX xsd: rdfs:comment "The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map."@en; rdfs:label "GenomeMap"@en . + + rdf:type owl:ObjectProperty; + rdfs:comment "markerPositions"@en; + rdfs:domain ; + rdfs:label "markerPositions"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; @@ -2569,13 +2792,6 @@ PREFIX xsd: rdfs:label "publicationPUI"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "markerPositions"@en; - rdfs:domain ; - rdfs:label "markerPositions"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. "@en; @@ -2583,6 +2799,13 @@ PREFIX xsd: rdfs:label "modality"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter."@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + rdf:type , owl:NamedIndividual , . @@ -2621,13 +2844,6 @@ PREFIX xsd: rdfs:label "plate"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter."@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The Cross associated with this Pollination Event"@en; @@ -2760,6 +2976,10 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "observationUnits"@en; @@ -2791,6 +3011,9 @@ PREFIX xsd: rdfs:label "variantType"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:Class; rdfs:comment "The date and time when this study was last modified"@en; @@ -2831,6 +3054,13 @@ PREFIX xsd: rdfs:label "seedLotDescription"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of institutes that were involved with breeding a material/germplasm\n
MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard.\n
MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available."@en; + rdfs:domain ; + rdfs:label "breedingInstitutes"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The primary objective of the program"@en; @@ -2855,9 +3085,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; @@ -2865,6 +3092,9 @@ PREFIX xsd: rdfs:label "sampleType"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)"@en; @@ -2898,6 +3128,10 @@ PREFIX xsd: rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; rdfs:label "GeoJSON"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "plates"@en; @@ -2926,13 +3160,6 @@ PREFIX xsd: rdfs:label "sampleDescription"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - rdf:type owl:NamedIndividual , . @@ -2957,6 +3184,13 @@ PREFIX xsd: rdfs:label "crossingProjectDbId"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3046,6 +3280,13 @@ PREFIX xsd: rdfs:label "variantSets"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed."@en; + rdfs:domain ; + rdfs:label "geometry"@en; + rdfs:range , . + rdf:type owl:Class; rdfs:comment "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')."@en; @@ -3065,13 +3306,6 @@ PREFIX xsd: rdfs:label "methodName"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed."@en; - rdfs:domain ; - rdfs:label "geometry"@en; - rdfs:range , . - rdf:type owl:DatatypeProperty; rdfs:comment "Name of institution submitting the variable"@en; @@ -3142,6 +3376,9 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "The type of tissue sampled. ex. 'Leaf', 'Root', etc.\n
MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology)."@en; @@ -3149,10 +3386,6 @@ PREFIX xsd: rdfs:label "tissueType"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -3162,6 +3395,13 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name."@en; + rdfs:domain ; + rdfs:label "speciesAuthority"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3197,6 +3437,13 @@ PREFIX xsd: rdfs:label "speciesAuthority"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; + rdfs:domain ; + rdfs:label "biologicalStatusOfAccessionCode"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . @@ -3285,6 +3532,13 @@ PREFIX xsd: rdfs:label "created"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The `GenomeMap` to which this `LinkageGroup` belongs "@en; + rdfs:domain ; + rdfs:label "genomeMap"@en; + rdfs:range . + rdf:type owl:Class; rdfs:comment "If the Scale is a categorical type, these objects define the valid options"@en; @@ -3352,6 +3606,20 @@ PREFIX xsd: rdfs:label "method"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level."@en; + rdfs:domain ; + rdfs:label "subtaxonAuthority"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville)."@en; + rdfs:domain ; + rdfs:label "locationDescription"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -3364,13 +3632,6 @@ PREFIX xsd: rdfs:comment "The dimension of the matrix being paginated"@en; rdfs:label "Dimension"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "Set of custom attributes associated with a cross"@en; - rdfs:domain ; - rdfs:label "crossAttributes"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "the human readable identifier for this breeding method"@en; @@ -3385,11 +3646,12 @@ PREFIX xsd: rdfs:label "version"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:domain ; - rdfs:label "validValues"@en; - rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "Set of custom attributes associated with a cross"@en; + rdfs:domain ; + rdfs:label "crossAttributes"@en; + rdfs:range . rdf:type owl:NamedIndividual , . @@ -3401,6 +3663,12 @@ PREFIX xsd: rdfs:label "studyType"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:domain ; + rdfs:label "validValues"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc"@en; @@ -3429,6 +3697,13 @@ PREFIX xsd: rdfs:label "genotypeMetadata"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology's list of authors (no specific format)"@en; + rdfs:domain ; + rdfs:label "authors"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; @@ -3443,6 +3718,11 @@ PREFIX xsd: rdfs:label "value"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; + rdfs:label "StorageTypeCode"@en . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3450,17 +3730,18 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; - rdfs:label "StorageTypeCode"@en . + + rdf:type owl:ObjectProperty; + rdfs:domain ; + rdfs:label "safetyDuplicateInstitutes"@en; + rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology's list of authors (no specific format)"@en; - rdfs:domain ; - rdfs:label "authors"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "Institutes which collected the sample"@en; + rdfs:domain ; + rdfs:label "collectingInstitutes"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -3484,7 +3765,7 @@ PREFIX xsd: rdfs:range xsd:string . - rdf:type owl:NamedIndividual , . + rdf:type , owl:NamedIndividual , . rdf:type owl:ObjectProperty; @@ -3493,10 +3774,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The type of positional coordinate used for the X coordinate of the position."@en; @@ -3509,13 +3786,6 @@ PREFIX xsd: rdfs:comment "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis."@en; rdfs:label "Plate"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The 4 digit year of the season."@en; @@ -3523,6 +3793,13 @@ PREFIX xsd: rdfs:label "year"@en; rdfs:range xsd:integer . + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; @@ -3544,6 +3821,9 @@ PREFIX xsd: rdfs:label "md5checksum"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3551,8 +3831,9 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -3608,10 +3889,6 @@ PREFIX xsd: rdfs:label "genotypeValue"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3652,6 +3929,17 @@ PREFIX xsd: rdfs:comment "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100."@en; rdfs:label "ContentMixture"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123)."@en; + rdfs:domain ; + rdfs:label "longitudeDecimal"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The human readable identifier for a `GenomeMap`"@en; @@ -3659,6 +3947,9 @@ PREFIX xsd: rdfs:label "mapName"@en; rdfs:range xsd:string . + + rdf:type , owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a location, associated with this study"@en; @@ -3666,9 +3957,6 @@ PREFIX xsd: rdfs:label "location"@en; rdfs:range . - - rdf:type , owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "The end of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event."@en; @@ -3742,6 +4030,11 @@ PREFIX xsd: rdfs:label "amount"@en; rdfs:range xsd:double . + + rdf:type owl:Class; + rdfs:comment "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")"@en; + rdfs:label "MlsStatus"@en . + rdf:type owl:Class; rdfs:label "Attribute"@en . @@ -3763,6 +4056,13 @@ PREFIX xsd: rdfs:label "dataFormat"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space."@en; + rdfs:domain ; + rdfs:label "instituteName"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3777,6 +4077,10 @@ PREFIX xsd: rdfs:label "observationVariables"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -3793,6 +4097,11 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . + + rdf:type owl:Class; + rdfs:comment "Information about the collection of a germplasm"@en; + rdfs:label "CollectingInfo"@en . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3831,6 +4140,11 @@ PREFIX xsd: rdfs:label "samples"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)"@en; + rdfs:label "AcquisitionSourceCode"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'."@en; @@ -3845,6 +4159,13 @@ PREFIX xsd: rdfs:label "abbreviation"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers\" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\"."@en; + rdfs:domain ; + rdfs:label "countryOfOrigin"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)"@en; @@ -3880,6 +4201,10 @@ PREFIX xsd: rdfs:label "study"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows."@en; @@ -3888,13 +4213,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:ObjectProperty; - rdfs:comment "plannedCrosses"@en; - rdfs:domain ; - rdfs:label "plannedCrosses"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The value of the data collected as an observation"@en; @@ -3902,6 +4220,13 @@ PREFIX xsd: rdfs:label "value"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "plannedCrosses"@en; + rdfs:domain ; + rdfs:label "plannedCrosses"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "Other variable names"@en; @@ -3961,6 +4286,9 @@ PREFIX xsd: rdfs:label "variants"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "List of seasons over which this study was performed."@en; @@ -3968,9 +4296,6 @@ PREFIX xsd: rdfs:label "seasons"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -4014,13 +4339,6 @@ PREFIX xsd: rdfs:comment "A persons contact information"@en; rdfs:label "Contact"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; - rdfs:domain ; - rdfs:label "method"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The number of Variants included in this VariantSet"@en; @@ -4028,6 +4346,13 @@ PREFIX xsd: rdfs:label "variantCount"@en; rdfs:range xsd:integer . + + rdf:type owl:ObjectProperty; + rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; + rdfs:domain ; + rdfs:label "method"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "the first parent used in the cross"@en; @@ -4047,6 +4372,13 @@ PREFIX xsd: rdfs:comment "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program."@en; rdfs:label "SeedLot"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'."@en; + rdfs:domain ; + rdfs:label "ancestralData"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)"@en; @@ -4104,6 +4436,10 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -4175,7 +4511,7 @@ PREFIX xsd: rdf:type owl:ObjectProperty; - rdfs:comment ""@en; + rdfs:comment "The child locations that belong to this Location. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; rdfs:domain ; rdfs:label "childLocations"@en; rdfs:range . @@ -4221,11 +4557,11 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - + rdf:type owl:DatatypeProperty; - rdfs:comment "Full scientific binomial format name. This includes Genus, Species, and Sub-species"@en; - rdfs:domain ; - rdfs:label "scientificName"@en; + rdfs:comment "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; + rdfs:domain ; + rdfs:label "donorAccessionNumber"@en; rdfs:range xsd:string . @@ -4235,6 +4571,13 @@ PREFIX xsd: rdfs:label "variant"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Full scientific binomial format name. This includes Genus, Species, and Sub-species"@en; + rdfs:domain ; + rdfs:label "scientificName"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor."@en; @@ -4247,6 +4590,13 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date this study started\n\nMIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started"@en; + rdfs:domain ; + rdfs:label "startDate"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "A single position"@en; @@ -4254,11 +4604,11 @@ PREFIX xsd: rdfs:label "coordinates"@en; rdfs:range xsd:double . - + rdf:type owl:DatatypeProperty; - rdfs:comment "The date this study started\n\nMIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started"@en; - rdfs:domain ; - rdfs:label "startDate"@en; + rdfs:comment "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum."@en; + rdfs:domain ; + rdfs:label "spatialReferenceSystem"@en; rdfs:range xsd:string . @@ -4271,6 +4621,11 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:Class; + rdfs:comment "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other."@en; + rdfs:label "AvailableFormat"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; @@ -4278,11 +4633,6 @@ PREFIX xsd: rdfs:label "defaultValue"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other."@en; - rdfs:label "AvailableFormat"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; @@ -4311,10 +4661,6 @@ PREFIX xsd: rdfs:label "plates"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "associated event"@en; @@ -4327,6 +4673,13 @@ PREFIX xsd: rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; rdfs:label "Trait"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10"@en; + rdfs:domain ; + rdfs:label "latitudeDegrees"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "A flag to indicate if a Trial is currently active and ongoing"@en; @@ -4341,6 +4694,17 @@ PREFIX xsd: rdfs:label "factor"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections."@en; + rdfs:domain ; + rdfs:label "collectingNumber"@en; + rdfs:range xsd:string . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "samples"@en; @@ -4362,6 +4726,13 @@ PREFIX xsd: rdfs:label "fieldAbbreviation"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The identifying information for the entity acting as an accession donor\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.\n
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available."@en; + rdfs:domain ; + rdfs:label "donorInstitute"@en; + rdfs:range . + rdf:type owl:Class; rdfs:comment "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data."@en; @@ -4372,23 +4743,6 @@ PREFIX xsd: rdfs:comment "An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. \n
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other"@en; rdfs:label "Event"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard."@en; - rdfs:domain ; - rdfs:label "fieldName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A permanent unique identifier associated with this study data. For example, a URI or DOI"@en; - rdfs:domain ; - rdfs:label "studyPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "The ID which uniquely identifies a `Variant`"@en; @@ -4396,18 +4750,8 @@ PREFIX xsd: rdfs:label "variantDbId"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A flag to indicate if a Study is currently active and ongoing"@en; - rdfs:domain ; - rdfs:label "active"@en; - rdfs:range xsd:boolean . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . + + rdf:type owl:NamedIndividual , . rdf:type owl:ObjectProperty; @@ -4416,6 +4760,26 @@ PREFIX xsd: rdfs:label "cross"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A flag to indicate if a Study is currently active and ongoing"@en; + rdfs:domain ; + rdfs:label "active"@en; + rdfs:range xsd:boolean . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A permanent unique identifier associated with this study data. For example, a URI or DOI"@en; + rdfs:domain ; + rdfs:label "studyPUI"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "A detailed, human-readable description of this event\n
MIAPPE V1.1 (DM-67) Event description - Description of the event, including details such as amount applied and possibly duration of the event. "@en; @@ -4430,11 +4794,11 @@ PREFIX xsd: rdfs:label "potentialParents"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name which identifies a germplasm within the given database server"@en; - rdfs:domain ; - rdfs:label "callSetName"@en; + rdfs:comment "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard."@en; + rdfs:domain ; + rdfs:label "fieldName"@en; rdfs:range xsd:string . @@ -4458,17 +4822,10 @@ PREFIX xsd: rdfs:label "defaultValue"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; - rdfs:label "Scale"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "events"@en; - rdfs:domain ; - rdfs:label "events"@en; - rdfs:range . + + rdf:type owl:Class; + rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; + rdfs:label "Scale"@en . rdf:type owl:ObjectProperty; @@ -4477,6 +4834,13 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "events"@en; + rdfs:domain ; + rdfs:label "events"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "The crossing project used to generate this germplasm"@en; @@ -4498,6 +4862,20 @@ PREFIX xsd: rdfs:label "levelOrder"@en; rdfs:range xsd:integer . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name which identifies a germplasm within the given database server"@en; + rdfs:domain ; + rdfs:label "callSetName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed."@en; + rdfs:domain ; + rdfs:label "elevation"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "images"@en; @@ -4574,13 +4952,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of markers present in a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "markerCount"@en; - rdfs:range xsd:integer . - rdf:type owl:ObjectProperty; rdfs:comment "the second parent used in the cross"@en; @@ -4588,6 +4959,13 @@ PREFIX xsd: rdfs:label "parent2"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of markers present in a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "markerCount"@en; + rdfs:range xsd:integer . + rdf:type owl:DatatypeProperty; rdfs:comment "A short human readable code for a study"@en; @@ -4619,6 +4997,11 @@ PREFIX xsd: rdfs:comment "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology"@en; rdfs:label "ExperimentalDesign"@en . + + rdf:type owl:Class; + rdfs:comment "Information about an accession donor"@en; + rdfs:label "DonorInfo"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; @@ -4633,6 +5016,13 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "PUI (DOI mostly) of the accession in the donor system."@en; + rdfs:domain ; + rdfs:label "donorAccessionPui"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "Formats associated with a variant set"@en; @@ -4664,6 +5054,20 @@ PREFIX xsd: rdfs:label "fieldValue"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The content of the image"@en; + rdfs:domain ; + rdfs:label "imageContent"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown."@en; + rdfs:domain ; + rdfs:label "coordinateUncertainty"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; @@ -4671,6 +5075,13 @@ PREFIX xsd: rdfs:label "analysis"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of markers associated with a `LinkageGroup`."@en; + rdfs:domain ; + rdfs:label "markerCount"@en; + rdfs:range xsd:integer . + rdf:type owl:ObjectProperty; rdfs:comment "The unique identifier for a Location\n
The Parent Location defines the encompassing Location that a smaller Location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; @@ -4706,6 +5117,13 @@ PREFIX xsd: rdfs:label "variantSets"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)"@en; + rdfs:domain ; + rdfs:label "acquisitionSourceCode"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "Internal database identifier"@en; @@ -4769,13 +5187,6 @@ PREFIX xsd: rdfs:label "samplePUI"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The season for this Observation"@en; @@ -4811,6 +5222,13 @@ PREFIX xsd: rdfs:label "toSeedLot"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -4823,6 +5241,10 @@ PREFIX xsd: rdfs:comment "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding "@en; rdfs:label "ProgramType"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of institution submitting the variable"@en; @@ -4830,9 +5252,12 @@ PREFIX xsd: rdfs:label "institution"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI"@en; + rdfs:domain ; + rdfs:label "eventParameters"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -4841,13 +5266,6 @@ PREFIX xsd: rdfs:label "code"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI"@en; - rdfs:domain ; - rdfs:label "eventParameters"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "the first parent used in the cross"@en; @@ -4856,7 +5274,7 @@ PREFIX xsd: rdfs:range . - rdf:type owl:NamedIndividual , . + rdf:type , owl:NamedIndividual , . rdf:type owl:DatatypeProperty; @@ -4902,10 +5320,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "The type of positional coordinate. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; @@ -4921,6 +5335,13 @@ PREFIX xsd: rdfs:comment "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)"@en; rdfs:label "EventDateRange"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies an observation"@en; + rdfs:domain ; + rdfs:label "observationDbId"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "List of possible values with optional labels"@en; @@ -4932,12 +5353,9 @@ PREFIX xsd: rdf:type owl:Class; rdfs:label "ExternalReference"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies an observation"@en; - rdfs:domain ; - rdfs:label "observationDbId"@en; - rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -5230,13 +5648,6 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."@en; - rdfs:domain ; - rdfs:label "orcid"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. "@en; @@ -5251,6 +5662,13 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation."@en; + rdfs:domain ; + rdfs:label "termURI"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "pedigreeNodes"@en; @@ -5258,11 +5676,18 @@ PREFIX xsd: rdfs:label "pedigreeNodes"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation."@en; - rdfs:domain ; - rdfs:label "termURI"@en; + rdfs:comment "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\")."@en; + rdfs:domain ; + rdfs:label "accessionNumber"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."@en; + rdfs:domain ; + rdfs:label "orcid"@en; rdfs:range xsd:string . @@ -5272,6 +5697,13 @@ PREFIX xsd: rdfs:label "methodDbId"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The offset position (0-based) of the given sequence from the start of this `Reference`. This value will differ for each page in a request."@en; + rdfs:domain ; + rdfs:label "offset"@en; + rdfs:range xsd:integer . + rdf:type owl:ObjectProperty; rdfs:comment "observationUnits"@en; @@ -5286,10 +5718,6 @@ PREFIX xsd: rdfs:label "trial"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -5297,6 +5725,13 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (REMARKS) 28. The remarks field is used to add notes or to elaborate on descriptors with value 99 or 999 (= Other). Prefix remarks with the field name they refer to and a colon (:) without space (e.g. COLLSRC:riverside). Distinct remarks referring to different fields are separated by semi-colons without space."@en; + rdfs:domain ; + rdfs:label "remarks"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "A specific panel/collection/population name this germplasm belongs to."@en; @@ -5337,6 +5772,10 @@ PREFIX xsd: rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; rdfs:label "ObservationUnitHierarchyLevel"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation"@en; @@ -5417,6 +5856,10 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a `Program` within the given database server"@en; @@ -5431,6 +5874,13 @@ PREFIX xsd: rdfs:label "geoCoordinates"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The maximum position of a marker within a `LinkageGroup`."@en; + rdfs:domain ; + rdfs:label "maxPosition"@en; + rdfs:range xsd:integer . + rdf:type owl:DatatypeProperty; rdfs:comment "The name of the institution which this contact is part of\n\nMIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to"@en; @@ -5452,12 +5902,21 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . rdf:type owl:NamedIndividual , . + + rdf:type owl:Class; + rdfs:comment "Information about the location where the sample was collected"@en; + rdfs:label "CollectingSite"@en . + rdf:type owl:NamedIndividual , . @@ -5468,10 +5927,20 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space."@en; + rdfs:domain ; + rdfs:label "instituteCode"@en; + rdfs:range xsd:string . + [ rdf:type owl:Class; - owl:oneOf ( ) + owl:oneOf ( ) ] . + + rdf:type owl:NamedIndividual , . + rdf:type owl:Class; rdfs:comment "A link to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; @@ -5593,6 +6062,10 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this attribute"@en; @@ -5614,6 +6087,11 @@ PREFIX xsd: rdfs:label "levelCode"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event."@en; + rdfs:label "EventParameter"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary."@en; @@ -5621,11 +6099,6 @@ PREFIX xsd: rdfs:label "germplasmPreprocessing"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event."@en; - rdfs:label "EventParameter"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "In the case of structural variants, start and end of the variant may not\nbe known with an exact base position. \"cipos\" provides an interval with\nhigh confidence for the start position. The interval is provided by 0 or\n2 signed integers which are added to the start position.\nBased on the use in VCF v4.2"@en; @@ -5654,12 +6127,9 @@ PREFIX xsd: rdfs:label "software"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -5680,6 +6150,13 @@ PREFIX xsd: rdfs:label "discreteDates"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "Last update associated with a study"@en; @@ -5788,6 +6265,11 @@ PREFIX xsd: rdfs:label "samples"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "The details of an Institute or other simular entity."@en; + rdfs:label "Institute"@en . + rdf:type owl:Class; rdfs:comment "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap."@en; @@ -5807,12 +6289,10 @@ PREFIX xsd: rdfs:label "mapDbId"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; - rdfs:domain ; - rdfs:label "defaultValue"@en; - rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group."@en; + rdfs:label "LinkageGroup"@en . rdf:type owl:DatatypeProperty; @@ -5835,6 +6315,13 @@ PREFIX xsd: rdfs:label "defaultDisplayName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; + rdfs:domain ; + rdfs:label "defaultValue"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; @@ -5856,6 +6343,9 @@ PREFIX xsd: rdfs:label "imageFileSize"@en; rdfs:range xsd:integer . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "The length of this `Reference` sequence."@en; @@ -5880,15 +6370,14 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)."@en; rdfs:label "EnvironmentParameter"@en . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of scientist submitting the variable."@en; @@ -5896,13 +6385,6 @@ PREFIX xsd: rdfs:label "scientist"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the entity was first created"@en; @@ -5998,7 +6480,7 @@ PREFIX xsd: rdfs:range . - rdf:type owl:NamedIndividual , . + rdf:type , owl:NamedIndividual , . rdf:type owl:DatatypeProperty; @@ -6021,9 +6503,6 @@ PREFIX xsd: rdfs:label "dataType"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; @@ -6031,6 +6510,9 @@ PREFIX xsd: rdfs:label "instituteAddress"@en; rdfs:range xsd:string . + + rdf:type , , owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value."@en; @@ -6051,6 +6533,8 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "The Well identifier for this `Sample` location in the `Plate`. Usually a concatenation of Row and Column, or just a number if the `Samples` are not part of an ordered `Plate`."@en; @@ -6058,10 +6542,6 @@ PREFIX xsd: rdfs:label "well"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\""@en; @@ -6076,10 +6556,6 @@ PREFIX xsd: rdfs:label "mainAbbreviation"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology."@en; @@ -6101,13 +6577,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a Location"@en; - rdfs:domain ; - rdfs:label "location"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; @@ -6115,6 +6584,13 @@ PREFIX xsd: rdfs:label "trait"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a Location"@en; + rdfs:domain ; + rdfs:label "location"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -6165,7 +6641,7 @@ PREFIX xsd: rdfs:range . - rdf:type owl:NamedIndividual , . + rdf:type , owl:NamedIndividual , . rdf:type owl:ObjectProperty; diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index 0ee9d91a..401d9015 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -1005,6 +1005,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details for a specific Germplasm Attribute", @@ -1087,6 +1098,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Germplasm Attribute", @@ -1415,6 +1437,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details for a specific Germplasm Attribute", @@ -1487,168 +1520,6 @@ }, "description" : "Unauthorized" }, - "403" : { - "content" : { - "application/json" : { - "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", - "schema" : { - "type" : "string" - } - } - }, - "description" : "Forbidden" - } - }, - "summary" : "Update an existing Germplasm Attribute Value", - "tags" : [ "Germplasm Attribute Values" ] - } - }, - "/breedingmethods" : { - "get" : { - "description" : "Get the list of germplasm breeding methods available in a system.", - "parameters" : [ { - "description" : "Used to request a specific page of data to be returned.\n\nThe page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", - "example" : "0", - "explode" : true, - "in" : "query", - "name" : "page", - "required" : false, - "schema" : { - "type" : "integer" - }, - "style" : "form" - }, { - "description" : "The size of the pages to be returned. Default is `1000`.", - "example" : 1000, - "explode" : true, - "in" : "query", - "name" : "pageSize", - "required" : false, - "schema" : { - "type" : "integer" - }, - "style" : "form" - }, { - "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", - "example" : "Bearer XXXX", - "explode" : false, - "in" : "header", - "name" : "Authorization", - "required" : false, - "schema" : { - "pattern" : "^Bearer .*$", - "type" : "string" - }, - "style" : "simple" - } ], - "responses" : { - "200" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/BreedingMethodListResponse" - } - } - }, - "description" : "OK" - }, - "400" : { - "content" : { - "application/json" : { - "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", - "schema" : { - "type" : "string" - } - } - }, - "description" : "Bad Request" - }, - "401" : { - "content" : { - "application/json" : { - "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", - "schema" : { - "type" : "string" - } - } - }, - "description" : "Unauthorized" - }, - "403" : { - "content" : { - "application/json" : { - "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", - "schema" : { - "type" : "string" - } - } - }, - "description" : "Forbidden" - } - }, - "summary" : "Get the Breeding Methods", - "tags" : [ "Germplasm" ] - } - }, - "/breedingmethods/{breedingMethodDbId}" : { - "get" : { - "description" : "Get the details of a specific Breeding Method used to produce Germplasm", - "parameters" : [ { - "description" : "Internal database identifier for a breeding method", - "explode" : false, - "in" : "path", - "name" : "breedingMethodDbId", - "required" : true, - "schema" : { - "type" : "string" - }, - "style" : "simple" - }, { - "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", - "example" : "Bearer XXXX", - "explode" : false, - "in" : "header", - "name" : "Authorization", - "required" : false, - "schema" : { - "pattern" : "^Bearer .*$", - "type" : "string" - }, - "style" : "simple" - } ], - "responses" : { - "200" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/BreedingMethodSingleResponse" - } - } - }, - "description" : "OK" - }, - "400" : { - "content" : { - "application/json" : { - "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", - "schema" : { - "type" : "string" - } - } - }, - "description" : "Bad Request" - }, - "401" : { - "content" : { - "application/json" : { - "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", - "schema" : { - "type" : "string" - } - } - }, - "description" : "Unauthorized" - }, "403" : { "content" : { "application/json" : { @@ -1672,96 +1543,269 @@ "description" : "Not Found" } }, - "summary" : "Get the details of a specific Breeding Method", - "tags" : [ "Germplasm" ] + "summary" : "Update an existing Germplasm Attribute Value", + "tags" : [ "Germplasm Attribute Values" ] } }, - "/calls" : { + "/breedingmethods" : { "get" : { - "description" : "Gets a filtered list of `Call` JSON objects.", + "description" : "Get the list of germplasm breeding methods available in a system.", "parameters" : [ { - "description" : "The ID which uniquely identifies a `CallSet` within the given database server", - "explode" : true, - "in" : "query", - "name" : "callSetDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "The ID which uniquely identifies a `Variant` within the given database server", - "explode" : true, - "in" : "query", - "name" : "variantDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "The ID which uniquely identifies a `VariantSet` within the given database server", - "explode" : true, - "in" : "query", - "name" : "variantSetDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", - "explode" : true, - "in" : "query", - "name" : "expandHomozygotes", - "required" : false, - "schema" : { - "type" : "boolean" - }, - "style" : "form" - }, { - "description" : "The string to use as a representation for missing data", - "explode" : true, - "in" : "query", - "name" : "unknownString", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "The string to use as a separator for phased allele calls", - "explode" : true, - "in" : "query", - "name" : "sepPhased", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "The string to use as a separator for unphased allele calls", - "explode" : true, - "in" : "query", - "name" : "sepUnphased", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
Used to request a specific page of data to be returned.\n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. ", - "example" : "33c27874", - "explode" : true, - "in" : "query", - "name" : "pageToken", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { + "description" : "Used to request a specific page of data to be returned.\n\nThe page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "example" : "0", + "explode" : true, + "in" : "query", + "name" : "page", + "required" : false, + "schema" : { + "type" : "integer" + }, + "style" : "form" + }, { + "description" : "The size of the pages to be returned. Default is `1000`.", + "example" : 1000, + "explode" : true, + "in" : "query", + "name" : "pageSize", + "required" : false, + "schema" : { + "type" : "integer" + }, + "style" : "form" + }, { + "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", + "example" : "Bearer XXXX", + "explode" : false, + "in" : "header", + "name" : "Authorization", + "required" : false, + "schema" : { + "pattern" : "^Bearer .*$", + "type" : "string" + }, + "style" : "simple" + } ], + "responses" : { + "200" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/BreedingMethodListResponse" + } + } + }, + "description" : "OK" + }, + "400" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" + }, + "401" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" + }, + "403" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" + } + }, + "summary" : "Get the Breeding Methods", + "tags" : [ "Germplasm" ] + } + }, + "/breedingmethods/{breedingMethodDbId}" : { + "get" : { + "description" : "Get the details of a specific Breeding Method used to produce Germplasm", + "parameters" : [ { + "description" : "Internal database identifier for a breeding method", + "explode" : false, + "in" : "path", + "name" : "breedingMethodDbId", + "required" : true, + "schema" : { + "type" : "string" + }, + "style" : "simple" + }, { + "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", + "example" : "Bearer XXXX", + "explode" : false, + "in" : "header", + "name" : "Authorization", + "required" : false, + "schema" : { + "pattern" : "^Bearer .*$", + "type" : "string" + }, + "style" : "simple" + } ], + "responses" : { + "200" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/BreedingMethodSingleResponse" + } + } + }, + "description" : "OK" + }, + "400" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" + }, + "401" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" + }, + "403" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" + } + }, + "summary" : "Get the details of a specific Breeding Method", + "tags" : [ "Germplasm" ] + } + }, + "/calls" : { + "get" : { + "description" : "Gets a filtered list of `Call` JSON objects.", + "parameters" : [ { + "description" : "The ID which uniquely identifies a `CallSet` within the given database server", + "explode" : true, + "in" : "query", + "name" : "callSetDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "The ID which uniquely identifies a `Variant` within the given database server", + "explode" : true, + "in" : "query", + "name" : "variantDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "The ID which uniquely identifies a `VariantSet` within the given database server", + "explode" : true, + "in" : "query", + "name" : "variantSetDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "explode" : true, + "in" : "query", + "name" : "expandHomozygotes", + "required" : false, + "schema" : { + "type" : "boolean" + }, + "style" : "form" + }, { + "description" : "The string to use as a representation for missing data", + "explode" : true, + "in" : "query", + "name" : "unknownString", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "The string to use as a separator for phased allele calls", + "explode" : true, + "in" : "query", + "name" : "sepPhased", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "The string to use as a separator for unphased allele calls", + "explode" : true, + "in" : "query", + "name" : "sepUnphased", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
Used to request a specific page of data to be returned.\n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. ", + "example" : "33c27874", + "explode" : true, + "in" : "query", + "name" : "pageToken", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { "description" : "Used to request a specific page of data to be returned.\n\nThe page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", "example" : "0", "explode" : true, @@ -2306,6 +2350,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Gets a list of `Calls` associated with a `CallSet`.", @@ -3094,6 +3149,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get a filtered list of Crossing Projects", @@ -3176,6 +3242,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Crossing Project", @@ -9128,6 +9205,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get a specific Ontology record by its ontologyDbId", @@ -9210,6 +9298,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update a specific Ontology record", @@ -11417,6 +11516,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get a breeding Program by Id", @@ -11499,6 +11609,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Program", @@ -12147,201 +12268,245 @@ } }, "description" : "A successful response." - } - }, - "summary" : "Gets a `ReferenceSet` by ID.", - "tags" : [ "Reference Sets" ] - } - }, - "/samples" : { - "get" : { - "description" : "Used to retrieve list of Samples from a Sample Tracking system based on some search criteria.", - "parameters" : [ { - "description" : "The unique identifier for a `Sample`", - "explode" : true, - "in" : "query", - "name" : "sampleDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "The human readable name of the `Sample`", - "explode" : true, - "in" : "query", - "name" : "sampleName", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "The unique identifier for a group of related `Samples`", - "explode" : true, - "in" : "query", - "name" : "sampleGroupDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "The ID which uniquely identifies an `ObservationUnit`", - "explode" : true, - "in" : "query", - "name" : "observationUnitDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "The ID which uniquely identifies a `Plate` of `Sample`", - "explode" : true, - "in" : "query", - "name" : "plateDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "The human readable name of a `Plate` of `Sample`", - "explode" : true, - "in" : "query", - "name" : "plateName", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crop. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "explode" : true, - "in" : "query", - "name" : "commonCropName", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "Use this parameter to only return results associated with the given `Program` unique identifier. \n
Use `GET /programs` to find the list of available `Programs` on a server.", - "explode" : true, - "in" : "query", - "name" : "programDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "Use this parameter to only return results associated with the given `Trial` unique identifier. \n
Use `GET /trials` to find the list of available `Trials` on a server.", - "explode" : true, - "in" : "query", - "name" : "trialDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "Use this parameter to only return results associated with the given `Study` unique identifier. \n
Use `GET /studies` to find the list of available `Studies` on a server.", - "explode" : true, - "in" : "query", - "name" : "studyDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "Use this parameter to only return results associated with the given `Germplasm` unique identifier. \n
Use `GET /germplasm` to find the list of available `Germplasm` on a server.", - "explode" : true, - "in" : "query", - "name" : "germplasmDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", - "explode" : true, - "in" : "query", - "name" : "externalReferenceID", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", - "explode" : true, - "in" : "query", - "name" : "externalReferenceId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "An identifier for the source system or database of an external reference (use with `externalReferenceId` parameter)", - "explode" : true, - "in" : "query", - "name" : "externalReferenceSource", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" - }, { - "description" : "Used to request a specific page of data to be returned.\n\nThe page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", - "example" : "0", - "explode" : true, - "in" : "query", - "name" : "page", - "required" : false, - "schema" : { - "type" : "integer" - }, - "style" : "form" - }, { - "description" : "The size of the pages to be returned. Default is `1000`.", - "example" : 1000, - "explode" : true, - "in" : "query", - "name" : "pageSize", - "required" : false, - "schema" : { - "type" : "integer" - }, - "style" : "form" - }, { - "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", - "example" : "Bearer XXXX", - "explode" : false, - "in" : "header", - "name" : "Authorization", - "required" : false, - "schema" : { - "pattern" : "^Bearer .*$", - "type" : "string" - }, - "style" : "simple" - } ], - "responses" : { - "200" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/SampleListResponse" - } - } - }, - "description" : "OK" + }, + "400" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Bad Request" + }, + "401" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Unauthorized" + }, + "403" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" + } + }, + "summary" : "Gets a `ReferenceSet` by ID.", + "tags" : [ "Reference Sets" ] + } + }, + "/samples" : { + "get" : { + "description" : "Used to retrieve list of Samples from a Sample Tracking system based on some search criteria.", + "parameters" : [ { + "description" : "The unique identifier for a `Sample`", + "explode" : true, + "in" : "query", + "name" : "sampleDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "The human readable name of the `Sample`", + "explode" : true, + "in" : "query", + "name" : "sampleName", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "The unique identifier for a group of related `Samples`", + "explode" : true, + "in" : "query", + "name" : "sampleGroupDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "The ID which uniquely identifies an `ObservationUnit`", + "explode" : true, + "in" : "query", + "name" : "observationUnitDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "The ID which uniquely identifies a `Plate` of `Sample`", + "explode" : true, + "in" : "query", + "name" : "plateDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "The human readable name of a `Plate` of `Sample`", + "explode" : true, + "in" : "query", + "name" : "plateName", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crop. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "explode" : true, + "in" : "query", + "name" : "commonCropName", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "Use this parameter to only return results associated with the given `Program` unique identifier. \n
Use `GET /programs` to find the list of available `Programs` on a server.", + "explode" : true, + "in" : "query", + "name" : "programDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "Use this parameter to only return results associated with the given `Trial` unique identifier. \n
Use `GET /trials` to find the list of available `Trials` on a server.", + "explode" : true, + "in" : "query", + "name" : "trialDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "Use this parameter to only return results associated with the given `Study` unique identifier. \n
Use `GET /studies` to find the list of available `Studies` on a server.", + "explode" : true, + "in" : "query", + "name" : "studyDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "Use this parameter to only return results associated with the given `Germplasm` unique identifier. \n
Use `GET /germplasm` to find the list of available `Germplasm` on a server.", + "explode" : true, + "in" : "query", + "name" : "germplasmDbId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "explode" : true, + "in" : "query", + "name" : "externalReferenceID", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "explode" : true, + "in" : "query", + "name" : "externalReferenceId", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "An identifier for the source system or database of an external reference (use with `externalReferenceId` parameter)", + "explode" : true, + "in" : "query", + "name" : "externalReferenceSource", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" + }, { + "description" : "Used to request a specific page of data to be returned.\n\nThe page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "example" : "0", + "explode" : true, + "in" : "query", + "name" : "page", + "required" : false, + "schema" : { + "type" : "integer" + }, + "style" : "form" + }, { + "description" : "The size of the pages to be returned. Default is `1000`.", + "example" : 1000, + "explode" : true, + "in" : "query", + "name" : "pageSize", + "required" : false, + "schema" : { + "type" : "integer" + }, + "style" : "form" + }, { + "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", + "example" : "Bearer XXXX", + "explode" : false, + "in" : "header", + "name" : "Authorization", + "required" : false, + "schema" : { + "pattern" : "^Bearer .*$", + "type" : "string" + }, + "style" : "simple" + } ], + "responses" : { + "200" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/SampleListResponse" + } + } + }, + "description" : "OK" }, "400" : { "content" : { @@ -13216,7 +13381,7 @@ } } }, - "description" : "Study Search request" + "description" : "AlleleMatrix Search request" }, "responses" : { "200" : { @@ -13790,7 +13955,7 @@ } } }, - "description" : "Study Search request" + "description" : "Calls Search request" }, "responses" : { "200" : { @@ -13990,11 +14155,11 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/callSetsSearchRequest" + "$ref" : "#/components/schemas/CallSetsSearchRequest" } } }, - "description" : "Study Search request" + "description" : "CallSet Search request" }, "responses" : { "200" : { @@ -17553,11 +17718,11 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/variantsSearchRequest" + "$ref" : "#/components/schemas/VariantsSearchRequest" } } }, - "description" : "Study Search request" + "description" : "Variant Search request" }, "responses" : { "200" : { @@ -17761,7 +17926,7 @@ } } }, - "description" : "Study Search request" + "description" : "VariantSet Search request" }, "responses" : { "200" : { @@ -18205,6 +18370,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the a single Season", @@ -18288,6 +18464,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update existing Seasons", @@ -21703,6 +21890,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Gets a list of `Calls` associated with a `Variant`.", @@ -21920,7 +22118,7 @@ } } }, - "description" : "Study Search request" + "description" : "VariantSet Search request" }, "responses" : { "200" : { @@ -22211,6 +22409,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Gets a list of `Calls` associated with a `VariantSet`.", @@ -24859,6 +25068,163 @@ "primaryModel" : true } }, + "CallSetsSearchRequest" : { + "properties" : { + "callSetDbIds" : { + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "example" : [ "6c7486b2", "49c36a73" ], + "items" : { + "type" : "string" + }, + "nullable" : true, + "type" : "array" + }, + "callSetNames" : { + "description" : "A list of human readable names associated with `CallSets`", + "example" : [ "Sample_123_DNA_Run_456", "Sample_789_DNA_Run_101" ], + "items" : { + "type" : "string" + }, + "nullable" : true, + "type" : "array" + }, + "commonCropNames" : { + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "example" : [ "Tomatillo", "Paw Paw" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "externalReferenceIDs" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "example" : [ "doi:10.155454/12341234", "14a19841" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "externalReferenceIds" : { + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "example" : [ "doi:10.155454/12341234", "14a19841" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "externalReferenceSources" : { + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "example" : [ "DOI", "Field App Name" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "germplasmDbIds" : { + "description" : "List of IDs which uniquely identify germplasm to search for", + "example" : [ "e9c6edd7", "1b1df4a6" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "germplasmNames" : { + "description" : "List of human readable names to identify germplasm to search for", + "example" : [ "A0000003", "A0000477" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "page" : { + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "example" : 0, + "type" : "integer" + }, + "pageSize" : { + "description" : "The size of the pages to be returned. Default is `1000`.", + "example" : 1000, + "type" : "integer" + }, + "programDbIds" : { + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "example" : [ "8f5de35b", "0e2d4a13" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "programNames" : { + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "example" : [ "Better Breeding Program", "Best Breeding Program" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "sampleDbIds" : { + "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "example" : [ "758d3f6d", "39c0a3f7" ], + "items" : { + "type" : "string" + }, + "nullable" : true, + "type" : "array" + }, + "sampleNames" : { + "description" : "A list of human readable names associated with `Samples`", + "example" : [ "Sample_123", "Sample_789" ], + "items" : { + "type" : "string" + }, + "nullable" : true, + "type" : "array" + }, + "studyDbIds" : { + "description" : "List of study identifiers to search for", + "example" : [ "cf6c4bd4", "691e69d6" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "studyNames" : { + "description" : "List of study names to filter search results", + "example" : [ "The First Bob Study 2017", "Wheat Yield Trial 246" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "trialDbIds" : { + "description" : "The ID which uniquely identifies a trial to search for", + "example" : [ "d2593dc2", "9431a731" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "trialNames" : { + "description" : "The human readable name of a trial to search for", + "example" : [ "All Yield Trials 2016", "Disease Resistance Study Comparison Group" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "variantSetDbIds" : { + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "example" : [ "8a9a8972", "32a2649a" ], + "items" : { + "type" : "string" + }, + "nullable" : true, + "type" : "array" + } + }, + "type" : "object" + }, "CallsSearchRequest" : { "properties" : { "callSetDbIds" : { @@ -36475,6 +36841,173 @@ }, "type" : "object" }, + "VariantsSearchRequest" : { + "properties" : { + "callSetDbIds" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", + "example" : [ "4639fe3e", "b60d900b" ], + "items" : { + "type" : "string" + }, + "nullable" : true, + "type" : "array" + }, + "commonCropNames" : { + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "example" : [ "Tomatillo", "Paw Paw" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "end" : { + "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", + "example" : 1500, + "nullable" : true, + "type" : "integer" + }, + "externalReferenceIDs" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "example" : [ "doi:10.155454/12341234", "14a19841" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "externalReferenceIds" : { + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "example" : [ "doi:10.155454/12341234", "14a19841" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "externalReferenceSources" : { + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "example" : [ "DOI", "Field App Name" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "page" : { + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "example" : 0, + "type" : "integer" + }, + "pageSize" : { + "description" : "The size of the pages to be returned. Default is `1000`.", + "example" : 1000, + "type" : "integer" + }, + "pageToken" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
Used to request a specific page of data to be returned.\n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. ", + "example" : "33c27874", + "type" : "string" + }, + "programDbIds" : { + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "example" : [ "8f5de35b", "0e2d4a13" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "programNames" : { + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "example" : [ "Better Breeding Program", "Best Breeding Program" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "referenceDbId" : { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", + "example" : "120a2d5c", + "nullable" : true, + "type" : "string" + }, + "referenceDbIds" : { + "description" : "The unique identifier representing a genotype `Reference`", + "example" : [ "89ab4d17", "74d3b63d" ], + "items" : { + "type" : "string" + }, + "nullable" : true, + "type" : "array" + }, + "referenceSetDbIds" : { + "description" : "The unique identifier representing a genotype `ReferenceSet`", + "example" : [ "d3b63d4d", "3b63d74b" ], + "items" : { + "type" : "string" + }, + "nullable" : true, + "type" : "array" + }, + "start" : { + "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", + "example" : 100, + "nullable" : true, + "type" : "integer" + }, + "studyDbIds" : { + "description" : "List of study identifiers to search for", + "example" : [ "cf6c4bd4", "691e69d6" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "studyNames" : { + "description" : "List of study names to filter search results", + "example" : [ "The First Bob Study 2017", "Wheat Yield Trial 246" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "trialDbIds" : { + "description" : "The ID which uniquely identifies a trial to search for", + "example" : [ "d2593dc2", "9431a731" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "trialNames" : { + "description" : "The human readable name of a trial to search for", + "example" : [ "All Yield Trials 2016", "Disease Resistance Study Comparison Group" ], + "items" : { + "type" : "string" + }, + "type" : "array" + }, + "variantDbIds" : { + "description" : "A list of IDs which uniquely identify `Variants`", + "example" : [ "3b63d889", "ab4d174d" ], + "items" : { + "type" : "string" + }, + "nullable" : true, + "type" : "array" + }, + "variantSetDbIds" : { + "description" : "A list of IDs which uniquely identify `VariantSets`", + "example" : [ "ba63d810", "434d1760" ], + "items" : { + "type" : "string" + }, + "nullable" : true, + "type" : "array" + } + }, + "type" : "object" + }, "VendorContact" : { "properties" : { "vendorAddress" : { @@ -36969,163 +37502,6 @@ "required" : [ "currentPage", "pageSize" ], "type" : "object" }, - "callSetsSearchRequest" : { - "properties" : { - "callSetDbIds" : { - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "example" : [ "6c7486b2", "49c36a73" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "callSetNames" : { - "description" : "A list of human readable names associated with `CallSets`", - "example" : [ "Sample_123_DNA_Run_456", "Sample_789_DNA_Run_101" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "commonCropNames" : { - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "example" : [ "Tomatillo", "Paw Paw" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "externalReferenceIDs" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "example" : [ "doi:10.155454/12341234", "14a19841" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "externalReferenceIds" : { - "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "example" : [ "doi:10.155454/12341234", "14a19841" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "externalReferenceSources" : { - "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", - "example" : [ "DOI", "Field App Name" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "germplasmDbIds" : { - "description" : "List of IDs which uniquely identify germplasm to search for", - "example" : [ "e9c6edd7", "1b1df4a6" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "germplasmNames" : { - "description" : "List of human readable names to identify germplasm to search for", - "example" : [ "A0000003", "A0000477" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "page" : { - "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", - "example" : 0, - "type" : "integer" - }, - "pageSize" : { - "description" : "The size of the pages to be returned. Default is `1000`.", - "example" : 1000, - "type" : "integer" - }, - "programDbIds" : { - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "example" : [ "8f5de35b", "0e2d4a13" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "programNames" : { - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "example" : [ "Better Breeding Program", "Best Breeding Program" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "sampleDbIds" : { - "description" : "A list of IDs which uniquely identify `Samples` within the given database server", - "example" : [ "758d3f6d", "39c0a3f7" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "sampleNames" : { - "description" : "A list of human readable names associated with `Samples`", - "example" : [ "Sample_123", "Sample_789" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "studyDbIds" : { - "description" : "List of study identifiers to search for", - "example" : [ "cf6c4bd4", "691e69d6" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "studyNames" : { - "description" : "List of study names to filter search results", - "example" : [ "The First Bob Study 2017", "Wheat Yield Trial 246" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "trialDbIds" : { - "description" : "The ID which uniquely identifies a trial to search for", - "example" : [ "d2593dc2", "9431a731" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "trialNames" : { - "description" : "The human readable name of a trial to search for", - "example" : [ "All Yield Trials 2016", "Disease Resistance Study Comparison Group" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "variantSetDbIds" : { - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "example" : [ "8a9a8972", "32a2649a" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - } - }, - "type" : "object" - }, "dataFile" : { "description" : "A dataFile contains a URL and the relevant file metadata to represent a file", "properties" : { @@ -37442,173 +37818,6 @@ "required" : [ "currentPage", "nextPageToken", "pageSize" ], "type" : "object" }, - "variantsSearchRequest" : { - "properties" : { - "callSetDbIds" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", - "example" : [ "4639fe3e", "b60d900b" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "commonCropNames" : { - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "example" : [ "Tomatillo", "Paw Paw" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "end" : { - "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", - "example" : 1500, - "nullable" : true, - "type" : "integer" - }, - "externalReferenceIDs" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "example" : [ "doi:10.155454/12341234", "14a19841" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "externalReferenceIds" : { - "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "example" : [ "doi:10.155454/12341234", "14a19841" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "externalReferenceSources" : { - "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", - "example" : [ "DOI", "Field App Name" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "page" : { - "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", - "example" : 0, - "type" : "integer" - }, - "pageSize" : { - "description" : "The size of the pages to be returned. Default is `1000`.", - "example" : 1000, - "type" : "integer" - }, - "pageToken" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
Used to request a specific page of data to be returned.\n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. ", - "example" : "33c27874", - "type" : "string" - }, - "programDbIds" : { - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "example" : [ "8f5de35b", "0e2d4a13" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "programNames" : { - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "example" : [ "Better Breeding Program", "Best Breeding Program" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "referenceDbId" : { - "deprecated" : true, - "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", - "example" : "120a2d5c", - "nullable" : true, - "type" : "string" - }, - "referenceDbIds" : { - "description" : "The unique identifier representing a genotype `Reference`", - "example" : [ "89ab4d17", "74d3b63d" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "referenceSetDbIds" : { - "description" : "The unique identifier representing a genotype `ReferenceSet`", - "example" : [ "d3b63d4d", "3b63d74b" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "start" : { - "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", - "example" : 100, - "nullable" : true, - "type" : "integer" - }, - "studyDbIds" : { - "description" : "List of study identifiers to search for", - "example" : [ "cf6c4bd4", "691e69d6" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "studyNames" : { - "description" : "List of study names to filter search results", - "example" : [ "The First Bob Study 2017", "Wheat Yield Trial 246" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "trialDbIds" : { - "description" : "The ID which uniquely identifies a trial to search for", - "example" : [ "d2593dc2", "9431a731" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "trialNames" : { - "description" : "The human readable name of a trial to search for", - "example" : [ "All Yield Trials 2016", "Disease Resistance Study Comparison Group" ], - "items" : { - "type" : "string" - }, - "type" : "array" - }, - "variantDbIds" : { - "description" : "A list of IDs which uniquely identify `Variants`", - "example" : [ "3b63d889", "ab4d174d" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - }, - "variantSetDbIds" : { - "description" : "A list of IDs which uniquely identify `VariantSets`", - "example" : [ "ba63d810", "434d1760" ], - "items" : { - "type" : "string" - }, - "nullable" : true, - "type" : "array" - } - }, - "type" : "object" - }, "AlleleMatrixResponse" : { "properties" : { "@context" : { diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index 82ecd7f0..df7cc557 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -3,18935 +3,4278 @@ ##### `GET` /allelematrix -> Use this endpoint to retrieve a two dimensional matrix of genotype data - - -##### `GET` /attributes/categories - -> Get the Categories of Germplasm Attributes - ##### `GET` /commoncropnames -> Get the Common Crop Names - ##### `POST` /delete/images -> Submit a delete request for `Images` - ##### `POST` /delete/observations -> Submit a delete request for `Observations` - - -##### `GET` /germplasm/{germplasmDbId}/mcpd - -> Get the details of a specific Germplasm in MCPD format - - -##### `PUT` /images/{imageDbId}/imagecontent - -> Attach an image binary file to an existing image metadata record - - -##### `POST` /lists/{listDbId}/data - -> Add new data members to a specific List - - -##### `GET` /maps/{mapDbId}/linkagegroups - -> Get the Linkage Groups of a specific Genomic Map - ##### `GET` /observationlevels -> Get the Observation Levels - ##### `GET` /observations/table -> Get a list of Observations in a table format - ##### `GET` /observationunits/table -> Get a list of Observations in a table format - - -##### `GET` /references/{referenceDbId}/bases - -> Lists `Reference` bases by ID and optional range. - ##### `GET` /seedlots/transactions -> Get a filtered list of Seed Lot Transactions - ##### `POST` /seedlots/transactions -> Add new Seed Lot Transaction to be recorded - ##### `GET` /seedlots/{seedLotDbId}/transactions -> Get all Transactions related to a specific Seed Lot - ##### `GET` /serverinfo -> Get the list of implemented Calls - - -##### `GET` /studytypes - -> Get the Study Types - ##### `POST` /variantsets/extract -> Create new `VariantSet` based on search results - - -##### `PUT` /calls -> Update existing `Calls` with new genotype value or metadata +##### `PUT` /observations/{observationDbId} ##### `PUT` /observationunits/{observationUnitDbId} -> Update an existing Observation Units - - -##### `PUT` /pedigree -> Send a list of pedigree nodes to update existing information on a server +##### `PUT` /calls ##### `PUT` /plates -> Update the details of existing Plates - - -##### `PUT` /observations/{observationDbId} -> Update an existing Observation +##### `PUT` /pedigree #### What's Changed --- -##### `GET` /attributes - -> Get a filtered list of GermplasmAttribute - - -###### Parameters: - -Changed: `attributeCategory` in `query` -> General category for the attribute. very similar to Trait class. - - -Changed: `attributeDbId` in `query` -> List of Germplasm Attribute IDs to search for - - -Changed: `attributeName` in `query` -> List of human readable Germplasm Attribute names to search for - - -Changed: `methodDbId` in `query` -> List of methods to filter search results - - -Changed: `scaleDbId` in `query` -> The unique identifier for a Scale - - -Changed: `scaleName` in `query` -> Name of the scale ->
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable - - -Changed: `traitDbId` in `query` -> The unique identifier for a Trait - - -Changed: `traitName` in `query` -> The human readable name of a trait ->
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for +##### `GET` /markerpositions ###### Return Type: -Changed response : **200 OK** -> OK - +Changed response : **200** * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - * Changed property `result` (object) * Changed property `data` (array) - Changed items (object): - > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit - + Changed items (array): - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` + New properties: `mapPUI` - New optional properties: - - `method` - - `scale` - - `trait` + Deleted properties: `variantName` - * Added property `attributeValueDbIds` (array) + * Changed property `mapDbId` (string): + - Nullable changed: `true` -> `null` - Items (string): + * Changed property `mapName` (string): + - Nullable changed: `true` -> `null` - * Added property `methodDbId` (string) + * Changed property `variantDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `methodName` (string) +##### `GET` /methods - * Added property `methodPUI` (string) - * Added property `ontologyReferenceDbId` (string) +###### Parameters: - * Added property `scaleDbId` (string) +Deleted: `externalReferenceID` in `query` - * Added property `scaleName` (string) +##### `GET` /observationunits/{observationUnitDbId} - * Added property `scalePUI` (string) - * Added property `traitDbId` (string) +###### Return Type: - * Added property `traitName` (string) +New response : **404** - * Added property `traitPUI` (string) +##### `POST` /ontologies - * Deleted property `attributeDbId` (string) - > The ID which uniquely identifies this attribute within the given database server +###### Request: - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) +* Changed content type : `application/json` + Changed items (array): - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `ontologyName` (string): + - Nullable changed: `true` -> `null` +##### `PUT` /ontologies/{ontologyDbId} - * Deleted property `method` (object) - * Deleted property `ontologyReference` (object) +###### Request: - * Deleted property `scale` (object) +* Changed content type : `application/json` - * Deleted property `synonyms` (array) - > Other variable names + * Changed property `ontologyName` (string): + - Nullable changed: `true` -> `null` +##### `GET` /scales - * Deleted property `trait` (object) - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +###### Parameters: +Deleted: `externalReferenceID` in `query` - * Added property `additionalProperties` (string) +##### `POST` /search/allelematrix - * Changed property `attributeCategory` (string) - * Changed property `attributeDescription` (string) +###### Request: - * Changed property `attributeName` (string) +* Changed content type : `application/json` - * Changed property `attributePUI` (string) + * Changed property `dataMatrixAbbreviations` (array): + - Nullable changed: `true` -> `null` - * Changed property `commonCropName` (string) + * Changed property `dataMatrixNames` (array): + - Nullable changed: `true` -> `null` - * Changed property `defaultValue` (string) + * Changed property `expandHomozygotes` (boolean): + - Nullable changed: `true` -> `null` - * Changed property `documentationURL` (string -> string) + * Changed property `germplasmDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `growthStage` (string) + * Changed property `germplasmNames` (array): + - Nullable changed: `true` -> `null` - * Changed property `institution` (string) + * Changed property `germplasmPUIs` (array): + - Nullable changed: `true` -> `null` - * Changed property `language` (string) + * Changed property `pagination` (array): + - Nullable changed: `true` -> `null` - * Changed property `scientist` (string) + * Changed property `positionRanges` (array): + - Nullable changed: `true` -> `null` - * Changed property `status` (string) + * Changed property `preview` (boolean): + - Default changed: `false` -> `none` - * Changed property `submissionTimestamp` (string -> string) + * Changed property `sampleDbIds` (array): + - Nullable changed: `true` -> `null` -##### `POST` /attributes + * Changed property `sepPhased` (string): + - Nullable changed: `true` -> `null` -> Create new GermplasmAttribute + * Changed property `sepUnphased` (string): + - Nullable changed: `true` -> `null` + * Changed property `unknownString` (string): + - Nullable changed: `true` -> `null` -###### Request: + * Changed property `variantDbIds` (array): + - Nullable changed: `true` -> `null` -Changed content type : `application/json` + * Changed property `variantSetDbIds` (array): + - Nullable changed: `true` -> `null` ###### Return Type: -Changed response : **200 OK** -> OK - +Changed response : **200** * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - * Changed property `result` (object) - * Changed property `data` (array) - - Changed items (object): - > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit - - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `attributeValueDbIds` (array) - - * Added property `methodDbId` (string) - - * Added property `methodName` (string) - - * Added property `methodPUI` (string) - - * Added property `ontologyReferenceDbId` (string) - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Added property `traitDbId` (string) - - * Added property `traitName` (string) - - * Added property `traitPUI` (string) - - * Deleted property `attributeDbId` (string) - > The ID which uniquely identifies this attribute within the given database server - - - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `method` (object) - - * Deleted property `ontologyReference` (object) - - * Deleted property `scale` (object) - - * Deleted property `synonyms` (array) - > Other variable names - - - * Deleted property `trait` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - + New properties: `data` - * Added property `additionalProperties` (string) + Deleted properties: `callSetDbIds`, `dataMatrices`, `expandHomozygotes`, `pagination`, `sepPhased`, `sepUnphased`, `unknownString`, `variantDbIds`, `variantSetDbIds` - * Changed property `attributeCategory` (string) - - * Changed property `attributeDescription` (string) - - * Changed property `attributeName` (string) - - * Changed property `attributePUI` (string) - - * Changed property `commonCropName` (string) - - * Changed property `defaultValue` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `growthStage` (string) - - * Changed property `institution` (string) - - * Changed property `language` (string) - - * Changed property `scientist` (string) - - * Changed property `status` (string) - - * Changed property `submissionTimestamp` (string -> string) - -##### `GET` /attributes/{attributeDbId} - -> Get the details of a specific GermplasmAttribute - - -###### Parameters: - -Deleted: `attributeDbId` in `path` -> The unique id for an attribute + New required properties: + - `data` + Removed required properties: + - `callSetDbIds` + - `variantSetDbIds` -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} +##### `GET` /search/allelematrix/{searchResultsDbId} ###### Return Type: -Changed response : **200 OK** -> OK +Deleted response : **202** +Changed response : **200** * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - * Changed property `result` (object) - > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit - - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `attributeValueDbIds` (array) - - * Added property `methodDbId` (string) - - * Added property `methodName` (string) - * Added property `methodPUI` (string) + New properties: `data` - * Added property `ontologyReferenceDbId` (string) + Deleted properties: `callSetDbIds`, `dataMatrices`, `expandHomozygotes`, `pagination`, `sepPhased`, `sepUnphased`, `unknownString`, `variantDbIds`, `variantSetDbIds` - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) + New required properties: + - `data` - * Added property `traitDbId` (string) + Removed required properties: + - `callSetDbIds` + - `variantSetDbIds` - * Added property `traitName` (string) +##### `POST` /search/attributes - * Added property `traitPUI` (string) - * Deleted property `attributeDbId` (string) - > The ID which uniquely identifies this attribute within the given database server +###### Request: +* Changed content type : `application/json` - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + * Changed property `attributeCategories` (array): + - Nullable changed: `true` -> `null` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `attributeDbIds` (array): + - Nullable changed: `true` -> `null` + * Changed property `attributeNames` (array): + - Nullable changed: `true` -> `null` - * Deleted property `method` (object) + * Changed property `attributePUIs` (array): + - Nullable changed: `true` -> `null` - * Deleted property `ontologyReference` (object) + * Changed property `studyDbId` (array): + - Deprecated status changed - * Deleted property `scale` (object) +##### `GET` /search/attributes/{searchResultsDbId} - * Deleted property `synonyms` (array) - > Other variable names +###### Return Type: - * Deleted property `trait` (object) +Deleted response : **202** - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +Deleted response : **404** +##### `POST` /search/attributevalues - * Added property `additionalProperties` (string) - * Changed property `attributeCategory` (string) +###### Request: - * Changed property `attributeDescription` (string) +* Changed content type : `application/json` - * Changed property `attributeName` (string) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `attributePUI` (string) + * Changed property `attributeDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `commonCropName` (string) + * Changed property `attributeNames` (array): + - Nullable changed: `true` -> `null` - * Changed property `defaultValue` (string) + * Changed property `attributeValueDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `documentationURL` (string -> string) + * Changed property `dataTypes` (array): + - Nullable changed: `true` -> `null` - * Changed property `growthStage` (string) + * Changed property `methodDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `institution` (string) + * Changed property `ontologyDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `language` (string) + * Changed property `scaleDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `scientist` (string) + * Changed property `traitClasses` (array): + - Nullable changed: `true` -> `null` - * Changed property `status` (string) + * Changed property `traitDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `submissionTimestamp` (string -> string) +##### `GET` /search/attributevalues/{searchResultsDbId} -##### `PUT` /attributes/{attributeDbId} -> Update the details for an existing GermplasmAttribute +###### Return Type: +Deleted response : **202** -###### Parameters: +Deleted response : **404** -Deleted: `attributeDbId` in `path` -> The unique id for an attribute +##### `POST` /search/germplasm ###### Request: -Changed content type : `application/json` - -New required properties: -- `attributeDbId` -- `methodDbId` -- `methodName` -- `scaleDbId` -- `scaleName` -- `traitName` +* Changed content type : `application/json` -New optional properties: -- `method` -- `scale` -- `trait` + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` -* Added property `attributeDbId` (string) + * Changed property `accessionNumbers` (array): + - Nullable changed: `true` -> `null` -* Added property `attributeValueDbIds` (array) + * Changed property `binomialNames` (array): + - Nullable changed: `true` -> `null` -* Added property `methodDbId` (string) + * Changed property `collections` (array): + - Nullable changed: `true` -> `null` -* Added property `methodName` (string) + * Changed property `familyCodes` (array): + - Nullable changed: `true` -> `null` -* Added property `methodPUI` (string) + * Changed property `genus` (array): + - Nullable changed: `true` -> `null` -* Added property `ontologyReferenceDbId` (string) + * Changed property `germplasmPUIs` (array): + - Nullable changed: `true` -> `null` -* Added property `scaleDbId` (string) + * Changed property `instituteCodes` (array): + - Nullable changed: `true` -> `null` -* Added property `scaleName` (string) + * Changed property `parentDbIds` (array): + - Nullable changed: `true` -> `null` -* Added property `scalePUI` (string) + * Changed property `progenyDbIds` (array): + - Nullable changed: `true` -> `null` -* Added property `traitDbId` (string) + * Changed property `species` (array): + - Nullable changed: `true` -> `null` -* Added property `traitName` (string) + * Changed property `synonyms` (array): + - Nullable changed: `true` -> `null` -* Added property `traitPUI` (string) +##### `GET` /search/germplasm/{searchResultsDbId} -* Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) +###### Return Type: -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. +Deleted response : **202** +Deleted response : **404** -* Deleted property `method` (object) +##### `GET` /search/images/{searchResultsDbId} -* Deleted property `ontologyReference` (object) -* Deleted property `scale` (object) +###### Return Type: -* Deleted property `synonyms` (array) - > Other variable names +Deleted response : **202** +Deleted response : **404** -* Deleted property `trait` (object) +##### `POST` /search/lists -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +###### Request: - * Added property `additionalProperties` (string) +* Changed content type : `application/json` -* Changed property `attributeCategory` (string) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` -* Changed property `attributeDescription` (string) + * Changed property `dateCreatedRangeEnd` (string): + - Nullable changed: `true` -> `null` -* Changed property `attributeName` (string) + * Changed property `dateCreatedRangeStart` (string): + - Nullable changed: `true` -> `null` -* Changed property `attributePUI` (string) + * Changed property `dateModifiedRangeEnd` (string): + - Nullable changed: `true` -> `null` -* Changed property `commonCropName` (string) + * Changed property `dateModifiedRangeStart` (string): + - Nullable changed: `true` -> `null` -* Changed property `defaultValue` (string) + * Changed property `listDbIds` (array): + - Nullable changed: `true` -> `null` -* Changed property `documentationURL` (string -> string) + * Changed property `listNames` (array): + - Nullable changed: `true` -> `null` -* Changed property `growthStage` (string) + * Changed property `listOwnerNames` (array): + - Nullable changed: `true` -> `null` -* Changed property `institution` (string) + * Changed property `listOwnerPersonDbIds` (array): + - Nullable changed: `true` -> `null` -* Changed property `language` (string) + * Changed property `listSources` (array): + - Nullable changed: `true` -> `null` -* Changed property `scientist` (string) + * Changed property `listType` (string): + - Nullable changed: `true` -> `null` -* Changed property `status` (string) +##### `GET` /search/lists/{searchResultsDbId} -* Changed property `submissionTimestamp` (string -> string) ###### Return Type: -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit - - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `attributeValueDbIds` (array) - - * Added property `methodDbId` (string) +Deleted response : **202** - * Added property `methodName` (string) - - * Added property `methodPUI` (string) +##### `GET` /search/locations/{searchResultsDbId} - * Added property `ontologyReferenceDbId` (string) - * Added property `scaleDbId` (string) +###### Return Type: - * Added property `scaleName` (string) +Deleted response : **202** - * Added property `scalePUI` (string) +##### `POST` /search/markerpositions - * Added property `traitDbId` (string) - * Added property `traitName` (string) +###### Request: - * Added property `traitPUI` (string) +* Changed content type : `application/json` - * Deleted property `attributeDbId` (string) - > The ID which uniquely identifies this attribute within the given database server + Deleted properties: `page`, `pageSize` + * Changed property `linkageGroupNames` (array): + - Nullable changed: `true` -> `null` - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) + * Changed property `mapDbIds` (array): + - Nullable changed: `true` -> `null` + * Changed property `variantDbIds` (array): + - Nullable changed: `true` -> `null` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. +###### Return Type: +Changed response : **200** - * Deleted property `method` (object) +* Changed content type : `application/json` - * Deleted property `ontologyReference` (object) + * Changed property `result` (object) - * Deleted property `scale` (object) + * Changed property `data` (array) - * Deleted property `synonyms` (array) - > Other variable names + Changed items (array): + New properties: `mapPUI` - * Deleted property `trait` (object) + Deleted properties: `variantName` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `mapDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `mapName` (string): + - Nullable changed: `true` -> `null` - * Added property `additionalProperties` (string) + * Changed property `variantDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `attributeCategory` (string) +##### `GET` /search/markerpositions/{searchResultsDbId} - * Changed property `attributeDescription` (string) - * Changed property `attributeName` (string) +###### Return Type: - * Changed property `attributePUI` (string) +Deleted response : **202** - * Changed property `commonCropName` (string) +Changed response : **200** - * Changed property `defaultValue` (string) +* Changed content type : `application/json` - * Changed property `documentationURL` (string -> string) + * Changed property `result` (object) - * Changed property `growthStage` (string) + * Changed property `data` (array) - * Changed property `institution` (string) + Changed items (array): - * Changed property `language` (string) + New properties: `mapPUI` - * Changed property `scientist` (string) + Deleted properties: `variantName` - * Changed property `status` (string) + * Changed property `mapDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `submissionTimestamp` (string -> string) + * Changed property `mapName` (string): + - Nullable changed: `true` -> `null` -##### `GET` /attributevalues + * Changed property `variantDbId` (string): + - Nullable changed: `true` -> `null` -> Get a filtered list of GermplasmAttributeValue +##### `GET` /search/observations/{searchResultsDbId} ###### Parameters: -Added: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `ontologyDbId` in `query` -> List of ontology IDs to search for - +Deleted: `Accept` in `header` -Added: `methodDbId` in `query` -> List of methods to filter search results +###### Return Type: +Deleted response : **202** -Added: `scaleDbId` in `query` -> List of scales to filter search results +##### `GET` /search/observationunits/{searchResultsDbId} -Added: `traitDbId` in `query` -> List of trait unique ID to filter search results +###### Return Type: +Deleted response : **202** -Added: `traitClass` in `query` -> List of trait classes to filter search results +Deleted response : **404** +##### `POST` /search/people -Added: `dataType` in `query` -> List of scale data types to filter search results +###### Request: -Changed: `attributeValueDbId` in `query` -> List of Germplasm Attribute Value IDs to search for +* Changed content type : `application/json` + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` -Changed: `attributeDbId` in `query` -> List of Germplasm Attribute IDs to search for + * Changed property `emailAddresses` (array): + - Nullable changed: `true` -> `null` + * Changed property `firstNames` (array): + - Nullable changed: `true` -> `null` -Changed: `attributeName` in `query` -> List of human readable Germplasm Attribute names to search for + * Changed property `lastNames` (array): + - Nullable changed: `true` -> `null` + * Changed property `mailingAddresses` (array): + - Nullable changed: `true` -> `null` -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. + * Changed property `middleNames` (array): + - Nullable changed: `true` -> `null` + * Changed property `personDbIds` (array): + - Nullable changed: `true` -> `null` -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. + * Changed property `phoneNumbers` (array): + - Nullable changed: `true` -> `null` + * Changed property `userIDs` (array): + - Nullable changed: `true` -> `null` -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for +##### `GET` /search/people/{searchResultsDbId} ###### Return Type: -Changed response : **200 OK** -> OK +Deleted response : **202** - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. - - - * Added property `attributePUI` (string) - - * Added property `germplasmPUI` (string) - - * Deleted property `attributeValueDbId` (string) - > The ID which uniquely identifies this attribute value within the given database server - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attributeDbId` (string) - - * Changed property `attributeName` (string) - - * Changed property `determinedDate` (string -> string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `value` (string) - -##### `POST` /attributevalues - -> Create new GermplasmAttributeValue - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. - - - * Added property `attributePUI` (string) - - * Added property `germplasmPUI` (string) - - * Deleted property `attributeValueDbId` (string) - > The ID which uniquely identifies this attribute value within the given database server - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attributeDbId` (string) - - * Changed property `attributeName` (string) - - * Changed property `determinedDate` (string -> string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `value` (string) - -##### `GET` /attributevalues/{attributeValueDbId} - -> Get the details of a specific GermplasmAttributeValue - - -###### Parameters: - -Deleted: `attributeValueDbId` in `path` -> The unique id for an attribute value - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. - - - * Added property `attributePUI` (string) - - * Added property `germplasmPUI` (string) - - * Deleted property `attributeValueDbId` (string) - > The ID which uniquely identifies this attribute value within the given database server - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attributeDbId` (string) - - * Changed property `attributeName` (string) - - * Changed property `determinedDate` (string -> string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `value` (string) - -##### `PUT` /attributevalues/{attributeValueDbId} - -> Update the details for an existing GermplasmAttributeValue - - -###### Parameters: - -Deleted: `attributeValueDbId` in `path` -> The unique id for an attribute value - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `attributeValueDbId` - -* Added property `attributePUI` (string) - -* Added property `attributeValueDbId` (string) - -* Added property `germplasmPUI` (string) - -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - -* Changed property `attributeDbId` (string) - -* Changed property `attributeName` (string) - -* Changed property `determinedDate` (string -> string) - -* Changed property `germplasmDbId` (string) - -* Changed property `germplasmName` (string) - -* Changed property `value` (string) - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. - - - * Added property `attributePUI` (string) - - * Added property `germplasmPUI` (string) - - * Deleted property `attributeValueDbId` (string) - > The ID which uniquely identifies this attribute value within the given database server - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attributeDbId` (string) - - * Changed property `attributeName` (string) - - * Changed property `determinedDate` (string -> string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `value` (string) - -##### `GET` /breedingmethods - -> Get a filtered list of BreedingMethod - - -###### Parameters: - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The techniques and protocol used to produce a Cross or Germplasm - - - New required properties: - - `abbreviation` - - `breedingMethodName` - - `description` - - * Changed property `abbreviation` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `description` (string) - -##### `GET` /breedingmethods/{breedingMethodDbId} - -> Get the details of a specific BreedingMethod - - -###### Parameters: - -Deleted: `breedingMethodDbId` in `path` -> Internal database identifier for a breeding method - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > The techniques and protocol used to produce a Cross or Germplasm - - - New required properties: - - `abbreviation` - - `breedingMethodName` - - `description` - - * Changed property `abbreviation` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `description` (string) - -##### `GET` /calls - -> Get a filtered list of Call - - -###### Parameters: - -Added: `expandHomozygote` in `query` -> Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - -Deleted: `expandHomozygotes` in `query` -> Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - -Deleted: `pageToken` in `query` -> **Deprecated in v2.1** Please use `page`. Github issue number #451 ->
Used to request a specific page of data to be returned. ->
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. - - -Changed: `callSetDbId` in `query` -> A list of IDs which uniquely identify `CallSets` within the given database server - - -Changed: `variantDbId` in `query` -> A list of IDs which uniquely identify `Variant` within the given database server - - -Changed: `variantSetDbId` in `query` -> A list of IDs which uniquely identify `VariantSets` within the given database server - - -Changed: `unknownString` in `query` -> The string used as a representation for missing data. - - -Changed: `sepPhased` in `query` -> The string used as a separator for phased allele calls. - - -Changed: `sepUnphased` in `query` -> The string used as a separator for unphased allele calls. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Deleted property `expandHomozygotes` (boolean) - > Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - - * Deleted property `sepPhased` (string) - > The string used as a separator for phased allele calls. - - - * Deleted property `sepUnphased` (string) - > The string used as a separator for unphased allele calls. - - - * Deleted property `unknownString` (string) - > The string used as a representation for missing data. - - - * Changed property `data` (array) - - Changed items (object): - > A `Call` represents the determination of genotype with respect to a particular `Variant`. - > - > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. - - - * Deleted property `genotype` (object) - - * Deleted property `genotypeMetadata` (array) - > Genotype Metadata are additional layers of metadata associated with each genotype. - - - * Deleted property `genotype_likelihood` (array) - > **Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491 - >
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec. - - - * Deleted property `variantName` (string) - > The name of the variant this call belongs to. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `genotypeValue` (string) - - * Changed property `phaseSet` (string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (string) - - * Changed property `variantSetName` (string) - -##### `GET` /callsets - -> Get a filtered list of CallSet - - -###### Parameters: - -Added: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Added: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Added: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyDbId` in `query` -> List of study identifiers to search for - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `sampleName` in `query` -> A list of human readable names associated with `Samples` - - -Added: `externalReferenceID` in `query` -> **Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 ->
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter) - - -Changed: `callSetDbId` in `query` -> A list of IDs which uniquely identify `CallSets` within the given database server - - -Changed: `callSetName` in `query` -> A list of human readable names associated with `CallSets` - - -Changed: `variantSetDbId` in `query` -> A list of IDs which uniquely identify `VariantSets` within the given database server - - -Changed: `sampleDbId` in `query` -> A list of IDs which uniquely identify `Samples` within the given database server - - -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A CallSet is a collection of Calls that were generated by the same analysis of the same Sample - - - * Added property `sampleName` (string) - - * Added property `samplePUI` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Deleted property `externalReferences` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `created` (string -> string) - - * Changed property `sampleDbId` (string) - - * Changed property `studyDbId` (string) - - * Changed property `updated` (string -> string) - - * Changed property `variantSetDbIds` (array) - -##### `GET` /callsets/{callSetDbId} - -> Get the details of a specific CallSet - - -###### Parameters: - -Deleted: `callSetDbId` in `path` -> The ID which uniquely identifies a `CallSet` within the given database server - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A CallSet is a collection of Calls that were generated by the same analysis of the same Sample - - - * Added property `sampleName` (string) - - * Added property `samplePUI` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Deleted property `externalReferences` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `created` (string -> string) - - * Changed property `sampleDbId` (string) - - * Changed property `studyDbId` (string) - - * Changed property `updated` (string -> string) - - * Changed property `variantSetDbIds` (array) - -##### `GET` /callsets/{callSetDbId}/calls - -> Get a filtered list of Call - - -###### Parameters: - -Added: `callSetDbId` in `query` -> A list of IDs which uniquely identify `CallSets` within the given database server - - -Added: `variantDbId` in `query` -> A list of IDs which uniquely identify `Variant` within the given database server - - -Added: `variantSetDbId` in `query` -> A list of IDs which uniquely identify `VariantSets` within the given database server - - -Added: `expandHomozygote` in `query` -> Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - -Deleted: `callSetDbId` in `path` -> The ID which uniquely identifies a `CallSet` within the given database server - - -Deleted: `expandHomozygotes` in `query` -> Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - -Deleted: `pageToken` in `query` -> **Deprecated in v2.1** Please use `page`. Github issue number #451 ->
Used to request a specific page of data to be returned. ->
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. - - -Changed: `unknownString` in `query` -> The string used as a representation for missing data. - - -Changed: `sepPhased` in `query` -> The string used as a separator for phased allele calls. - - -Changed: `sepUnphased` in `query` -> The string used as a separator for unphased allele calls. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Deleted property `expandHomozygotes` (boolean) - > Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - - * Deleted property `sepPhased` (string) - > The string used as a separator for phased allele calls. - - - * Deleted property `sepUnphased` (string) - > The string used as a separator for unphased allele calls. - - - * Deleted property `unknownString` (string) - > The string used as a representation for missing data. - - - * Changed property `data` (array) - - Changed items (object): - > A `Call` represents the determination of genotype with respect to a particular `Variant`. - > - > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. - - - * Deleted property `genotype` (object) - - * Deleted property `genotypeMetadata` (array) - > Genotype Metadata are additional layers of metadata associated with each genotype. - - - * Deleted property `genotype_likelihood` (array) - > **Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491 - >
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec. - - - * Deleted property `variantName` (string) - > The name of the variant this call belongs to. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `genotypeValue` (string) - - * Changed property `phaseSet` (string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (string) - - * Changed property `variantSetName` (string) - -##### `GET` /crossingprojects - -> Get a filtered list of CrossingProject - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `includePotentialParent` in `query` -> If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object. - - -Deleted: `includePotentialParents` in `query` -> If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object. - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented. - - - * Deleted property `crossingProjectDbId` (string) - > The unique identifier for a crossing project - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `potentialParents` (array) - > A list of all the potential parents in the crossing block, available in the crossing project - >
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `crossingProjectDescription` (string) - - * Changed property `crossingProjectName` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - -##### `POST` /crossingprojects - -> Create new CrossingProject - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented. - - - * Deleted property `crossingProjectDbId` (string) - > The unique identifier for a crossing project - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `potentialParents` (array) - > A list of all the potential parents in the crossing block, available in the crossing project - >
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `crossingProjectDescription` (string) - - * Changed property `crossingProjectName` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - -##### `GET` /crossingprojects/{crossingProjectDbId} - -> Get the details of a specific CrossingProject - - -###### Parameters: - -Deleted: `crossingProjectDbId` in `path` -> The unique identifier for a crossing project - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented. - - - * Deleted property `crossingProjectDbId` (string) - > The unique identifier for a crossing project - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `potentialParents` (array) - > A list of all the potential parents in the crossing block, available in the crossing project - >
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `crossingProjectDescription` (string) - - * Changed property `crossingProjectName` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - -##### `PUT` /crossingprojects/{crossingProjectDbId} - -> Update the details for an existing CrossingProject - - -###### Parameters: - -Deleted: `crossingProjectDbId` in `path` -> Search for Crossing Projects with this unique id - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `crossingProjectDbId` -- `crossingProjectDbId` - -* Added property `crossingProjectDbId` (string) - -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - -* Deleted property `potentialParents` (array) - > A list of all the potential parents in the crossing block, available in the crossing project - >
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object. - - -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - -* Changed property `commonCropName` (string) - -* Changed property `crossingProjectDescription` (string) - -* Changed property `crossingProjectName` (string) - -* Changed property `programDbId` (string) - -* Changed property `programName` (string) - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented. - - - * Deleted property `crossingProjectDbId` (string) - > The unique identifier for a crossing project - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `potentialParents` (array) - > A list of all the potential parents in the crossing block, available in the crossing project - >
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `crossingProjectDescription` (string) - - * Changed property `crossingProjectName` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - -##### `GET` /events - -> Get a filtered list of Event - - -###### Parameters: - -Added: `studyName` in `query` -> List of study names to filter search results - - -Changed: `observationUnitDbId` in `query` -> The ID which uniquely identifies an observation unit. - - -Changed: `eventDbId` in `query` -> Filter based on an Event DbId. - - -Changed: `dateRangeStart` in `query` -> Filter based on an Event start date. - - -Changed: `dateRangeEnd` in `query` -> Filter based on an Event start date. - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. - >
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other - - - * Added property `studyPUI` (string) - - * Deleted property `date` (array) - > **Deprecated in v2.1** Please use `eventDateRange.discreteDates`. Github issue number #440 - >
A list of dates when the event occurred - >
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. - - - * Deleted property `eventDateRange` (object) - - * Deleted property `eventParameters` (array) - > A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `eventDbId` (string) - - * Changed property `eventDescription` (string) - - * Changed property `eventType` (string) - - * Changed property `eventTypeDbId` (string) - - * Changed property `observationUnitDbIds` (array) - - * Changed property `studyDbId` (string) - - * Changed property `studyName` (string) - -##### `GET` /germplasm - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `familyCode` in `query` -> A familyCode representing the family this germplasm belongs to. - - -Added: `instituteCode` in `query` -> The code for the institute that maintains the material. ->
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with "obsolete" codes, see "Common formatting rules (v)". - - -Added: `genu` in `query` -> List of Genus names to identify germplasm - - -Added: `specy` in `query` -> List of Species names to identify germplasm - - -Deleted: `genus` in `query` -> Genus name to identify germplasm - - -Deleted: `species` in `query` -> Species name to identify germplasm - - -Changed: `accessionNumber` in `query` -> A collection of unique identifiers for materials or germplasm within a genebank -> -> MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). - - -Changed: `binomialName` in `query` -> List of the full binomial name (scientific name) to identify a germplasm - - -Changed: `synonym` in `query` -> List of alternative names or IDs used to reference this germplasm - - -Changed: `parentDbId` in `query` -> Search for Germplasm with these parents - - -Changed: `progenyDbId` in `query` -> Search for Germplasm with these children - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -Changed: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Changed: `germplasmPUI` in `query` -> List of Permanent Unique Identifiers to identify germplasm - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `sampleDbIds` (array) - - * Deleted property `donors` (array) - > List of donor institutes - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `germplasmDbId` (string) - > The ID which uniquely identifies a germplasm within the given database server - >
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. - - - * Deleted property `germplasmOrigin` (array) - > Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm. - - - * Deleted property `storageTypes` (array) - > The type of storage this germplasm is kept in at a genebank. - - - * Deleted property `synonyms` (array) - > List of alternative names or IDs used to reference this germplasm - > - > MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. - - - * Deleted property `taxonIds` (array) - > The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. - > - > MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. - - - * Changed property `accessionNumber` (string) - - * Changed property `acquisitionDate` (string -> string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `biologicalStatusOfAccessionCode` (string) - > MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. - > - > 100) Wild - > 110) Natural - > 120) Semi-natural/wild - > 130) Semi-natural/sown - > 200) Weedy - > 300) Traditional cultivar/landrace - > 400) Breeding/research material - > 410) Breeders line - > 411) Synthetic population - > 412) Hybrid - > 413) Founder stock/base population - > 414) Inbred line (parent of hybrid cultivar) - > 415) Segregating population - > 416) Clonal selection - > 420) Genetic stock - > 421) Mutant (e.g. induced/insertion mutants, tilling populations) - > 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) - > 423) Other genetic stocks (e.g. mapping populations) - > 500) Advanced or improved cultivar (conventional breeding methods) - > 600) GMO (by genetic engineering) - > 999) Other (Elaborate in REMARKS field) - - - * Changed property `biologicalStatusOfAccessionDescription` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `collection` (string) - - * Changed property `commonCropName` (string) - - * Changed property `countryOfOriginCode` (string) - - * Changed property `defaultDisplayName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `genus` (string) - - * Changed property `germplasmName` (string) - - * Changed property `germplasmPUI` (string) - - * Changed property `germplasmPreprocessing` (string) - - * Changed property `instituteCode` (string) - - * Changed property `instituteName` (string) - - * Changed property `pedigree` (string) - - * Changed property `seedSource` (string) - - * Changed property `seedSourceDescription` (string) - - * Changed property `species` (string) - - * Changed property `speciesAuthority` (string) - - * Changed property `subtaxa` (string) - - * Changed property `subtaxaAuthority` (string) - -##### `POST` /germplasm - -> Create new Germplasm - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `sampleDbIds` (array) - - * Deleted property `donors` (array) - > List of donor institutes - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `germplasmDbId` (string) - > The ID which uniquely identifies a germplasm within the given database server - >
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. - - - * Deleted property `germplasmOrigin` (array) - > Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm. - - - * Deleted property `storageTypes` (array) - > The type of storage this germplasm is kept in at a genebank. - - - * Deleted property `synonyms` (array) - > List of alternative names or IDs used to reference this germplasm - > - > MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. - - - * Deleted property `taxonIds` (array) - > The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. - > - > MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. - - - * Changed property `accessionNumber` (string) - - * Changed property `acquisitionDate` (string -> string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `biologicalStatusOfAccessionCode` (string) - > MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. - > - > 100) Wild - > 110) Natural - > 120) Semi-natural/wild - > 130) Semi-natural/sown - > 200) Weedy - > 300) Traditional cultivar/landrace - > 400) Breeding/research material - > 410) Breeders line - > 411) Synthetic population - > 412) Hybrid - > 413) Founder stock/base population - > 414) Inbred line (parent of hybrid cultivar) - > 415) Segregating population - > 416) Clonal selection - > 420) Genetic stock - > 421) Mutant (e.g. induced/insertion mutants, tilling populations) - > 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) - > 423) Other genetic stocks (e.g. mapping populations) - > 500) Advanced or improved cultivar (conventional breeding methods) - > 600) GMO (by genetic engineering) - > 999) Other (Elaborate in REMARKS field) - - - * Changed property `biologicalStatusOfAccessionDescription` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `collection` (string) - - * Changed property `commonCropName` (string) - - * Changed property `countryOfOriginCode` (string) - - * Changed property `defaultDisplayName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `genus` (string) - - * Changed property `germplasmName` (string) - - * Changed property `germplasmPUI` (string) - - * Changed property `germplasmPreprocessing` (string) - - * Changed property `instituteCode` (string) - - * Changed property `instituteName` (string) - - * Changed property `pedigree` (string) - - * Changed property `seedSource` (string) - - * Changed property `seedSourceDescription` (string) - - * Changed property `species` (string) - - * Changed property `speciesAuthority` (string) - - * Changed property `subtaxa` (string) - - * Changed property `subtaxaAuthority` (string) - -##### `GET` /germplasm/{germplasmDbId} - - -###### Parameters: - -Deleted: `germplasmDbId` in `path` -> The internal id of the germplasm - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `sampleDbIds` (array) - - * Deleted property `donors` (array) - > List of donor institutes - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `germplasmDbId` (string) - > The ID which uniquely identifies a germplasm within the given database server - >
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. - - - * Deleted property `germplasmOrigin` (array) - > Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm. - - - * Deleted property `storageTypes` (array) - > The type of storage this germplasm is kept in at a genebank. - - - * Deleted property `synonyms` (array) - > List of alternative names or IDs used to reference this germplasm - > - > MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. - - - * Deleted property `taxonIds` (array) - > The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. - > - > MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. - - - * Changed property `accessionNumber` (string) - - * Changed property `acquisitionDate` (string -> string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `biologicalStatusOfAccessionCode` (string) - > MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. - > - > 100) Wild - > 110) Natural - > 120) Semi-natural/wild - > 130) Semi-natural/sown - > 200) Weedy - > 300) Traditional cultivar/landrace - > 400) Breeding/research material - > 410) Breeders line - > 411) Synthetic population - > 412) Hybrid - > 413) Founder stock/base population - > 414) Inbred line (parent of hybrid cultivar) - > 415) Segregating population - > 416) Clonal selection - > 420) Genetic stock - > 421) Mutant (e.g. induced/insertion mutants, tilling populations) - > 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) - > 423) Other genetic stocks (e.g. mapping populations) - > 500) Advanced or improved cultivar (conventional breeding methods) - > 600) GMO (by genetic engineering) - > 999) Other (Elaborate in REMARKS field) - - - * Changed property `biologicalStatusOfAccessionDescription` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `collection` (string) - - * Changed property `commonCropName` (string) - - * Changed property `countryOfOriginCode` (string) - - * Changed property `defaultDisplayName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `genus` (string) - - * Changed property `germplasmName` (string) - - * Changed property `germplasmPUI` (string) - - * Changed property `germplasmPreprocessing` (string) - - * Changed property `instituteCode` (string) - - * Changed property `instituteName` (string) - - * Changed property `pedigree` (string) - - * Changed property `seedSource` (string) - - * Changed property `seedSourceDescription` (string) - - * Changed property `species` (string) - - * Changed property `speciesAuthority` (string) - - * Changed property `subtaxa` (string) - - * Changed property `subtaxaAuthority` (string) - -##### `PUT` /germplasm/{germplasmDbId} - -> Update the details for an existing Germplasm - - -###### Parameters: - -Deleted: `germplasmDbId` in `path` -> The internal id of the germplasm - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `germplasmDbId` -- `germplasmDbId` - -* Added property `germplasmDbId` (string) - -* Added property `sampleDbIds` (array) - -* Deleted property `donors` (array) - > List of donor institutes - - -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - -* Deleted property `germplasmOrigin` (array) - > Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm. - - -* Deleted property `storageTypes` (array) - > The type of storage this germplasm is kept in at a genebank. - - -* Deleted property `synonyms` (array) - > List of alternative names or IDs used to reference this germplasm - > - > MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. - - -* Deleted property `taxonIds` (array) - > The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. - > - > MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. - - -* Changed property `accessionNumber` (string) - -* Changed property `acquisitionDate` (string -> string) - -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - -* Changed property `biologicalStatusOfAccessionCode` (string) - > MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. - > - > 100) Wild - > 110) Natural - > 120) Semi-natural/wild - > 130) Semi-natural/sown - > 200) Weedy - > 300) Traditional cultivar/landrace - > 400) Breeding/research material - > 410) Breeders line - > 411) Synthetic population - > 412) Hybrid - > 413) Founder stock/base population - > 414) Inbred line (parent of hybrid cultivar) - > 415) Segregating population - > 416) Clonal selection - > 420) Genetic stock - > 421) Mutant (e.g. induced/insertion mutants, tilling populations) - > 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) - > 423) Other genetic stocks (e.g. mapping populations) - > 500) Advanced or improved cultivar (conventional breeding methods) - > 600) GMO (by genetic engineering) - > 999) Other (Elaborate in REMARKS field) - - -* Changed property `biologicalStatusOfAccessionDescription` (string) - -* Changed property `breedingMethodDbId` (string) - -* Changed property `breedingMethodName` (string) - -* Changed property `collection` (string) - -* Changed property `commonCropName` (string) - -* Changed property `countryOfOriginCode` (string) - -* Changed property `defaultDisplayName` (string) - -* Changed property `documentationURL` (string -> string) - -* Changed property `genus` (string) - -* Changed property `germplasmName` (string) - -* Changed property `germplasmPUI` (string) - -* Changed property `germplasmPreprocessing` (string) - -* Changed property `instituteCode` (string) - -* Changed property `instituteName` (string) - -* Changed property `pedigree` (string) - -* Changed property `seedSource` (string) - -* Changed property `seedSourceDescription` (string) - -* Changed property `species` (string) - -* Changed property `speciesAuthority` (string) - -* Changed property `subtaxa` (string) - -* Changed property `subtaxaAuthority` (string) - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `sampleDbIds` (array) - - * Deleted property `donors` (array) - > List of donor institutes - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `germplasmDbId` (string) - > The ID which uniquely identifies a germplasm within the given database server - >
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. - - - * Deleted property `germplasmOrigin` (array) - > Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm. - - - * Deleted property `storageTypes` (array) - > The type of storage this germplasm is kept in at a genebank. - - - * Deleted property `synonyms` (array) - > List of alternative names or IDs used to reference this germplasm - > - > MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. - - - * Deleted property `taxonIds` (array) - > The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. - > - > MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. - - - * Changed property `accessionNumber` (string) - - * Changed property `acquisitionDate` (string -> string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `biologicalStatusOfAccessionCode` (string) - > MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. - > - > 100) Wild - > 110) Natural - > 120) Semi-natural/wild - > 130) Semi-natural/sown - > 200) Weedy - > 300) Traditional cultivar/landrace - > 400) Breeding/research material - > 410) Breeders line - > 411) Synthetic population - > 412) Hybrid - > 413) Founder stock/base population - > 414) Inbred line (parent of hybrid cultivar) - > 415) Segregating population - > 416) Clonal selection - > 420) Genetic stock - > 421) Mutant (e.g. induced/insertion mutants, tilling populations) - > 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) - > 423) Other genetic stocks (e.g. mapping populations) - > 500) Advanced or improved cultivar (conventional breeding methods) - > 600) GMO (by genetic engineering) - > 999) Other (Elaborate in REMARKS field) - - - * Changed property `biologicalStatusOfAccessionDescription` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `collection` (string) - - * Changed property `commonCropName` (string) - - * Changed property `countryOfOriginCode` (string) - - * Changed property `defaultDisplayName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `genus` (string) - - * Changed property `germplasmName` (string) - - * Changed property `germplasmPUI` (string) - - * Changed property `germplasmPreprocessing` (string) - - * Changed property `instituteCode` (string) - - * Changed property `instituteName` (string) - - * Changed property `pedigree` (string) - - * Changed property `seedSource` (string) - - * Changed property `seedSourceDescription` (string) - - * Changed property `species` (string) - - * Changed property `speciesAuthority` (string) - - * Changed property `subtaxa` (string) - - * Changed property `subtaxaAuthority` (string) - -##### `GET` /lists - -> Get a filtered list of List - - -###### Parameters: - -Added: `dateCreatedRangeStart` in `query` -> Define the beginning for an interval of time and only include Lists that are created within this interval. - - -Added: `dateCreatedRangeEnd` in `query` -> Define the end for an interval of time and only include Lists that are created within this interval. - - -Added: `dateModifiedRangeStart` in `query` -> Define the beginning for an interval of time and only include Lists that are modified within this interval. - - -Added: `dateModifiedRangeEnd` in `query` -> Define the end for an interval of time and only include Lists that are modified within this interval. - - -Added: `listOwnerName` in `query` -> An array of names for the people or entities who are responsible for a set of Lists - - -Added: `listOwnerPersonDbId` in `query` -> An array of primary database identifiers to identify people or entities who are responsible for a set of Lists - - -Deleted: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crop. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Deleted: `programDbId` in `query` -> Use this parameter to only return results associated with the given `Program` unique identifier. ->
Use `GET /programs` to find the list of available `Programs` on a server. - - -Changed: `listName` in `query` -> An array of human readable names to identify a set of Lists - - -Changed: `listDbId` in `query` -> An array of primary database identifiers to identify a set of Lists - - -Changed: `listSource` in `query` -> An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc) - - -Changed: `listType` in `query` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. - - - * Added property `personDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `listDbId` (string) - > The unique identifier for a List - - - * Deleted property `listOwnerPersonDbId` (string) - > The unique identifier for a List Owner. (usually a user or person) - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `dateCreated` (string -> string) - - * Changed property `dateModified` (string -> string) - - * Changed property `listDescription` (string) - - * Changed property `listName` (string) - - * Changed property `listOwnerName` (string) - - * Changed property `listSize` (integer -> integer) - - * Changed property `listSource` (string) - - * Changed property `listType` (string) - > The type of objects that are referenced in a List - - -##### `POST` /lists - -> Create new List - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. - - - * Added property `personDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `listDbId` (string) - > The unique identifier for a List - - - * Deleted property `listOwnerPersonDbId` (string) - > The unique identifier for a List Owner. (usually a user or person) - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `dateCreated` (string -> string) - - * Changed property `dateModified` (string -> string) - - * Changed property `listDescription` (string) - - * Changed property `listName` (string) - - * Changed property `listOwnerName` (string) - - * Changed property `listSize` (integer -> integer) - - * Changed property `listSource` (string) - - * Changed property `listType` (string) - > The type of objects that are referenced in a List - - -##### `GET` /lists/{listDbId} - - -###### Parameters: - -Deleted: `listDbId` in `path` -> The unique identifier of a List - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. - - - * Added property `personDbId` (string) - - * Deleted property `data` (array) - > The array of DbIds of the BrAPI objects contained in a List - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `listDbId` (string) - > The unique identifier for a List - - - * Deleted property `listOwnerPersonDbId` (string) - > The unique identifier for a List Owner. (usually a user or person) - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `dateCreated` (string -> string) - - * Changed property `dateModified` (string -> string) - - * Changed property `listDescription` (string) - - * Changed property `listName` (string) - - * Changed property `listOwnerName` (string) - - * Changed property `listSize` (integer -> integer) - - * Changed property `listSource` (string) - - * Changed property `listType` (string) - > The type of objects that are referenced in a List - - -##### `PUT` /lists/{listDbId} - -> Update the details for an existing List - - -###### Parameters: - -Deleted: `listDbId` in `path` -> The unique identifier of a List - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `listDbId` -- `listDbId` - -* Added property `listDbId` (string) - -* Added property `personDbId` (string) - -* Deleted property `data` (array) - > The array of DbIds of the BrAPI objects contained in a List - - -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - -* Deleted property `listOwnerPersonDbId` (string) - > The unique identifier for a List Owner. (usually a user or person) - - -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - -* Changed property `dateCreated` (string -> string) - -* Changed property `dateModified` (string -> string) - -* Changed property `listDescription` (string) - -* Changed property `listName` (string) - -* Changed property `listOwnerName` (string) - -* Changed property `listSize` (integer -> integer) - -* Changed property `listSource` (string) - -* Changed property `listType` (string) - > The type of objects that are referenced in a List - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. - - - * Added property `personDbId` (string) - - * Deleted property `data` (array) - > The array of DbIds of the BrAPI objects contained in a List - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `listDbId` (string) - > The unique identifier for a List - - - * Deleted property `listOwnerPersonDbId` (string) - > The unique identifier for a List Owner. (usually a user or person) - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `dateCreated` (string -> string) - - * Changed property `dateModified` (string -> string) - - * Changed property `listDescription` (string) - - * Changed property `listName` (string) - - * Changed property `listOwnerName` (string) - - * Changed property `listSize` (integer -> integer) - - * Changed property `listSource` (string) - - * Changed property `listType` (string) - > The type of objects that are referenced in a List - - -##### `GET` /maps - -> Get a filtered list of GenomeMap - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map. - - - New optional properties: - - `mapName` - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `comments` (string) - - * Changed property `commonCropName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `linkageGroupCount` (integer -> integer) - - * Changed property `mapDbId` (string) - - * Changed property `mapName` (string) - - * Changed property `mapPUI` (string) - - * Changed property `markerCount` (integer -> integer) - - * Changed property `publishedDate` (string -> string) - - * Changed property `scientificName` (string) - - * Changed property `type` (string) - - * Changed property `unit` (string) - -##### `GET` /maps/{mapDbId} - -> Get the details of a specific GenomeMap - - -###### Parameters: - -Deleted: `mapDbId` in `path` -> The ID which uniquely identifies a `GenomeMap` - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map. - - - New optional properties: - - `mapName` - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `comments` (string) - - * Changed property `commonCropName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `linkageGroupCount` (integer -> integer) - - * Changed property `mapDbId` (string) - - * Changed property `mapName` (string) - - * Changed property `mapPUI` (string) - - * Changed property `markerCount` (integer -> integer) - - * Changed property `publishedDate` (string -> string) - - * Changed property `scientificName` (string) - - * Changed property `type` (string) - - * Changed property `unit` (string) - -##### `GET` /markerpositions - -> Get a filtered list of MarkerPosition - - -###### Parameters: - -Changed: `mapDbId` in `query` -> A list of IDs which uniquely identify `GenomeMaps` within the given database server - - -Changed: `linkageGroupName` in `query` -> A list of Uniquely Identifiable linkage group names - - -Changed: `variantDbId` in `query` -> A list of IDs which uniquely identify `Variants` within the given database server - - -Changed: `minPosition` in `query` -> The minimum position of markers in a given map - - -Changed: `maxPosition` in `query` -> The maximum position of markers in a given map - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap. - - - * Added property `mapPUI` (string) - - * Deleted property `variantName` (string) - > The human readable name for a `Variant` - >
A `Variant` can also represent a Marker - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `linkageGroupName` (string) - - * Changed property `mapDbId` (string) - - * Changed property `mapName` (string) - - * Changed property `position` (integer -> integer) - - * Changed property `variantDbId` (string) - -##### `GET` /methods - -> Get a filtered list of Method - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `scaleDbId` in `query` -> The unique identifier for a method. - - -Deleted: `methodDbId` in `query` -> The unique identifier for a method - - -Changed: `observationVariableDbId` in `query` -> The unique identifier for an observation variable. - - -Changed: `ontologyDbId` in `query` -> The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology -> -> Use `GET /ontologies` to find the list of available ontologies on a server. - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A description of the way an Observation should be collected. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `methodDbId` (string) - > Method unique identifier - - - * Deleted property `ontologyReference` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `bibliographicalReference` (string) - - * Changed property `description` (string) - - * Changed property `formula` (string) - - * Changed property `methodClass` (string) - - * Changed property `methodName` (string) - - * Changed property `methodPUI` (string) - -##### `POST` /methods - -> Create new Method - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A description of the way an Observation should be collected. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `methodDbId` (string) - > Method unique identifier - - - * Deleted property `ontologyReference` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `bibliographicalReference` (string) - - * Changed property `description` (string) - - * Changed property `formula` (string) - - * Changed property `methodClass` (string) - - * Changed property `methodName` (string) - - * Changed property `methodPUI` (string) - -##### `GET` /methods/{methodDbId} - -> Get the details of a specific Method - - -###### Parameters: - -Deleted: `methodDbId` in `path` -> Id of the method to retrieve details of. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A description of the way an Observation should be collected. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `methodDbId` (string) - > Method unique identifier - - - * Deleted property `ontologyReference` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `bibliographicalReference` (string) - - * Changed property `description` (string) - - * Changed property `formula` (string) - - * Changed property `methodClass` (string) - - * Changed property `methodName` (string) - - * Changed property `methodPUI` (string) - -##### `PUT` /methods/{methodDbId} - -> Update the details for an existing Method - - -###### Parameters: - -Deleted: `methodDbId` in `path` -> Id of the method to retrieve details of. - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A description of the way an Observation should be collected. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `methodDbId` (string) - > Method unique identifier - - - * Deleted property `ontologyReference` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `bibliographicalReference` (string) - - * Changed property `description` (string) - - * Changed property `formula` (string) - - * Changed property `methodClass` (string) - - * Changed property `methodName` (string) - - * Changed property `methodPUI` (string) - -##### `GET` /observationunits - -> Get a filtered list of ObservationUnit - - -###### Parameters: - -Added: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Added: `locationName` in `query` -> A human readable names to search for - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `observationVariableDbId` in `query` -> The DbIds of Variables to search for - - -Added: `observationVariableName` in `query` -> The names of Variables to search for - - -Added: `observationVariablePUI` in `query` -> The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `observationLevel` in `query` -> Searches for values in ObservationUnit->observationUnitPosition->observationLevel - - -Added: `observationLevelRelationship` in `query` -> Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships - - -Added: `includeObservation` in `query` -> Use this parameter to include a list of observations embedded in each ObservationUnit object. -> -> CAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to. - - -Deleted: `includeObservations` in `query` -> Use this parameter to include a list of observations embedded in each ObservationUnit object. -> -> CAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to. - - -Deleted: `observationUnitLevelName` in `query` -> The Observation Unit Level. Returns only the observation unit of the specified Level. ->
References ObservationUnit->observationUnitPosition->observationLevel->levelName ->
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ->
For more information on Observation Levels, please review the Observation Levels documentation. - - -Deleted: `observationUnitLevelOrder` in `query` -> The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. -> References ObservationUnit->observationUnitPosition->observationLevel->levelOrder ->
For more information on Observation Levels, please review the Observation Levels documentation. - - -Deleted: `observationUnitLevelCode` in `query` -> The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` -> or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode ->
For more information on Observation Levels, please review the Observation Levels documentation. - - -Deleted: `observationUnitLevelRelationshipName` in `query` -> The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. ->
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. ->
Use this parameter to identify groups of observation units that share a relationship level. ->
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ->
For more information on Observation Levels, please review the Observation Levels documentation. - - -Deleted: `observationUnitLevelRelationshipOrder` in `query` -> The Observation Unit Level Order Number. ->
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder ->
For more information on Observation Levels, please review the Observation Levels documentation. - - -Deleted: `observationUnitLevelRelationshipCode` in `query` -> The Observation Unit Level Code. ->
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode ->
For more information on Observation Levels, please review the Observation Levels documentation. - - -Deleted: `observationUnitLevelRelationshipDbId` in `query` -> The observationUnitDbId associated with a particular level and code. ->
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId ->
For more information on Observation Levels, please review the Observation Levels documentation. - - -Changed: `observationUnitDbId` in `query` -> The unique id of an observation unit - - -Changed: `locationDbId` in `query` -> The location ids to search for - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. - - - * Added property `germplasmPUI` (string) - - * Added property `studyPUI` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `observationUnitDbId` (string) - > The ID which uniquely identifies an observation unit - > - > MIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. - - - * Deleted property `observationUnitPosition` (object) - - * Deleted property `observations` (array) - > All observations attached to this observation unit. - > - > Default for this field is null or omitted. Do NOT include data in this field unless the 'includeObservations' flag is explicitly set to True. - - - * Deleted property `treatments` (array) - > List of treatments applied to an observation unit. - > - > MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossDbId` (string) - - * Changed property `crossName` (string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `observationUnitPUI` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `seedLotDbId` (string) - - * Changed property `seedLotName` (string) - - * Changed property `studyDbId` (string) - - * Changed property `studyName` (string) - - * Changed property `trialDbId` (string) - - * Changed property `trialName` (string) - -##### `PUT` /observationunits - -> Update the details for an existing ObservationUnit - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `observationUnitDbId` -- `observationUnitDbId` - -* Added property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Property `additionalProperties` (string) - -* Added property `crossDbId` (string) - -* Added property `crossName` (string) - -* Added property `germplasmDbId` (string) - -* Added property `germplasmName` (string) - -* Added property `germplasmPUI` (string) - -* Added property `locationDbId` (string) - -* Added property `locationName` (string) - -* Added property `observationUnitDbId` (string) - -* Added property `observationUnitName` (string) - -* Added property `observationUnitPUI` (string) - -* Added property `programDbId` (string) - -* Added property `programName` (string) - -* Added property `seedLotDbId` (string) - -* Added property `seedLotName` (string) - -* Added property `studyDbId` (string) - -* Added property `studyName` (string) - -* Added property `studyPUI` (string) - -* Added property `trialDbId` (string) - -* Added property `trialName` (string) - -* Added property `trialPUI` (string) - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. - - - * Added property `germplasmPUI` (string) - - * Added property `studyPUI` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `observationUnitDbId` (string) - > The ID which uniquely identifies an observation unit - > - > MIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. - - - * Deleted property `observationUnitPosition` (object) - - * Deleted property `observations` (array) - > All observations attached to this observation unit. - > - > Default for this field is null or omitted. Do NOT include data in this field unless the 'includeObservations' flag is explicitly set to True. - - - * Deleted property `treatments` (array) - > List of treatments applied to an observation unit. - > - > MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossDbId` (string) - - * Changed property `crossName` (string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `observationUnitPUI` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `seedLotDbId` (string) - - * Changed property `seedLotName` (string) - - * Changed property `studyDbId` (string) - - * Changed property `studyName` (string) - - * Changed property `trialDbId` (string) - - * Changed property `trialName` (string) - -##### `POST` /observationunits - -> Create new ObservationUnit - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. - - - * Added property `germplasmPUI` (string) - - * Added property `studyPUI` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `observationUnitDbId` (string) - > The ID which uniquely identifies an observation unit - > - > MIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. - - - * Deleted property `observationUnitPosition` (object) - - * Deleted property `observations` (array) - > All observations attached to this observation unit. - > - > Default for this field is null or omitted. Do NOT include data in this field unless the 'includeObservations' flag is explicitly set to True. - - - * Deleted property `treatments` (array) - > List of treatments applied to an observation unit. - > - > MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossDbId` (string) - - * Changed property `crossName` (string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `observationUnitPUI` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `seedLotDbId` (string) - - * Changed property `seedLotName` (string) - - * Changed property `studyDbId` (string) - - * Changed property `studyName` (string) - - * Changed property `trialDbId` (string) - - * Changed property `trialName` (string) - -##### `GET` /observationunits/{observationUnitDbId} - -> Get the details of a specific ObservationUnit - - -###### Parameters: - -Deleted: `observationUnitDbId` in `path` -> The unique ID of the specific Observation Unit - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. - - - * Added property `germplasmPUI` (string) - - * Added property `studyPUI` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `observationUnitDbId` (string) - > The ID which uniquely identifies an observation unit - > - > MIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. - - - * Deleted property `observationUnitPosition` (object) - - * Deleted property `observations` (array) - > All observations attached to this observation unit. - > - > Default for this field is null or omitted. Do NOT include data in this field unless the 'includeObservations' flag is explicitly set to True. - - - * Deleted property `treatments` (array) - > List of treatments applied to an observation unit. - > - > MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossDbId` (string) - - * Changed property `crossName` (string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `observationUnitPUI` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `seedLotDbId` (string) - - * Changed property `seedLotName` (string) - - * Changed property `studyDbId` (string) - - * Changed property `studyName` (string) - - * Changed property `trialDbId` (string) - - * Changed property `trialName` (string) - -##### `GET` /ontologies - -> Get a filtered list of Ontology - - -###### Parameters: - -Changed: `ontologyName` in `query` -> The human readable identifier for an ontology definition. - - -Changed: `ontologyDbId` in `query` -> The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology -> -> Use `GET /ontologies` to find the list of available ontologies on a server. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The identifier and metadata needed to reference an external controlled vocabulary - - - * Deleted property `ontologyDbId` (string) - > Ontology database unique identifier - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `authors` (string) - - * Changed property `copyright` (string) - - * Changed property `description` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `licence` (string) - - * Changed property `ontologyName` (string) - - * Changed property `version` (string) - -##### `POST` /ontologies - -> Create new Ontology - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The identifier and metadata needed to reference an external controlled vocabulary - - - * Deleted property `ontologyDbId` (string) - > Ontology database unique identifier - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `authors` (string) - - * Changed property `copyright` (string) - - * Changed property `description` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `licence` (string) - - * Changed property `ontologyName` (string) - - * Changed property `version` (string) - -##### `GET` /ontologies/{ontologyDbId} - -> Get the details of a specific Ontology - - -###### Parameters: - -Deleted: `ontologyDbId` in `path` -> The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology -> -> Use `GET /ontologies` to find the list of available ontologies on a server. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > The identifier and metadata needed to reference an external controlled vocabulary - - - * Deleted property `ontologyDbId` (string) - > Ontology database unique identifier - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `authors` (string) - - * Changed property `copyright` (string) - - * Changed property `description` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `licence` (string) - - * Changed property `ontologyName` (string) - - * Changed property `version` (string) - -##### `PUT` /ontologies/{ontologyDbId} - -> Update the details for an existing Ontology - - -###### Parameters: - -Deleted: `ontologyDbId` in `path` -> The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology -> -> Use `GET /ontologies` to find the list of available ontologies on a server. - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `ontologyDbId` -- `ontologyDbId` - -* Added property `ontologyDbId` (string) - -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - -* Changed property `authors` (string) - -* Changed property `copyright` (string) - -* Changed property `description` (string) - -* Changed property `documentationURL` (string -> string) - -* Changed property `licence` (string) - -* Changed property `ontologyName` (string) - -* Changed property `version` (string) - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > The identifier and metadata needed to reference an external controlled vocabulary - - - * Deleted property `ontologyDbId` (string) - > Ontology database unique identifier - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `authors` (string) - - * Changed property `copyright` (string) - - * Changed property `description` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `licence` (string) - - * Changed property `ontologyName` (string) - - * Changed property `version` (string) - -##### `GET` /pedigree - -> Get a filtered list of PedigreeNode - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `instituteCode` in `query` -> The code for the institute that maintains the material. ->
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with "obsolete" codes, see "Common formatting rules (v)". - - -Added: `genu` in `query` -> List of Genus names to identify germplasm - - -Added: `specy` in `query` -> List of Species names to identify germplasm - - -Added: `includeParent` in `query` -> If this parameter is true, include the array of parents in the response - - -Added: `includeSibling` in `query` -> If this parameter is true, include the array of siblings in the response - - -Added: `externalReferenceID` in `query` -> **Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 ->
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter) - - -Deleted: `genus` in `query` -> The scientific genus of a germplasm - - -Deleted: `species` in `query` -> The scientific species of a germplasm - - -Deleted: `includeParents` in `query` -> If this parameter is true, include the array of parents in the response - - -Deleted: `includeSiblings` in `query` -> If this parameter is true, include the array of siblings in the response - - -Changed: `accessionNumber` in `query` -> A collection of unique identifiers for materials or germplasm within a genebank -> -> MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). - - -Changed: `binomialName` in `query` -> List of the full binomial name (scientific name) to identify a germplasm - - -Changed: `synonym` in `query` -> List of alternative names or IDs used to reference this germplasm - - -Changed: `includeFullTree` in `query` -> If this parameter is true, recursively include ALL of the nodes available in this pedigree tree - - -Changed: `pedigreeDepth` in `query` -> Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc) - - -Changed: `progenyDepth` in `query` -> Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc) - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -Changed: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Changed: `germplasmPUI` in `query` -> List of Permanent Unique Identifiers to identify germplasm - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances. - - - New required properties: - - `germplasmPUI` - - * Added property `crossingProjectName` (string) - - * Added property `pedigreeNodeDbId` (string) - - * Added property `siblingDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `parents` (array) - > A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. - >
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. - >
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response. - - - * Deleted property `progeny` (array) - > A list of germplasm references that are direct children of this germplasm. These represent edges in the tree, connecting to other nodes. - >
The given germplasm could have a large number of progeny, across a number of different breeding methods. The 'parentType' shows - > the type of parent this germplasm is to each of the child germplasm references. - >
If the parameter 'includeProgeny' is set to false, then this array should be empty, null, or not present in the response. - - - * Deleted property `siblings` (array) - > A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. - >
Siblings share at least one parent with the given germplasm. - >
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `crossingProjectDbId` (string) - - * Changed property `crossingYear` (integer -> integer) - - * Changed property `defaultDisplayName` (string) - - * Changed property `familyCode` (string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `germplasmPUI` (string) - - * Changed property `pedigreeString` (string) - -##### `POST` /pedigree - -> Create new PedigreeNode - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances. - - - New required properties: - - `germplasmPUI` - - * Added property `crossingProjectName` (string) - - * Added property `pedigreeNodeDbId` (string) - - * Added property `siblingDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `parents` (array) - > A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. - >
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. - >
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response. - - - * Deleted property `progeny` (array) - > A list of germplasm references that are direct children of this germplasm. These represent edges in the tree, connecting to other nodes. - >
The given germplasm could have a large number of progeny, across a number of different breeding methods. The 'parentType' shows - > the type of parent this germplasm is to each of the child germplasm references. - >
If the parameter 'includeProgeny' is set to false, then this array should be empty, null, or not present in the response. - - - * Deleted property `siblings` (array) - > A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. - >
Siblings share at least one parent with the given germplasm. - >
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `crossingProjectDbId` (string) - - * Changed property `crossingYear` (integer -> integer) - - * Changed property `defaultDisplayName` (string) - - * Changed property `familyCode` (string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `germplasmPUI` (string) - - * Changed property `pedigreeString` (string) - -##### `GET` /people - -> Get a filtered list of Person - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `emailAddress` in `query` -> email address for this person - - -Added: `mailingAddress` in `query` -> physical address of this person - - -Added: `middleName` in `query` -> Persons middle name - - -Added: `phoneNumber` in `query` -> phone number of this person - - -Changed: `firstName` in `query` -> Persons first name - - -Changed: `lastName` in `query` -> Persons last name - - -Changed: `personDbId` in `query` -> Unique ID for this person - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `personDbId` (string) - > Unique ID for a person - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `description` (string) - - * Changed property `emailAddress` (string) - - * Changed property `firstName` (string) - - * Changed property `lastName` (string) - - * Changed property `mailingAddress` (string) - - * Changed property `middleName` (string) - - * Changed property `phoneNumber` (string) - - * Changed property `userID` (string) - -##### `POST` /people - -> Create new Person - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `personDbId` (string) - > Unique ID for a person - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `description` (string) - - * Changed property `emailAddress` (string) - - * Changed property `firstName` (string) - - * Changed property `lastName` (string) - - * Changed property `mailingAddress` (string) - - * Changed property `middleName` (string) - - * Changed property `phoneNumber` (string) - - * Changed property `userID` (string) - -##### `GET` /people/{personDbId} - -> Get the details of a specific Person - - -###### Parameters: - -Deleted: `personDbId` in `path` -> The unique ID of a person - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `personDbId` (string) - > Unique ID for a person - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `description` (string) - - * Changed property `emailAddress` (string) - - * Changed property `firstName` (string) - - * Changed property `lastName` (string) - - * Changed property `mailingAddress` (string) - - * Changed property `middleName` (string) - - * Changed property `phoneNumber` (string) - - * Changed property `userID` (string) - -##### `PUT` /people/{personDbId} - -> Update the details for an existing Person - - -###### Parameters: - -Deleted: `personDbId` in `path` -> The unique ID of a person - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `personDbId` -- `personDbId` - -* Added property `personDbId` (string) - -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - -* Changed property `description` (string) - -* Changed property `emailAddress` (string) - -* Changed property `firstName` (string) - -* Changed property `lastName` (string) - -* Changed property `mailingAddress` (string) - -* Changed property `middleName` (string) - -* Changed property `phoneNumber` (string) - -* Changed property `userID` (string) - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `personDbId` (string) - > Unique ID for a person - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `description` (string) - - * Changed property `emailAddress` (string) - - * Changed property `firstName` (string) - - * Changed property `lastName` (string) - - * Changed property `mailingAddress` (string) - - * Changed property `middleName` (string) - - * Changed property `phoneNumber` (string) - - * Changed property `userID` (string) - -##### `GET` /plates - -> Get a filtered list of Plate - - -###### Parameters: - -Added: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `plateBarcode` in `query` -> A unique identifier physically attached to the plate - - -Added: `germplasmDbId` in `query` -> The ID which uniquely identifies a germplasm - - -Changed: `sampleDbId` in `query` -> The ID which uniquely identifies a sample - - -Changed: `sampleName` in `query` -> The human readable name of the sample - - -Changed: `sampleGroupDbId` in `query` -> The unique identifier for a group of related Samples - - -Changed: `observationUnitDbId` in `query` -> The ID which uniquely identifies an observation unit - - -Changed: `plateDbId` in `query` -> The ID which uniquely identifies a plate of samples - - -Changed: `plateName` in `query` -> The human readable name of a plate of samples - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. - - - * Added property `programName` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `plateDbId` (string) - > The ID which uniquely identifies a `Plate` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `plateBarcode` (string) - - * Changed property `plateFormat` (string) - > Enum for plate formats, usually "PLATE_96" for a 96 well plate or "TUBES" for plateless format - - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `sampleType` (string) - > The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc - - - * Changed property `studyDbId` (string) - - * Changed property `trialDbId` (string) - -##### `POST` /plates - -> Create new Plate - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. - - - * Added property `programName` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `plateDbId` (string) - > The ID which uniquely identifies a `Plate` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `plateBarcode` (string) - - * Changed property `plateFormat` (string) - > Enum for plate formats, usually "PLATE_96" for a 96 well plate or "TUBES" for plateless format - - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `sampleType` (string) - > The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc - - - * Changed property `studyDbId` (string) - - * Changed property `trialDbId` (string) - -##### `GET` /plates/{plateDbId} - -> Get the details of a specific Plate - - -###### Parameters: - -Deleted: `plateDbId` in `path` -> The ID which uniquely identifies a `Plate` - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. - - - * Added property `programName` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `plateDbId` (string) - > The ID which uniquely identifies a `Plate` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `plateBarcode` (string) - - * Changed property `plateFormat` (string) - > Enum for plate formats, usually "PLATE_96" for a 96 well plate or "TUBES" for plateless format - - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `sampleType` (string) - > The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc - - - * Changed property `studyDbId` (string) - - * Changed property `trialDbId` (string) - -##### `GET` /programs - -> Get a filtered list of Program - - -###### Parameters: - -Added: `leadPersonDbId` in `query` -> The person DbIds of the program leader to search for - - -Added: `leadPersonName` in `query` -> The names of the program leader to search for - - -Added: `objectife` in `query` -> A program objective to search for - - -Changed: `abbreviation` in `query` -> A list of shortened human readable names for a set of Programs - - -Changed: `programType` in `query` -> The type of program entity this object represents ->
'STANDARD' represents a standard, permanent breeding program ->
'PROJECT' represents a short term project, usually with a set time limit based on funding - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. - - - * Added property `personDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `leadPersonDbId` (string) - > The unique identifier of the program leader - - - * Deleted property `leadPersonName` (string) - > The name of the program leader - - - * Deleted property `programDbId` (string) - > The ID which uniquely identifies the program - - - * Changed property `abbreviation` (string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `fundingInformation` (string) - - * Changed property `objective` (string) - - * Changed property `programName` (string) - - * Changed property `programType` (string) - > The type of program entity this object represents - >
'STANDARD' represents a standard, permanent breeding program - >
'PROJECT' represents a short term project, usually with a set time limit based on funding - - -##### `POST` /programs - -> Create new Program - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. - - - * Added property `personDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `leadPersonDbId` (string) - > The unique identifier of the program leader - - - * Deleted property `leadPersonName` (string) - > The name of the program leader - - - * Deleted property `programDbId` (string) - > The ID which uniquely identifies the program - - - * Changed property `abbreviation` (string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `fundingInformation` (string) - - * Changed property `objective` (string) - - * Changed property `programName` (string) - - * Changed property `programType` (string) - > The type of program entity this object represents - >
'STANDARD' represents a standard, permanent breeding program - >
'PROJECT' represents a short term project, usually with a set time limit based on funding - - -##### `GET` /programs/{programDbId} - -> Get the details of a specific Program - - -###### Parameters: - -Deleted: `programDbId` in `path` -> Filter by the common crop name. Exact match. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. - - - * Added property `personDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `leadPersonDbId` (string) - > The unique identifier of the program leader - - - * Deleted property `leadPersonName` (string) - > The name of the program leader - - - * Deleted property `programDbId` (string) - > The ID which uniquely identifies the program - - - * Changed property `abbreviation` (string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `fundingInformation` (string) - - * Changed property `objective` (string) - - * Changed property `programName` (string) - - * Changed property `programType` (string) - > The type of program entity this object represents - >
'STANDARD' represents a standard, permanent breeding program - >
'PROJECT' represents a short term project, usually with a set time limit based on funding - - -##### `PUT` /programs/{programDbId} - -> Update the details for an existing Program - - -###### Parameters: - -Deleted: `programDbId` in `path` -> Filter by the common crop name. Exact match. - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `programDbId` -- `programDbId` - -* Added property `personDbId` (string) - -* Added property `programDbId` (string) - -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - -* Deleted property `leadPersonDbId` (string) - > The unique identifier of the program leader - - -* Deleted property `leadPersonName` (string) - > The name of the program leader - - -* Changed property `abbreviation` (string) - -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - -* Changed property `commonCropName` (string) - -* Changed property `documentationURL` (string -> string) - -* Changed property `fundingInformation` (string) - -* Changed property `objective` (string) - -* Changed property `programName` (string) - -* Changed property `programType` (string) - > The type of program entity this object represents - >
'STANDARD' represents a standard, permanent breeding program - >
'PROJECT' represents a short term project, usually with a set time limit based on funding - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. - - - * Added property `personDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `leadPersonDbId` (string) - > The unique identifier of the program leader - - - * Deleted property `leadPersonName` (string) - > The name of the program leader - - - * Deleted property `programDbId` (string) - > The ID which uniquely identifies the program - - - * Changed property `abbreviation` (string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `fundingInformation` (string) - - * Changed property `objective` (string) - - * Changed property `programName` (string) - - * Changed property `programType` (string) - > The type of program entity this object represents - >
'STANDARD' represents a standard, permanent breeding program - >
'PROJECT' represents a short term project, usually with a set time limit based on funding - - -##### `GET` /samples - -> Get a filtered list of Sample - - -###### Parameters: - -Added: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `germplasmDbId` in `query` -> The ID which uniquely identifies a `Germplasm` - - -Changed: `sampleDbId` in `query` -> The ID which uniquely identifies a `Sample` - - -Changed: `plateDbId` in `query` -> The ID which uniquely identifies a `Plate` of `Samples` - - -Changed: `plateName` in `query` -> The human readable name of a `Plate` of `Samples` - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). - - - New required properties: - - `sampleDbId` - - * Added property `callSetDbIds` (array) - - * Added property `germplasmName` (string) - - * Added property `germplasmPUI` (string) - - * Added property `observationUnitName` (string) - - * Added property `observationUnitPUI` (string) - - * Added property `programName` (string) - - * Added property `sampleGroupId` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `sampleGroupDbId` (string) - > The ID which uniquely identifies a group of `Samples` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `column` (integer -> integer) - - * Changed property `germplasmDbId` (string) - - * Changed property `observationUnitDbId` (string) - - * Changed property `plateDbId` (string) - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `row` (string) - - * Changed property `sampleBarcode` (string) - - * Changed property `sampleDescription` (string) - - * Changed property `sampleName` (string) - - * Changed property `samplePUI` (string) - - * Changed property `sampleTimestamp` (string -> string) - - * Changed property `sampleType` (string) - - * Changed property `studyDbId` (string) - - * Changed property `takenBy` (string) - - * Changed property `tissueType` (string) - - * Changed property `trialDbId` (string) - - * Changed property `well` (string) - -##### `PUT` /samples - -> Update the details for an existing Sample - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `sampleDbId` -- `sampleName` - -* Added property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - -* Added property `callSetDbIds` (array) - -* Added property `column` (integer) - -* Added property `germplasmDbId` (string) - -* Added property `germplasmName` (string) - -* Added property `germplasmPUI` (string) - -* Added property `observationUnitDbId` (string) - -* Added property `observationUnitName` (string) - -* Added property `observationUnitPUI` (string) - -* Added property `plateDbId` (string) - -* Added property `plateName` (string) - -* Added property `programDbId` (string) - -* Added property `programName` (string) - -* Added property `row` (string) - -* Added property `sampleBarcode` (string) - -* Added property `sampleDbId` (string) - -* Added property `sampleDescription` (string) - -* Added property `sampleGroupId` (string) - -* Added property `sampleName` (string) - -* Added property `samplePUI` (string) - -* Added property `sampleTimestamp` (string) - -* Added property `sampleType` (string) - -* Added property `studyDbId` (string) - -* Added property `studyName` (string) - -* Added property `studyPUI` (string) - -* Added property `takenBy` (string) - -* Added property `tissueType` (string) - -* Added property `trialDbId` (string) - -* Added property `trialName` (string) - -* Added property `trialPUI` (string) - -* Added property `well` (string) - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). - - - New required properties: - - `sampleDbId` - - * Added property `callSetDbIds` (array) - - * Added property `germplasmName` (string) - - * Added property `germplasmPUI` (string) - - * Added property `observationUnitName` (string) - - * Added property `observationUnitPUI` (string) - - * Added property `programName` (string) - - * Added property `sampleGroupId` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `sampleGroupDbId` (string) - > The ID which uniquely identifies a group of `Samples` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `column` (integer -> integer) - - * Changed property `germplasmDbId` (string) - - * Changed property `observationUnitDbId` (string) - - * Changed property `plateDbId` (string) - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `row` (string) - - * Changed property `sampleBarcode` (string) - - * Changed property `sampleDescription` (string) - - * Changed property `sampleName` (string) - - * Changed property `samplePUI` (string) - - * Changed property `sampleTimestamp` (string -> string) - - * Changed property `sampleType` (string) - - * Changed property `studyDbId` (string) - - * Changed property `takenBy` (string) - - * Changed property `tissueType` (string) - - * Changed property `trialDbId` (string) - - * Changed property `well` (string) - -##### `POST` /samples - -> Create new Sample - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). - - - New required properties: - - `sampleDbId` - - * Added property `callSetDbIds` (array) - - * Added property `germplasmName` (string) - - * Added property `germplasmPUI` (string) - - * Added property `observationUnitName` (string) - - * Added property `observationUnitPUI` (string) - - * Added property `programName` (string) - - * Added property `sampleGroupId` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `sampleGroupDbId` (string) - > The ID which uniquely identifies a group of `Samples` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `column` (integer -> integer) - - * Changed property `germplasmDbId` (string) - - * Changed property `observationUnitDbId` (string) - - * Changed property `plateDbId` (string) - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `row` (string) - - * Changed property `sampleBarcode` (string) - - * Changed property `sampleDescription` (string) - - * Changed property `sampleName` (string) - - * Changed property `samplePUI` (string) - - * Changed property `sampleTimestamp` (string -> string) - - * Changed property `sampleType` (string) - - * Changed property `studyDbId` (string) - - * Changed property `takenBy` (string) - - * Changed property `tissueType` (string) - - * Changed property `trialDbId` (string) - - * Changed property `well` (string) - -##### `GET` /samples/{sampleDbId} - - -###### Parameters: - -Deleted: `sampleDbId` in `path` -> The unique identifier for a `Sample` - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). - - - New required properties: - - `sampleDbId` - - * Added property `callSetDbIds` (array) - - * Added property `germplasmName` (string) - - * Added property `germplasmPUI` (string) - - * Added property `observationUnitName` (string) - - * Added property `observationUnitPUI` (string) - - * Added property `programName` (string) - - * Added property `sampleGroupId` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `sampleGroupDbId` (string) - > The ID which uniquely identifies a group of `Samples` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `column` (integer -> integer) - - * Changed property `germplasmDbId` (string) - - * Changed property `observationUnitDbId` (string) - - * Changed property `plateDbId` (string) - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `row` (string) - - * Changed property `sampleBarcode` (string) - - * Changed property `sampleDescription` (string) - - * Changed property `sampleName` (string) - - * Changed property `samplePUI` (string) - - * Changed property `sampleTimestamp` (string -> string) - - * Changed property `sampleType` (string) - - * Changed property `studyDbId` (string) - - * Changed property `takenBy` (string) - - * Changed property `tissueType` (string) - - * Changed property `trialDbId` (string) - - * Changed property `well` (string) - -##### `POST` /search/allelematrix - -> Submit a search request for `AlleleMatrix` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `result` (object) - - New required properties: - - `data` - - New optional properties: - - `callSetDbIds` - - `variantSetDbIds` - - * Added property `data` (array) - - Items (object): - > The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier. - - - * Property `callSetDbIds` (array) - - * Property `expandHomozygotes` (boolean) - - * Property `sepPhased` (string) - - * Property `sepUnphased` (string) - - * Property `unknownString` (string) - - * Property `variantDbIds` (array) - - * Property `variantSetDbIds` (array) - - * Deleted property `callSetDbIds` (array) - > A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case. - - - * Deleted property `dataMatrices` (array) - > The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the "callSetDbIds" as columns and the "variantDbIds" as rows. - - - * Deleted property `expandHomozygotes` (boolean) - > Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - - * Deleted property `pagination` (array) - > Pagination for the matrix - - - * Deleted property `sepPhased` (string) - > The string used as a separator for phased allele calls. - - - * Deleted property `sepUnphased` (string) - > The string used as a separator for unphased allele calls. - - - * Deleted property `unknownString` (string) - > The string used as a representation for missing data. - - - * Deleted property `variantDbIds` (array) - > A list of unique identifiers for the Variants contained in the matrix response. This array should match the ordering for rows in the matrix. - - - * Deleted property `variantSetDbIds` (array) - > A list of unique identifiers for the VariantSets contained in the matrix response. A VariantSet is a data set originating from a sequencing event. Often, users will only be interested in data from a single VariantSet, but in some cases a user might be interested in a matrix with data from multiple VariantSets. - - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/allelematrix/{searchResultsDbId} - -> Submit a search request for `AlleleMatrix`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `result` (object) - - New required properties: - - `data` - - New optional properties: - - `callSetDbIds` - - `variantSetDbIds` - - * Added property `data` (array) - - * Deleted property `callSetDbIds` (array) - > A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case. - - - * Deleted property `dataMatrices` (array) - > The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the "callSetDbIds" as columns and the "variantDbIds" as rows. - - - * Deleted property `expandHomozygotes` (boolean) - > Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - - * Deleted property `pagination` (array) - > Pagination for the matrix - - - * Deleted property `sepPhased` (string) - > The string used as a separator for phased allele calls. - - - * Deleted property `sepUnphased` (string) - > The string used as a separator for unphased allele calls. - - - * Deleted property `unknownString` (string) - > The string used as a representation for missing data. - - - * Deleted property `variantDbIds` (array) - > A list of unique identifiers for the Variants contained in the matrix response. This array should match the ordering for rows in the matrix. - - - * Deleted property `variantSetDbIds` (array) - > A list of unique identifiers for the VariantSets contained in the matrix response. A VariantSet is a data set originating from a sequencing event. Often, users will only be interested in data from a single VariantSet, but in some cases a user might be interested in a matrix with data from multiple VariantSets. - - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `POST` /search/attributes - -> Submit a search request for `GermplasmAttribute` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit - - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `attributeValueDbIds` (array) - - * Added property `methodDbId` (string) - - * Added property `methodName` (string) - - * Added property `methodPUI` (string) - - * Added property `ontologyReferenceDbId` (string) - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Added property `traitDbId` (string) - - * Added property `traitName` (string) - - * Added property `traitPUI` (string) - - * Deleted property `attributeDbId` (string) - > The ID which uniquely identifies this attribute within the given database server - - - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `method` (object) - - * Deleted property `ontologyReference` (object) - - * Deleted property `scale` (object) - - * Deleted property `synonyms` (array) - > Other variable names - - - * Deleted property `trait` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attributeCategory` (string) - - * Changed property `attributeDescription` (string) - - * Changed property `attributeName` (string) - - * Changed property `attributePUI` (string) - - * Changed property `commonCropName` (string) - - * Changed property `defaultValue` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `growthStage` (string) - - * Changed property `institution` (string) - - * Changed property `language` (string) - - * Changed property `scientist` (string) - - * Changed property `status` (string) - - * Changed property `submissionTimestamp` (string -> string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/attributes/{searchResultsDbId} - -> Submit a search request for `GermplasmAttribute`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit - - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `attributeValueDbIds` (array) - - * Added property `methodDbId` (string) - - * Added property `methodName` (string) - - * Added property `methodPUI` (string) - - * Added property `ontologyReferenceDbId` (string) - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Added property `traitDbId` (string) - - * Added property `traitName` (string) - - * Added property `traitPUI` (string) - - * Deleted property `attributeDbId` (string) - > The ID which uniquely identifies this attribute within the given database server - - - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `method` (object) - - * Deleted property `ontologyReference` (object) - - * Deleted property `scale` (object) - - * Deleted property `synonyms` (array) - > Other variable names - - - * Deleted property `trait` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attributeCategory` (string) - - * Changed property `attributeDescription` (string) - - * Changed property `attributeName` (string) - - * Changed property `attributePUI` (string) - - * Changed property `commonCropName` (string) - - * Changed property `defaultValue` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `growthStage` (string) - - * Changed property `institution` (string) - - * Changed property `language` (string) - - * Changed property `scientist` (string) - - * Changed property `status` (string) - - * Changed property `submissionTimestamp` (string -> string) - -##### `POST` /search/attributevalues - -> Submit a search request for `GermplasmAttributeValue` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. - - - * Added property `attributePUI` (string) - - * Added property `germplasmPUI` (string) - - * Deleted property `attributeValueDbId` (string) - > The ID which uniquely identifies this attribute value within the given database server - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attributeDbId` (string) - - * Changed property `attributeName` (string) - - * Changed property `determinedDate` (string -> string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `value` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/attributevalues/{searchResultsDbId} - -> Submit a search request for `GermplasmAttributeValue`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit. - - - * Added property `attributePUI` (string) - - * Added property `germplasmPUI` (string) - - * Deleted property `attributeValueDbId` (string) - > The ID which uniquely identifies this attribute value within the given database server - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attributeDbId` (string) - - * Changed property `attributeName` (string) - - * Changed property `determinedDate` (string -> string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `value` (string) - -##### `POST` /search/calls - -> Submit a search request for `Call` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Deleted property `expandHomozygotes` (boolean) - > Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - - * Deleted property `sepPhased` (string) - > The string used as a separator for phased allele calls. - - - * Deleted property `sepUnphased` (string) - > The string used as a separator for unphased allele calls. - - - * Deleted property `unknownString` (string) - > The string used as a representation for missing data. - - - * Changed property `data` (array) - - Changed items (object): - > A `Call` represents the determination of genotype with respect to a particular `Variant`. - > - > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. - - - * Deleted property `genotype` (object) - - * Deleted property `genotypeMetadata` (array) - > Genotype Metadata are additional layers of metadata associated with each genotype. - - - * Deleted property `genotype_likelihood` (array) - > **Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491 - >
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec. - - - * Deleted property `variantName` (string) - > The name of the variant this call belongs to. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `genotypeValue` (string) - - * Changed property `phaseSet` (string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (string) - - * Changed property `variantSetName` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/calls/{searchResultsDbId} - -> Submit a search request for `Call`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `pageToken` in `query` -> **Deprecated in v2.1** Please use `page`. Github issue number #451 ->
Used to request a specific page of data to be returned. ->
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Deleted property `expandHomozygotes` (boolean) - > Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - - * Deleted property `sepPhased` (string) - > The string used as a separator for phased allele calls. - - - * Deleted property `sepUnphased` (string) - > The string used as a separator for unphased allele calls. - - - * Deleted property `unknownString` (string) - > The string used as a representation for missing data. - - - * Changed property `data` (array) - - Changed items (object): - > A `Call` represents the determination of genotype with respect to a particular `Variant`. - > - > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. - - - * Deleted property `genotype` (object) - - * Deleted property `genotypeMetadata` (array) - > Genotype Metadata are additional layers of metadata associated with each genotype. - - - * Deleted property `genotype_likelihood` (array) - > **Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491 - >
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec. - - - * Deleted property `variantName` (string) - > The name of the variant this call belongs to. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `genotypeValue` (string) - - * Changed property `phaseSet` (string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (string) - - * Changed property `variantSetName` (string) - -##### `POST` /search/callsets - -> Submit a search request for `CallSet` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A CallSet is a collection of Calls that were generated by the same analysis of the same Sample - - - * Added property `sampleName` (string) - - * Added property `samplePUI` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Deleted property `externalReferences` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `created` (string -> string) - - * Changed property `sampleDbId` (string) - - * Changed property `studyDbId` (string) - - * Changed property `updated` (string -> string) - - * Changed property `variantSetDbIds` (array) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/callsets/{searchResultsDbId} - -> Submit a search request for `CallSet`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A CallSet is a collection of Calls that were generated by the same analysis of the same Sample - - - * Added property `sampleName` (string) - - * Added property `samplePUI` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Deleted property `externalReferences` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `created` (string -> string) - - * Changed property `sampleDbId` (string) - - * Changed property `studyDbId` (string) - - * Changed property `updated` (string -> string) - - * Changed property `variantSetDbIds` (array) - -##### `POST` /search/germplasm - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `sampleDbIds` (array) - - * Deleted property `donors` (array) - > List of donor institutes - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `germplasmDbId` (string) - > The ID which uniquely identifies a germplasm within the given database server - >
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. - - - * Deleted property `germplasmOrigin` (array) - > Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm. - - - * Deleted property `storageTypes` (array) - > The type of storage this germplasm is kept in at a genebank. - - - * Deleted property `synonyms` (array) - > List of alternative names or IDs used to reference this germplasm - > - > MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. - - - * Deleted property `taxonIds` (array) - > The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. - > - > MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. - - - * Changed property `accessionNumber` (string) - - * Changed property `acquisitionDate` (string -> string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `biologicalStatusOfAccessionCode` (string) - > MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. - > - > 100) Wild - > 110) Natural - > 120) Semi-natural/wild - > 130) Semi-natural/sown - > 200) Weedy - > 300) Traditional cultivar/landrace - > 400) Breeding/research material - > 410) Breeders line - > 411) Synthetic population - > 412) Hybrid - > 413) Founder stock/base population - > 414) Inbred line (parent of hybrid cultivar) - > 415) Segregating population - > 416) Clonal selection - > 420) Genetic stock - > 421) Mutant (e.g. induced/insertion mutants, tilling populations) - > 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) - > 423) Other genetic stocks (e.g. mapping populations) - > 500) Advanced or improved cultivar (conventional breeding methods) - > 600) GMO (by genetic engineering) - > 999) Other (Elaborate in REMARKS field) - - - * Changed property `biologicalStatusOfAccessionDescription` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `collection` (string) - - * Changed property `commonCropName` (string) - - * Changed property `countryOfOriginCode` (string) - - * Changed property `defaultDisplayName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `genus` (string) - - * Changed property `germplasmName` (string) - - * Changed property `germplasmPUI` (string) - - * Changed property `germplasmPreprocessing` (string) - - * Changed property `instituteCode` (string) - - * Changed property `instituteName` (string) - - * Changed property `pedigree` (string) - - * Changed property `seedSource` (string) - - * Changed property `seedSourceDescription` (string) - - * Changed property `species` (string) - - * Changed property `speciesAuthority` (string) - - * Changed property `subtaxa` (string) - - * Changed property `subtaxaAuthority` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/germplasm/{searchResultsDbId} - -> Submit a search request for `Germplasm`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/germplasm/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `sampleDbIds` (array) - - * Deleted property `donors` (array) - > List of donor institutes - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `germplasmDbId` (string) - > The ID which uniquely identifies a germplasm within the given database server - >
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. - - - * Deleted property `germplasmOrigin` (array) - > Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm. - - - * Deleted property `storageTypes` (array) - > The type of storage this germplasm is kept in at a genebank. - - - * Deleted property `synonyms` (array) - > List of alternative names or IDs used to reference this germplasm - > - > MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. - - - * Deleted property `taxonIds` (array) - > The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. - > - > MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. - - - * Changed property `accessionNumber` (string) - - * Changed property `acquisitionDate` (string -> string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `biologicalStatusOfAccessionCode` (string) - > MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. - > - > 100) Wild - > 110) Natural - > 120) Semi-natural/wild - > 130) Semi-natural/sown - > 200) Weedy - > 300) Traditional cultivar/landrace - > 400) Breeding/research material - > 410) Breeders line - > 411) Synthetic population - > 412) Hybrid - > 413) Founder stock/base population - > 414) Inbred line (parent of hybrid cultivar) - > 415) Segregating population - > 416) Clonal selection - > 420) Genetic stock - > 421) Mutant (e.g. induced/insertion mutants, tilling populations) - > 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) - > 423) Other genetic stocks (e.g. mapping populations) - > 500) Advanced or improved cultivar (conventional breeding methods) - > 600) GMO (by genetic engineering) - > 999) Other (Elaborate in REMARKS field) - - - * Changed property `biologicalStatusOfAccessionDescription` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `collection` (string) - - * Changed property `commonCropName` (string) - - * Changed property `countryOfOriginCode` (string) - - * Changed property `defaultDisplayName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `genus` (string) - - * Changed property `germplasmName` (string) - - * Changed property `germplasmPUI` (string) - - * Changed property `germplasmPreprocessing` (string) - - * Changed property `instituteCode` (string) - - * Changed property `instituteName` (string) - - * Changed property `pedigree` (string) - - * Changed property `seedSource` (string) - - * Changed property `seedSourceDescription` (string) - - * Changed property `species` (string) - - * Changed property `speciesAuthority` (string) - - * Changed property `subtaxa` (string) - - * Changed property `subtaxaAuthority` (string) - -##### `POST` /search/lists - -> Submit a search request for `List` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. - - - * Added property `personDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `listDbId` (string) - > The unique identifier for a List - - - * Deleted property `listOwnerPersonDbId` (string) - > The unique identifier for a List Owner. (usually a user or person) - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `dateCreated` (string -> string) - - * Changed property `dateModified` (string -> string) - - * Changed property `listDescription` (string) - - * Changed property `listName` (string) - - * Changed property `listOwnerName` (string) - - * Changed property `listSize` (integer -> integer) - - * Changed property `listSource` (string) - - * Changed property `listType` (string) - > The type of objects that are referenced in a List - - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/lists/{searchResultsDbId} - -> Submit a search request for `List`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study. - - - * Added property `personDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `listDbId` (string) - > The unique identifier for a List - - - * Deleted property `listOwnerPersonDbId` (string) - > The unique identifier for a List Owner. (usually a user or person) - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `dateCreated` (string -> string) - - * Changed property `dateModified` (string -> string) - - * Changed property `listDescription` (string) - - * Changed property `listName` (string) - - * Changed property `listOwnerName` (string) - - * Changed property `listSize` (integer -> integer) - - * Changed property `listSource` (string) - - * Changed property `listType` (string) - > The type of objects that are referenced in a List - - -##### `POST` /search/markerpositions - -> Submit a search request for `MarkerPosition` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap. - - - * Added property `mapPUI` (string) - - * Deleted property `variantName` (string) - > The human readable name for a `Variant` - >
A `Variant` can also represent a Marker - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `linkageGroupName` (string) - - * Changed property `mapDbId` (string) - - * Changed property `mapName` (string) - - * Changed property `position` (integer -> integer) - - * Changed property `variantDbId` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/markerpositions/{searchResultsDbId} - -> Submit a search request for `MarkerPosition`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/markerPosition/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap. - - - * Added property `mapPUI` (string) - - * Deleted property `variantName` (string) - > The human readable name for a `Variant` - >
A `Variant` can also represent a Marker - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `linkageGroupName` (string) - - * Changed property `mapDbId` (string) - - * Changed property `mapName` (string) - - * Changed property `position` (integer -> integer) - - * Changed property `variantDbId` (string) - -##### `POST` /search/observationunits - -> Submit a search request for `ObservationUnit` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. - - - * Added property `germplasmPUI` (string) - - * Added property `studyPUI` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `observationUnitDbId` (string) - > The ID which uniquely identifies an observation unit - > - > MIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. - - - * Deleted property `observationUnitPosition` (object) - - * Deleted property `observations` (array) - > All observations attached to this observation unit. - > - > Default for this field is null or omitted. Do NOT include data in this field unless the 'includeObservations' flag is explicitly set to True. - - - * Deleted property `treatments` (array) - > List of treatments applied to an observation unit. - > - > MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossDbId` (string) - - * Changed property `crossName` (string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `observationUnitPUI` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `seedLotDbId` (string) - - * Changed property `seedLotName` (string) - - * Changed property `studyDbId` (string) - - * Changed property `studyName` (string) - - * Changed property `trialDbId` (string) - - * Changed property `trialName` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/observationunits/{searchResultsDbId} - -> Submit a search request for `ObservationUnit`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/observationUnit/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples. - - - * Added property `germplasmPUI` (string) - - * Added property `studyPUI` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `observationUnitDbId` (string) - > The ID which uniquely identifies an observation unit - > - > MIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. - - - * Deleted property `observationUnitPosition` (object) - - * Deleted property `observations` (array) - > All observations attached to this observation unit. - > - > Default for this field is null or omitted. Do NOT include data in this field unless the 'includeObservations' flag is explicitly set to True. - - - * Deleted property `treatments` (array) - > List of treatments applied to an observation unit. - > - > MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossDbId` (string) - - * Changed property `crossName` (string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `observationUnitPUI` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `seedLotDbId` (string) - - * Changed property `seedLotName` (string) - - * Changed property `studyDbId` (string) - - * Changed property `studyName` (string) - - * Changed property `trialDbId` (string) - - * Changed property `trialName` (string) - -##### `POST` /search/pedigree - -> Submit a search request for `PedigreeNode` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances. - - - New required properties: - - `germplasmPUI` - - * Added property `crossingProjectName` (string) - - * Added property `pedigreeNodeDbId` (string) - - * Added property `siblingDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `parents` (array) - > A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. - >
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. - >
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response. - - - * Deleted property `progeny` (array) - > A list of germplasm references that are direct children of this germplasm. These represent edges in the tree, connecting to other nodes. - >
The given germplasm could have a large number of progeny, across a number of different breeding methods. The 'parentType' shows - > the type of parent this germplasm is to each of the child germplasm references. - >
If the parameter 'includeProgeny' is set to false, then this array should be empty, null, or not present in the response. - - - * Deleted property `siblings` (array) - > A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. - >
Siblings share at least one parent with the given germplasm. - >
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `crossingProjectDbId` (string) - - * Changed property `crossingYear` (integer -> integer) - - * Changed property `defaultDisplayName` (string) - - * Changed property `familyCode` (string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `germplasmPUI` (string) - - * Changed property `pedigreeString` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/pedigree/{searchResultsDbId} - -> Submit a search request for `PedigreeNode`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/pedigreeNode/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances. - - - New required properties: - - `germplasmPUI` - - * Added property `crossingProjectName` (string) - - * Added property `pedigreeNodeDbId` (string) - - * Added property `siblingDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `parents` (array) - > A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. - >
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. - >
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response. - - - * Deleted property `progeny` (array) - > A list of germplasm references that are direct children of this germplasm. These represent edges in the tree, connecting to other nodes. - >
The given germplasm could have a large number of progeny, across a number of different breeding methods. The 'parentType' shows - > the type of parent this germplasm is to each of the child germplasm references. - >
If the parameter 'includeProgeny' is set to false, then this array should be empty, null, or not present in the response. - - - * Deleted property `siblings` (array) - > A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. - >
Siblings share at least one parent with the given germplasm. - >
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `breedingMethodDbId` (string) - - * Changed property `breedingMethodName` (string) - - * Changed property `crossingProjectDbId` (string) - - * Changed property `crossingYear` (integer -> integer) - - * Changed property `defaultDisplayName` (string) - - * Changed property `familyCode` (string) - - * Changed property `germplasmDbId` (string) - - * Changed property `germplasmName` (string) - - * Changed property `germplasmPUI` (string) - - * Changed property `pedigreeString` (string) - -##### `POST` /search/people - -> Submit a search request for `Person` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `personDbId` (string) - > Unique ID for a person - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `description` (string) - - * Changed property `emailAddress` (string) - - * Changed property `firstName` (string) - - * Changed property `lastName` (string) - - * Changed property `mailingAddress` (string) - - * Changed property `middleName` (string) - - * Changed property `phoneNumber` (string) - - * Changed property `userID` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/people/{searchResultsDbId} - -> Submit a search request for `Person`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/person/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `personDbId` (string) - > Unique ID for a person - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `description` (string) - - * Changed property `emailAddress` (string) - - * Changed property `firstName` (string) - - * Changed property `lastName` (string) - - * Changed property `mailingAddress` (string) - - * Changed property `middleName` (string) - - * Changed property `phoneNumber` (string) - - * Changed property `userID` (string) - -##### `POST` /search/plates - -> Submit a search request for `Plate` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. - - - * Added property `programName` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `plateDbId` (string) - > The ID which uniquely identifies a `Plate` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `plateBarcode` (string) - - * Changed property `plateFormat` (string) - > Enum for plate formats, usually "PLATE_96" for a 96 well plate or "TUBES" for plateless format - - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `sampleType` (string) - > The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc - - - * Changed property `studyDbId` (string) - - * Changed property `trialDbId` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/plates/{searchResultsDbId} - -> Submit a search request for `Plate`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. - - - * Added property `programName` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `plateDbId` (string) - > The ID which uniquely identifies a `Plate` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `plateBarcode` (string) - - * Changed property `plateFormat` (string) - > Enum for plate formats, usually "PLATE_96" for a 96 well plate or "TUBES" for plateless format - - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `sampleType` (string) - > The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc - - - * Changed property `studyDbId` (string) - - * Changed property `trialDbId` (string) - -##### `POST` /search/programs - -> Submit a search request for `Program` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. - - - * Added property `personDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `leadPersonDbId` (string) - > The unique identifier of the program leader - - - * Deleted property `leadPersonName` (string) - > The name of the program leader - - - * Deleted property `programDbId` (string) - > The ID which uniquely identifies the program - - - * Changed property `abbreviation` (string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `fundingInformation` (string) - - * Changed property `objective` (string) - - * Changed property `programName` (string) - - * Changed property `programType` (string) - > The type of program entity this object represents - >
'STANDARD' represents a standard, permanent breeding program - >
'PROJECT' represents a short term project, usually with a set time limit based on funding - - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/programs/{searchResultsDbId} - -> Submit a search request for `Program`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/program/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies. - - - * Added property `personDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `leadPersonDbId` (string) - > The unique identifier of the program leader - - - * Deleted property `leadPersonName` (string) - > The name of the program leader - - - * Deleted property `programDbId` (string) - > The ID which uniquely identifies the program - - - * Changed property `abbreviation` (string) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `fundingInformation` (string) - - * Changed property `objective` (string) - - * Changed property `programName` (string) - - * Changed property `programType` (string) - > The type of program entity this object represents - >
'STANDARD' represents a standard, permanent breeding program - >
'PROJECT' represents a short term project, usually with a set time limit based on funding - - -##### `POST` /search/samples - -> Submit a search request for `Sample` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). - - - New required properties: - - `sampleDbId` - - * Added property `callSetDbIds` (array) - - * Added property `germplasmName` (string) - - * Added property `germplasmPUI` (string) - - * Added property `observationUnitName` (string) - - * Added property `observationUnitPUI` (string) - - * Added property `programName` (string) - - * Added property `sampleGroupId` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `sampleGroupDbId` (string) - > The ID which uniquely identifies a group of `Samples` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `column` (integer -> integer) - - * Changed property `germplasmDbId` (string) - - * Changed property `observationUnitDbId` (string) - - * Changed property `plateDbId` (string) - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `row` (string) - - * Changed property `sampleBarcode` (string) - - * Changed property `sampleDescription` (string) - - * Changed property `sampleName` (string) - - * Changed property `samplePUI` (string) - - * Changed property `sampleTimestamp` (string -> string) - - * Changed property `sampleType` (string) - - * Changed property `studyDbId` (string) - - * Changed property `takenBy` (string) - - * Changed property `tissueType` (string) - - * Changed property `trialDbId` (string) - - * Changed property `well` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/samples/{searchResultsDbId} - -> Submit a search request for `Sample`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/sample/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc). - - - New required properties: - - `sampleDbId` - - * Added property `callSetDbIds` (array) - - * Added property `germplasmName` (string) - - * Added property `germplasmPUI` (string) - - * Added property `observationUnitName` (string) - - * Added property `observationUnitPUI` (string) - - * Added property `programName` (string) - - * Added property `sampleGroupId` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Added property `trialName` (string) - - * Added property `trialPUI` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `sampleGroupDbId` (string) - > The ID which uniquely identifies a group of `Samples` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `column` (integer -> integer) - - * Changed property `germplasmDbId` (string) - - * Changed property `observationUnitDbId` (string) - - * Changed property `plateDbId` (string) - - * Changed property `plateName` (string) - - * Changed property `programDbId` (string) - - * Changed property `row` (string) - - * Changed property `sampleBarcode` (string) - - * Changed property `sampleDescription` (string) - - * Changed property `sampleName` (string) - - * Changed property `samplePUI` (string) - - * Changed property `sampleTimestamp` (string -> string) - - * Changed property `sampleType` (string) - - * Changed property `studyDbId` (string) - - * Changed property `takenBy` (string) - - * Changed property `tissueType` (string) - - * Changed property `trialDbId` (string) - - * Changed property `well` (string) - -##### `POST` /search/variables - -> Submit a search request for `ObservationVariable` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `methodDbId` (string) - - * Added property `methodName` (string) - - * Added property `methodPUI` (string) - - * Added property `ontologyReferenceDbId` (string) - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Added property `traitDbId` (string) - - * Added property `traitName` (string) - - * Added property `traitPUI` (string) - - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `method` (object) - - * Deleted property `observationVariableDbId` (string) - > Variable unique identifier - > - > MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `scale` (object) - - * Deleted property `synonyms` (array) - > Other variable names - - - * Deleted property `trait` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `defaultValue` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `growthStage` (string) - - * Changed property `institution` (string) - - * Changed property `language` (string) - - * Changed property `observationVariableName` (string) - - * Changed property `observationVariablePUI` (string) - - * Changed property `scientist` (string) - - * Changed property `status` (string) - - * Changed property `submissionTimestamp` (string -> string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/variables/{searchResultsDbId} - -> Submit a search request for `ObservationVariable`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `methodDbId` (string) - - * Added property `methodName` (string) - - * Added property `methodPUI` (string) - - * Added property `ontologyReferenceDbId` (string) - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Added property `traitDbId` (string) - - * Added property `traitName` (string) - - * Added property `traitPUI` (string) - - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `method` (object) - - * Deleted property `observationVariableDbId` (string) - > Variable unique identifier - > - > MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `scale` (object) - - * Deleted property `synonyms` (array) - > Other variable names - - - * Deleted property `trait` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `defaultValue` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `growthStage` (string) - - * Changed property `institution` (string) - - * Changed property `language` (string) - - * Changed property `observationVariableName` (string) - - * Changed property `observationVariablePUI` (string) - - * Changed property `scientist` (string) - - * Changed property `status` (string) - - * Changed property `submissionTimestamp` (string -> string) - -##### `POST` /search/variants - -> Submit a search request for `Variant` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF. - - - * Added property `variantSetName` (string) - - * Deleted property `alternateBases` (array) - > The bases that appear instead of the reference bases. Multiple alternate alleles are possible. - - - * Deleted property `alternate_bases` (array) - > **Deprecated in v2.1** Please use `alternateBases`. Github issue number #549 - >
The bases that appear instead of the reference bases. Multiple alternate alleles are possible. - - - * Deleted property `ciend` (array) - > Similar to "cipos", but for the variant's end position (which is derived from start + svlen). - - - * Deleted property `cipos` (array) - > In the case of structural variants, start and end of the variant may not - > be known with an exact base position. "cipos" provides an interval with - > high confidence for the start position. The interval is provided by 0 or - > 2 signed integers which are added to the start position. - > Based on the use in VCF v4.2 - - - * Deleted property `externalReferences` (object) - - * Deleted property `filtersFailed` (array) - > Zero or more filters that failed for this variant. VCF column 7 "FILTER" shared across all alleles in the same VCF record. - - - * Deleted property `variantNames` (array) - > A human readable name associated with a `Variant` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `created` (string -> string) - - * Changed property `end` (integer -> integer) - - * Changed property `filtersApplied` (boolean -> boolean) - - * Changed property `filtersPassed` (boolean -> boolean) - - * Changed property `referenceBases` (string) - - * Changed property `referenceDbId` (string) - - * Changed property `referenceName` (string) - - * Changed property `referenceSetDbId` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `start` (integer -> integer) - - * Changed property `svlen` (integer -> integer) - - * Changed property `updated` (string -> string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (array -> string) - - * Changed property `variantType` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/variants/{searchResultsDbId} - -> Submit a search request for `Variant`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/variant/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `pageToken` in `query` -> **Deprecated in v2.1** Please use `page`. Github issue number #451 ->
Used to request a specific page of data to be returned. ->
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF. - - - * Added property `variantSetName` (string) - - * Deleted property `alternateBases` (array) - > The bases that appear instead of the reference bases. Multiple alternate alleles are possible. - - - * Deleted property `alternate_bases` (array) - > **Deprecated in v2.1** Please use `alternateBases`. Github issue number #549 - >
The bases that appear instead of the reference bases. Multiple alternate alleles are possible. - - - * Deleted property `ciend` (array) - > Similar to "cipos", but for the variant's end position (which is derived from start + svlen). - - - * Deleted property `cipos` (array) - > In the case of structural variants, start and end of the variant may not - > be known with an exact base position. "cipos" provides an interval with - > high confidence for the start position. The interval is provided by 0 or - > 2 signed integers which are added to the start position. - > Based on the use in VCF v4.2 - - - * Deleted property `externalReferences` (object) - - * Deleted property `filtersFailed` (array) - > Zero or more filters that failed for this variant. VCF column 7 "FILTER" shared across all alleles in the same VCF record. - - - * Deleted property `variantNames` (array) - > A human readable name associated with a `Variant` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `created` (string -> string) - - * Changed property `end` (integer -> integer) - - * Changed property `filtersApplied` (boolean -> boolean) - - * Changed property `filtersPassed` (boolean -> boolean) - - * Changed property `referenceBases` (string) - - * Changed property `referenceDbId` (string) - - * Changed property `referenceName` (string) - - * Changed property `referenceSetDbId` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `start` (integer -> integer) - - * Changed property `svlen` (integer -> integer) - - * Changed property `updated` (string -> string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (array -> string) - - * Changed property `variantType` (string) - -##### `POST` /search/variantsets - -> Submit a search request for `VariantSet` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A VariantSet is a collection of variants and variant calls intended to be analyzed together. - - - * Added property `analysiDbIds` (array) - - * Added property `referenceSetName` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Deleted property `analysis` (array) - > Set of Analysis descriptors for this VariantSet - - - * Deleted property `availableFormats` (array) - > When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. - >
'dataFormat' defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc) - >
'fileFormat' defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response. - - - * Deleted property `externalReferences` (object) - - * Deleted property `metadataFields` (array) - > The 'metadataFields' array indicates which types of genotyping data and metadata are available in the VariantSet. - >
When possible, these field names and abbreviations should follow the VCF standard - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetCount` (integer -> integer) - - * Changed property `referenceSetDbId` (string) - - * Changed property `studyDbId` (string) - - * Changed property `variantCount` (integer -> integer) - - * Changed property `variantSetDbId` (string) - - * Changed property `variantSetName` (string) - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -##### `GET` /search/variantsets/{searchResultsDbId} - -> Submit a search request for `VariantSet`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/variantSet/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A VariantSet is a collection of variants and variant calls intended to be analyzed together. - - - * Added property `analysiDbIds` (array) - - * Added property `referenceSetName` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Deleted property `analysis` (array) - > Set of Analysis descriptors for this VariantSet - - - * Deleted property `availableFormats` (array) - > When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. - >
'dataFormat' defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc) - >
'fileFormat' defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response. - - - * Deleted property `externalReferences` (object) - - * Deleted property `metadataFields` (array) - > The 'metadataFields' array indicates which types of genotyping data and metadata are available in the VariantSet. - >
When possible, these field names and abbreviations should follow the VCF standard - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetCount` (integer -> integer) - - * Changed property `referenceSetDbId` (string) - - * Changed property `studyDbId` (string) - - * Changed property `variantCount` (integer -> integer) - - * Changed property `variantSetDbId` (string) - - * Changed property `variantSetName` (string) - -##### `GET` /seasons - -> Get a filtered list of Season - - -###### Parameters: - -Changed: `seasonDbId` in `query` -> The unique identifier for a season. For backward compatibility it can be a string like '2012', '1957-2004'. - - -Changed: `season` in `query` -> The term to describe a given season. Example "Spring" OR "May" OR "Planting_Time_7". - - -Changed: `seasonName` in `query` -> The term to describe a given season. Example "Spring" OR "May" OR "Planting_Time_7". - - -Changed: `year` in `query` -> The 4 digit year of a season. Example "2017" - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like "Spring" or "Summer", or this term could be a month, like "May" or "June", or this could be an arbitrary season name which is meaningful to the breeding Program like "PlantingTime_3" or "Season E". - - - * Changed property `seasonDbId` (string) - - * Changed property `seasonName` (string) - - * Changed property `year` (integer -> integer) - -##### `POST` /seasons - -> Create new Season - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like "Spring" or "Summer", or this term could be a month, like "May" or "June", or this could be an arbitrary season name which is meaningful to the breeding Program like "PlantingTime_3" or "Season E". - - - * Changed property `seasonDbId` (string) - - * Changed property `seasonName` (string) - - * Changed property `year` (integer -> integer) - -##### `GET` /seasons/{seasonDbId} - -> Get the details of a specific Season - - -###### Parameters: - -Deleted: `seasonDbId` in `path` -> The unique identifier for a season. For backward compatibility it can be a string like '2012', '1957-2004' - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like "Spring" or "Summer", or this term could be a month, like "May" or "June", or this could be an arbitrary season name which is meaningful to the breeding Program like "PlantingTime_3" or "Season E". - - - * Changed property `seasonDbId` (string) - - * Changed property `seasonName` (string) - - * Changed property `year` (integer -> integer) - -##### `PUT` /seasons/{seasonDbId} - -> Update the details for an existing Season - - -###### Parameters: - -Deleted: `seasonDbId` in `path` -> The unique identifier for a season. For backward compatibility it can be a string like '2012', '1957-2004' - - -###### Request: - -Changed content type : `application/json` - -* Changed property `seasonDbId` (string) - -* Changed property `seasonName` (string) - -* Changed property `year` (integer -> integer) - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like "Spring" or "Summer", or this term could be a month, like "May" or "June", or this could be an arbitrary season name which is meaningful to the breeding Program like "PlantingTime_3" or "Season E". - - - * Changed property `seasonDbId` (string) - - * Changed property `seasonName` (string) - - * Changed property `year` (integer -> integer) - -##### `GET` /seedlots - -> Get a filtered list of SeedLot - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -Changed: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program. - - - * Deleted property `contentMixture` (array) - > The mixture of germplasm present in the seed lot. - >
- > If this seed lot only contains a single germplasm, the response should contain the name - > and DbId of that germplasm with a mixturePercentage value of 100 - >
- > If the seed lot contains a mixture of different germplasm, the response should contain - > the name and DbId every germplasm present. The mixturePercentage field should contain - > the ratio of each germplasm in the total mixture. All of the mixturePercentage values - > in this array should sum to equal 100. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `seedLotDbId` (string) - > Unique DbId for the Seed Lot - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `amount` (number) - - * Changed property `createdDate` (string -> string) - - * Changed property `lastUpdated` (string -> string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `seedLotDescription` (string) - - * Changed property `seedLotName` (string) - - * Changed property `sourceCollection` (string) - - * Changed property `storageLocation` (string) - - * Changed property `units` (string) - -##### `POST` /seedlots - -> Create new SeedLot - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program. - - - * Deleted property `contentMixture` (array) - > The mixture of germplasm present in the seed lot. - >
- > If this seed lot only contains a single germplasm, the response should contain the name - > and DbId of that germplasm with a mixturePercentage value of 100 - >
- > If the seed lot contains a mixture of different germplasm, the response should contain - > the name and DbId every germplasm present. The mixturePercentage field should contain - > the ratio of each germplasm in the total mixture. All of the mixturePercentage values - > in this array should sum to equal 100. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `seedLotDbId` (string) - > Unique DbId for the Seed Lot - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `amount` (number) - - * Changed property `createdDate` (string -> string) - - * Changed property `lastUpdated` (string -> string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `seedLotDescription` (string) - - * Changed property `seedLotName` (string) - - * Changed property `sourceCollection` (string) - - * Changed property `storageLocation` (string) - - * Changed property `units` (string) - -##### `GET` /seedlots/{seedLotDbId} - -> Get the details of a specific SeedLot - - -###### Parameters: - -Deleted: `seedLotDbId` in `path` -> Unique id for a seed lot on this server - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program. - - - * Deleted property `contentMixture` (array) - > The mixture of germplasm present in the seed lot. - >
- > If this seed lot only contains a single germplasm, the response should contain the name - > and DbId of that germplasm with a mixturePercentage value of 100 - >
- > If the seed lot contains a mixture of different germplasm, the response should contain - > the name and DbId every germplasm present. The mixturePercentage field should contain - > the ratio of each germplasm in the total mixture. All of the mixturePercentage values - > in this array should sum to equal 100. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `seedLotDbId` (string) - > Unique DbId for the Seed Lot - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `amount` (number) - - * Changed property `createdDate` (string -> string) - - * Changed property `lastUpdated` (string -> string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `seedLotDescription` (string) - - * Changed property `seedLotName` (string) - - * Changed property `sourceCollection` (string) - - * Changed property `storageLocation` (string) - - * Changed property `units` (string) - -##### `PUT` /seedlots/{seedLotDbId} - -> Update the details for an existing SeedLot - - -###### Parameters: - -Deleted: `seedLotDbId` in `path` -> Unique id for a seed lot on this server - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `seedLotDbId` -- `seedLotDbId` - -* Added property `seedLotDbId` (string) - -* Deleted property `contentMixture` (array) - > The mixture of germplasm present in the seed lot. - >
- > If this seed lot only contains a single germplasm, the response should contain the name - > and DbId of that germplasm with a mixturePercentage value of 100 - >
- > If the seed lot contains a mixture of different germplasm, the response should contain - > the name and DbId every germplasm present. The mixturePercentage field should contain - > the ratio of each germplasm in the total mixture. All of the mixturePercentage values - > in this array should sum to equal 100. - - -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - -* Changed property `amount` (number) - -* Changed property `createdDate` (string -> string) - -* Changed property `lastUpdated` (string -> string) - -* Changed property `locationDbId` (string) - -* Changed property `locationName` (string) - -* Changed property `programDbId` (string) - -* Changed property `programName` (string) - -* Changed property `seedLotDescription` (string) - -* Changed property `seedLotName` (string) - -* Changed property `sourceCollection` (string) - -* Changed property `storageLocation` (string) - -* Changed property `units` (string) - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program. - - - * Deleted property `contentMixture` (array) - > The mixture of germplasm present in the seed lot. - >
- > If this seed lot only contains a single germplasm, the response should contain the name - > and DbId of that germplasm with a mixturePercentage value of 100 - >
- > If the seed lot contains a mixture of different germplasm, the response should contain - > the name and DbId every germplasm present. The mixturePercentage field should contain - > the ratio of each germplasm in the total mixture. All of the mixturePercentage values - > in this array should sum to equal 100. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `seedLotDbId` (string) - > Unique DbId for the Seed Lot - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `amount` (number) - - * Changed property `createdDate` (string -> string) - - * Changed property `lastUpdated` (string -> string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `seedLotDescription` (string) - - * Changed property `seedLotName` (string) - - * Changed property `sourceCollection` (string) - - * Changed property `storageLocation` (string) - - * Changed property `units` (string) - -##### `GET` /traits - -> Get a filtered list of Trait - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `traitDbId` in `query` -> The unique identifier for a trait. - - -Changed: `observationVariableDbId` in `query` -> The unique identifier for an observation variable. - - -Changed: `ontologyDbId` in `query` -> The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology -> -> Use `GET /ontologies` to find the list of available ontologies on a server. - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Trait describes what property is being observed. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `alternativeAbbreviations` (array) - > A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `synonyms` (array) - > Other trait names - - - * Deleted property `traitDbId` (string) - > The ID which uniquely identifies a trait - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attribute` (string) - - * Changed property `attributePUI` (string) - - * Changed property `entity` (string) - - * Changed property `entityPUI` (string) - - * Changed property `mainAbbreviation` (string) - - * Changed property `status` (string) - - * Changed property `traitClass` (string) - - * Changed property `traitDescription` (string) - - * Changed property `traitName` (string) - - * Changed property `traitPUI` (string) - -##### `POST` /traits - -> Create new Trait - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Trait describes what property is being observed. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `alternativeAbbreviations` (array) - > A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `synonyms` (array) - > Other trait names - - - * Deleted property `traitDbId` (string) - > The ID which uniquely identifies a trait - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attribute` (string) - - * Changed property `attributePUI` (string) - - * Changed property `entity` (string) - - * Changed property `entityPUI` (string) - - * Changed property `mainAbbreviation` (string) - - * Changed property `status` (string) - - * Changed property `traitClass` (string) - - * Changed property `traitDescription` (string) - - * Changed property `traitName` (string) - - * Changed property `traitPUI` (string) - -##### `GET` /traits/{traitDbId} - - -###### Parameters: - -Deleted: `traitDbId` in `path` -> Id of the trait to retrieve details of. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A Trait describes what property is being observed. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `alternativeAbbreviations` (array) - > A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `synonyms` (array) - > Other trait names - - - * Deleted property `traitDbId` (string) - > The ID which uniquely identifies a trait - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attribute` (string) - - * Changed property `attributePUI` (string) - - * Changed property `entity` (string) - - * Changed property `entityPUI` (string) - - * Changed property `mainAbbreviation` (string) - - * Changed property `status` (string) - - * Changed property `traitClass` (string) - - * Changed property `traitDescription` (string) - - * Changed property `traitName` (string) - - * Changed property `traitPUI` (string) - -##### `PUT` /traits/{traitDbId} - -> Update the details for an existing Trait - - -###### Parameters: - -Deleted: `traitDbId` in `path` -> Id of the trait to retrieve details of. - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A Trait describes what property is being observed. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `alternativeAbbreviations` (array) - > A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `synonyms` (array) - > Other trait names - - - * Deleted property `traitDbId` (string) - > The ID which uniquely identifies a trait - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `attribute` (string) - - * Changed property `attributePUI` (string) - - * Changed property `entity` (string) - - * Changed property `entityPUI` (string) - - * Changed property `mainAbbreviation` (string) - - * Changed property `status` (string) - - * Changed property `traitClass` (string) - - * Changed property `traitDescription` (string) - - * Changed property `traitName` (string) - - * Changed property `traitPUI` (string) - -##### `GET` /variables - -> Get a filtered list of ObservationVariable - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `studyDbId` in `query` -> **Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 ->
The unique ID of a studies to filter on - - -Added: `dataType` in `query` -> List of scale data types to filter search results - - -Added: `traitAttribute` in `query` -> A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" - - -Added: `traitAttributePUI` in `query` -> The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI ->
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" - - -Added: `traitEntity` in `query` -> A trait can be decomposed as "Trait" = "Entity" + "Attribute", the entity is the part of the plant that the trait refers to e.g., for "grain colour", entity = "grain" - - -Added: `traitEntityPUI` in `query` -> The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI ->
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the entity is the part of the plant that the trait refers to e.g., for "grain colour", entity = "grain" - - -Changed: `observationVariableDbId` in `query` -> The DbIds of Variables to search for - - -Changed: `observationVariableName` in `query` -> The names of Variables to search for - - -Changed: `observationVariablePUI` in `query` -> The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI - - -Changed: `traitClass` in `query` -> List of trait classes to filter search results - - -Changed: `methodDbId` in `query` -> List of methods to filter search results - - -Changed: `scaleDbId` in `query` -> The unique identifier for a Scale - - -Changed: `scaleName` in `query` -> Name of the scale ->
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable - - -Changed: `traitDbId` in `query` -> The unique identifier for a Trait - - -Changed: `traitName` in `query` -> The human readable name of a trait ->
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation - - -Changed: `ontologyDbId` in `query` -> List of ontology IDs to search for - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `methodDbId` (string) - - * Added property `methodName` (string) - - * Added property `methodPUI` (string) - - * Added property `ontologyReferenceDbId` (string) - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Added property `traitDbId` (string) - - * Added property `traitName` (string) - - * Added property `traitPUI` (string) - - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `method` (object) - - * Deleted property `observationVariableDbId` (string) - > Variable unique identifier - > - > MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `scale` (object) - - * Deleted property `synonyms` (array) - > Other variable names - - - * Deleted property `trait` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `defaultValue` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `growthStage` (string) - - * Changed property `institution` (string) - - * Changed property `language` (string) - - * Changed property `observationVariableName` (string) - - * Changed property `observationVariablePUI` (string) - - * Changed property `scientist` (string) - - * Changed property `status` (string) - - * Changed property `submissionTimestamp` (string -> string) - -##### `POST` /variables - -> Create new ObservationVariable - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `methodDbId` (string) - - * Added property `methodName` (string) - - * Added property `methodPUI` (string) - - * Added property `ontologyReferenceDbId` (string) - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Added property `traitDbId` (string) - - * Added property `traitName` (string) - - * Added property `traitPUI` (string) - - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `method` (object) - - * Deleted property `observationVariableDbId` (string) - > Variable unique identifier - > - > MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `scale` (object) - - * Deleted property `synonyms` (array) - > Other variable names - - - * Deleted property `trait` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `defaultValue` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `growthStage` (string) - - * Changed property `institution` (string) - - * Changed property `language` (string) - - * Changed property `observationVariableName` (string) - - * Changed property `observationVariablePUI` (string) - - * Changed property `scientist` (string) - - * Changed property `status` (string) - - * Changed property `submissionTimestamp` (string -> string) - -##### `GET` /variables/{observationVariableDbId} - -> Get the details of a specific ObservationVariable - - -###### Parameters: - -Deleted: `observationVariableDbId` in `path` -> string id of the variable - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `methodDbId` (string) - - * Added property `methodName` (string) - - * Added property `methodPUI` (string) - - * Added property `ontologyReferenceDbId` (string) - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Added property `traitDbId` (string) - - * Added property `traitName` (string) - - * Added property `traitPUI` (string) - - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `method` (object) - - * Deleted property `observationVariableDbId` (string) - > Variable unique identifier - > - > MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `scale` (object) - - * Deleted property `synonyms` (array) - > Other variable names - - - * Deleted property `trait` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `defaultValue` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `growthStage` (string) - - * Changed property `institution` (string) - - * Changed property `language` (string) - - * Changed property `observationVariableName` (string) - - * Changed property `observationVariablePUI` (string) - - * Changed property `scientist` (string) - - * Changed property `status` (string) - - * Changed property `submissionTimestamp` (string -> string) - -##### `PUT` /variables/{observationVariableDbId} - -> Update the details for an existing ObservationVariable - - -###### Parameters: - -Deleted: `observationVariableDbId` in `path` -> string id of the variable - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `methodDbId` -- `methodName` -- `observationVariableDbId` -- `observationVariableDbId` -- `scaleDbId` -- `scaleName` -- `traitName` - -New optional properties: -- `method` -- `scale` -- `trait` - -* Added property `methodDbId` (string) - -* Added property `methodName` (string) - -* Added property `methodPUI` (string) - -* Added property `observationVariableDbId` (string) - -* Added property `ontologyReferenceDbId` (string) - -* Added property `scaleDbId` (string) - -* Added property `scaleName` (string) - -* Added property `scalePUI` (string) - -* Added property `traitDbId` (string) - -* Added property `traitName` (string) - -* Added property `traitPUI` (string) - -* Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) - - -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - -* Deleted property `method` (object) - -* Deleted property `ontologyReference` (object) - -* Deleted property `scale` (object) - -* Deleted property `synonyms` (array) - > Other variable names - - -* Deleted property `trait` (object) - -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - -* Changed property `commonCropName` (string) - -* Changed property `defaultValue` (string) - -* Changed property `documentationURL` (string -> string) - -* Changed property `growthStage` (string) - -* Changed property `institution` (string) - -* Changed property `language` (string) - -* Changed property `observationVariableName` (string) - -* Changed property `observationVariablePUI` (string) - -* Changed property `scientist` (string) - -* Changed property `status` (string) - -* Changed property `submissionTimestamp` (string -> string) - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - New optional properties: - - `method` - - `scale` - - `trait` - - * Added property `methodDbId` (string) - - * Added property `methodName` (string) - - * Added property `methodPUI` (string) - - * Added property `ontologyReferenceDbId` (string) - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Added property `traitDbId` (string) - - * Added property `traitName` (string) - - * Added property `traitPUI` (string) - - * Deleted property `contextOfUse` (array) - > Indication of how trait is routinely used. (examples: ["Trial evaluation", "Nursery evaluation"]) - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `method` (object) - - * Deleted property `observationVariableDbId` (string) - > Variable unique identifier - > - > MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `scale` (object) - - * Deleted property `synonyms` (array) - > Other variable names - - - * Deleted property `trait` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `defaultValue` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `growthStage` (string) - - * Changed property `institution` (string) - - * Changed property `language` (string) - - * Changed property `observationVariableName` (string) - - * Changed property `observationVariablePUI` (string) - - * Changed property `scientist` (string) - - * Changed property `status` (string) - - * Changed property `submissionTimestamp` (string -> string) - -##### `GET` /variants - -> Get a filtered list of Variant - - -###### Parameters: - -Added: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Added: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyDbId` in `query` -> List of study identifiers to search for - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `callSetDbId` in `query` -> **Deprecated in v2.1** Parameter unnecessary. Github issue number #474 ->
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects. - - -Added: `end` in `query` -> The end of the window (0-based, exclusive) for which overlapping variants should be returned. - - -Added: `referenceDbId` in `query` -> The unique identifier representing a genotype `Reference` - - -Added: `start` in `query` -> The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0). - - -Added: `externalReferenceID` in `query` -> **Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 ->
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter) - - -Deleted: `pageToken` in `query` -> **Deprecated in v2.1** Please use `page`. Github issue number #451 ->
Used to request a specific page of data to be returned. ->
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. - - -Changed: `variantDbId` in `query` -> A list of IDs which uniquely identify `Variants` - - -Changed: `variantSetDbId` in `query` -> A list of IDs which uniquely identify `VariantSets` - - -Changed: `referenceDbId` in `query` -> **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 ->
Only return variants on this reference. - - -Changed: `referenceSetDbId` in `query` -> The unique identifier representing a genotype `ReferenceSet` - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF. - - - * Added property `variantSetName` (string) - - * Deleted property `alternateBases` (array) - > The bases that appear instead of the reference bases. Multiple alternate alleles are possible. - - - * Deleted property `alternate_bases` (array) - > **Deprecated in v2.1** Please use `alternateBases`. Github issue number #549 - >
The bases that appear instead of the reference bases. Multiple alternate alleles are possible. - - - * Deleted property `ciend` (array) - > Similar to "cipos", but for the variant's end position (which is derived from start + svlen). - - - * Deleted property `cipos` (array) - > In the case of structural variants, start and end of the variant may not - > be known with an exact base position. "cipos" provides an interval with - > high confidence for the start position. The interval is provided by 0 or - > 2 signed integers which are added to the start position. - > Based on the use in VCF v4.2 - - - * Deleted property `externalReferences` (object) - - * Deleted property `filtersFailed` (array) - > Zero or more filters that failed for this variant. VCF column 7 "FILTER" shared across all alleles in the same VCF record. - - - * Deleted property `variantNames` (array) - > A human readable name associated with a `Variant` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `created` (string -> string) - - * Changed property `end` (integer -> integer) - - * Changed property `filtersApplied` (boolean -> boolean) - - * Changed property `filtersPassed` (boolean -> boolean) - - * Changed property `referenceBases` (string) - - * Changed property `referenceDbId` (string) - - * Changed property `referenceName` (string) - - * Changed property `referenceSetDbId` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `start` (integer -> integer) - - * Changed property `svlen` (integer -> integer) - - * Changed property `updated` (string -> string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (array -> string) - - * Changed property `variantType` (string) - -##### `GET` /variants/{variantDbId} - -> Get the details of a specific Variant - - -###### Parameters: - -Deleted: `variantDbId` in `path` -> The ID which uniquely identifies a `Variant` - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF. - - - * Added property `variantSetName` (string) - - * Deleted property `alternateBases` (array) - > The bases that appear instead of the reference bases. Multiple alternate alleles are possible. - - - * Deleted property `alternate_bases` (array) - > **Deprecated in v2.1** Please use `alternateBases`. Github issue number #549 - >
The bases that appear instead of the reference bases. Multiple alternate alleles are possible. - - - * Deleted property `ciend` (array) - > Similar to "cipos", but for the variant's end position (which is derived from start + svlen). - - - * Deleted property `cipos` (array) - > In the case of structural variants, start and end of the variant may not - > be known with an exact base position. "cipos" provides an interval with - > high confidence for the start position. The interval is provided by 0 or - > 2 signed integers which are added to the start position. - > Based on the use in VCF v4.2 - - - * Deleted property `externalReferences` (object) - - * Deleted property `filtersFailed` (array) - > Zero or more filters that failed for this variant. VCF column 7 "FILTER" shared across all alleles in the same VCF record. - - - * Deleted property `variantNames` (array) - > A human readable name associated with a `Variant` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `created` (string -> string) - - * Changed property `end` (integer -> integer) - - * Changed property `filtersApplied` (boolean -> boolean) - - * Changed property `filtersPassed` (boolean -> boolean) - - * Changed property `referenceBases` (string) - - * Changed property `referenceDbId` (string) - - * Changed property `referenceName` (string) - - * Changed property `referenceSetDbId` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `start` (integer -> integer) - - * Changed property `svlen` (integer -> integer) - - * Changed property `updated` (string -> string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (array -> string) - - * Changed property `variantType` (string) - -##### `GET` /variants/{variantDbId}/calls - -> Get a filtered list of Call - - -###### Parameters: - -Added: `callSetDbId` in `query` -> A list of IDs which uniquely identify `CallSets` within the given database server - - -Added: `variantDbId` in `query` -> A list of IDs which uniquely identify `Variant` within the given database server - - -Added: `variantSetDbId` in `query` -> A list of IDs which uniquely identify `VariantSets` within the given database server - - -Added: `expandHomozygote` in `query` -> Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - -Deleted: `variantDbId` in `path` -> The ID which uniquely identifies a `Variant` - - -Deleted: `expandHomozygotes` in `query` -> Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - -Deleted: `pageToken` in `query` -> **Deprecated in v2.1** Please use `page`. Github issue number #451 ->
Used to request a specific page of data to be returned. ->
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. - - -Changed: `unknownString` in `query` -> The string used as a representation for missing data. - - -Changed: `sepPhased` in `query` -> The string used as a separator for phased allele calls. - - -Changed: `sepUnphased` in `query` -> The string used as a separator for unphased allele calls. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Deleted property `expandHomozygotes` (boolean) - > Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - - * Deleted property `sepPhased` (string) - > The string used as a separator for phased allele calls. - - - * Deleted property `sepUnphased` (string) - > The string used as a separator for unphased allele calls. - - - * Deleted property `unknownString` (string) - > The string used as a representation for missing data. - - - * Changed property `data` (array) - - Changed items (object): - > A `Call` represents the determination of genotype with respect to a particular `Variant`. - > - > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. - - - * Deleted property `genotype` (object) - - * Deleted property `genotypeMetadata` (array) - > Genotype Metadata are additional layers of metadata associated with each genotype. - - - * Deleted property `genotype_likelihood` (array) - > **Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491 - >
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec. - - - * Deleted property `variantName` (string) - > The name of the variant this call belongs to. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `genotypeValue` (string) - - * Changed property `phaseSet` (string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (string) - - * Changed property `variantSetName` (string) - -##### `GET` /variantsets - -> Get a filtered list of VariantSet - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `referenceDbId` in `query` -> The unique identifier representing a genotype Reference - - -Added: `externalReferenceID` in `query` -> **Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 ->
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter) - - -Changed: `variantSetDbId` in `query` -> The unique identifier representing a VariantSet - - -Changed: `variantDbId` in `query` -> The unique identifier representing a Variant - - -Changed: `callSetDbId` in `query` -> The unique identifier representing a CallSet - - -Changed: `referenceSetDbId` in `query` -> The unique identifier representing a genotype ReferenceSet - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -Changed: `studyName` in `query` -> List of study names to filter search results - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A VariantSet is a collection of variants and variant calls intended to be analyzed together. - - - * Added property `analysiDbIds` (array) - - * Added property `referenceSetName` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Deleted property `analysis` (array) - > Set of Analysis descriptors for this VariantSet - - - * Deleted property `availableFormats` (array) - > When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. - >
'dataFormat' defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc) - >
'fileFormat' defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response. - - - * Deleted property `externalReferences` (object) - - * Deleted property `metadataFields` (array) - > The 'metadataFields' array indicates which types of genotyping data and metadata are available in the VariantSet. - >
When possible, these field names and abbreviations should follow the VCF standard - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetCount` (integer -> integer) - - * Changed property `referenceSetDbId` (string) - - * Changed property `studyDbId` (string) - - * Changed property `variantCount` (integer -> integer) - - * Changed property `variantSetDbId` (string) - - * Changed property `variantSetName` (string) - -##### `GET` /variantsets/{variantSetDbId} - -> Get the details of a specific VariantSet - - -###### Parameters: - -Deleted: `variantSetDbId` in `path` -> The ID of the `Variant` to be retrieved. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A VariantSet is a collection of variants and variant calls intended to be analyzed together. - - - * Added property `analysiDbIds` (array) - - * Added property `referenceSetName` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Deleted property `analysis` (array) - > Set of Analysis descriptors for this VariantSet - - - * Deleted property `availableFormats` (array) - > When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. - >
'dataFormat' defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc) - >
'fileFormat' defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response. - - - * Deleted property `externalReferences` (object) - - * Deleted property `metadataFields` (array) - > The 'metadataFields' array indicates which types of genotyping data and metadata are available in the VariantSet. - >
When possible, these field names and abbreviations should follow the VCF standard - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetCount` (integer -> integer) - - * Changed property `referenceSetDbId` (string) - - * Changed property `studyDbId` (string) - - * Changed property `variantCount` (integer -> integer) - - * Changed property `variantSetDbId` (string) - - * Changed property `variantSetName` (string) - -##### `GET` /variantsets/{variantSetDbId}/calls - -> Get a filtered list of Call - - -###### Parameters: - -Added: `callSetDbId` in `query` -> A list of IDs which uniquely identify `CallSets` within the given database server - - -Added: `variantDbId` in `query` -> A list of IDs which uniquely identify `Variant` within the given database server - - -Added: `variantSetDbId` in `query` -> A list of IDs which uniquely identify `VariantSets` within the given database server - - -Added: `expandHomozygote` in `query` -> Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - -Deleted: `variantSetDbId` in `path` -> The ID of the `VariantSet` to be retrieved. - - -Deleted: `expandHomozygotes` in `query` -> Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - -Deleted: `pageToken` in `query` -> **Deprecated in v2.1** Please use `page`. Github issue number #451 ->
Used to request a specific page of data to be returned. ->
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. - - -Changed: `unknownString` in `query` -> The string used as a representation for missing data. - - -Changed: `sepPhased` in `query` -> The string used as a separator for phased allele calls. - - -Changed: `sepUnphased` in `query` -> The string used as a separator for unphased allele calls. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Deleted property `expandHomozygotes` (boolean) - > Should homozygotes be expanded (true) or collapsed into a single occurrence (false) - - - * Deleted property `sepPhased` (string) - > The string used as a separator for phased allele calls. - - - * Deleted property `sepUnphased` (string) - > The string used as a separator for unphased allele calls. - - - * Deleted property `unknownString` (string) - > The string used as a representation for missing data. - - - * Changed property `data` (array) - - Changed items (object): - > A `Call` represents the determination of genotype with respect to a particular `Variant`. - > - > It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345. - - - * Deleted property `genotype` (object) - - * Deleted property `genotypeMetadata` (array) - > Genotype Metadata are additional layers of metadata associated with each genotype. - - - * Deleted property `genotype_likelihood` (array) - > **Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491 - >
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec. - - - * Deleted property `variantName` (string) - > The name of the variant this call belongs to. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `genotypeValue` (string) - - * Changed property `phaseSet` (string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (string) - - * Changed property `variantSetName` (string) - -##### `GET` /variantsets/{variantSetDbId}/callsets - -> Get a filtered list of CallSet - - -###### Parameters: - -Added: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Added: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -Added: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Added: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyDbId` in `query` -> List of study identifiers to search for - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `sampleDbId` in `query` -> A list of IDs which uniquely identify `Samples` within the given database server - - -Added: `sampleName` in `query` -> A list of human readable names associated with `Samples` - - -Added: `variantSetDbId` in `query` -> A list of IDs which uniquely identify `VariantSets` within the given database server - - -Added: `externalReferenceID` in `query` -> **Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 ->
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter) - - -Added: `externalReferenceId` in `query` -> An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter) - - -Added: `externalReferenceSource` in `query` -> An identifier for the source system or database of an external reference (use with `externalReferenceId` parameter) - - -Deleted: `variantSetDbId` in `path` -> The ID of the `VariantSet` to be retrieved. - - -Changed: `callSetDbId` in `query` -> A list of IDs which uniquely identify `CallSets` within the given database server - - -Changed: `callSetName` in `query` -> A list of human readable names associated with `CallSets` - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A CallSet is a collection of Calls that were generated by the same analysis of the same Sample - - - * Added property `sampleName` (string) - - * Added property `samplePUI` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Deleted property `externalReferences` (object) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `callSetDbId` (string) - - * Changed property `callSetName` (string) - - * Changed property `created` (string -> string) - - * Changed property `sampleDbId` (string) - - * Changed property `studyDbId` (string) - - * Changed property `updated` (string -> string) - - * Changed property `variantSetDbIds` (array) - -##### `GET` /variantsets/{variantSetDbId}/variants - -> Get a filtered list of Variant - - -###### Parameters: - -Added: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Added: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyDbId` in `query` -> List of study identifiers to search for - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `callSetDbId` in `query` -> **Deprecated in v2.1** Parameter unnecessary. Github issue number #474 ->
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects. - - -Added: `end` in `query` -> The end of the window (0-based, exclusive) for which overlapping variants should be returned. - - -Added: `referenceDbId` in `query` -> **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 ->
Only return variants on this reference. - - -Added: `referenceDbId` in `query` -> The unique identifier representing a genotype `Reference` - - -Added: `referenceSetDbId` in `query` -> The unique identifier representing a genotype `ReferenceSet` - - -Added: `start` in `query` -> The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0). - - -Added: `variantSetDbId` in `query` -> A list of IDs which uniquely identify `VariantSets` - - -Added: `externalReferenceID` in `query` -> **Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 ->
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter) - - -Added: `externalReferenceId` in `query` -> An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter) - - -Added: `externalReferenceSource` in `query` -> An identifier for the source system or database of an external reference (use with `externalReferenceId` parameter) - - -Deleted: `variantSetDbId` in `path` -> The ID of the `VariantSet` to be retrieved. - - -Deleted: `pageToken` in `query` -> **Deprecated in v2.1** Please use `page`. Github issue number #451 ->
Used to request a specific page of data to be returned. ->
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. - - -Changed: `variantDbId` in `query` -> A list of IDs which uniquely identify `Variants` - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF. - - - * Added property `variantSetName` (string) - - * Deleted property `alternateBases` (array) - > The bases that appear instead of the reference bases. Multiple alternate alleles are possible. - - - * Deleted property `alternate_bases` (array) - > **Deprecated in v2.1** Please use `alternateBases`. Github issue number #549 - >
The bases that appear instead of the reference bases. Multiple alternate alleles are possible. - - - * Deleted property `ciend` (array) - > Similar to "cipos", but for the variant's end position (which is derived from start + svlen). - - - * Deleted property `cipos` (array) - > In the case of structural variants, start and end of the variant may not - > be known with an exact base position. "cipos" provides an interval with - > high confidence for the start position. The interval is provided by 0 or - > 2 signed integers which are added to the start position. - > Based on the use in VCF v4.2 - - - * Deleted property `externalReferences` (object) - - * Deleted property `filtersFailed` (array) - > Zero or more filters that failed for this variant. VCF column 7 "FILTER" shared across all alleles in the same VCF record. - - - * Deleted property `variantNames` (array) - > A human readable name associated with a `Variant` - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `created` (string -> string) - - * Changed property `end` (integer -> integer) - - * Changed property `filtersApplied` (boolean -> boolean) - - * Changed property `filtersPassed` (boolean -> boolean) - - * Changed property `referenceBases` (string) - - * Changed property `referenceDbId` (string) - - * Changed property `referenceName` (string) - - * Changed property `referenceSetDbId` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `start` (integer -> integer) - - * Changed property `svlen` (integer -> integer) - - * Changed property `updated` (string -> string) - - * Changed property `variantDbId` (string) - - * Changed property `variantSetDbId` (array -> string) - - * Changed property `variantType` (string) - -##### `GET` /crosses - -> Get a filtered list of Cross - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present. - - - * Deleted property `crossAttributes` (array) - > Set of custom attributes associated with a cross - - - * Deleted property `crossDbId` (string) - > the unique identifier for a cross - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `pollinationEvents` (array) - > The list of pollination events that occurred for this cross - - - * Deleted property `pollinationTimeStamp` (string) - > **Deprecated in v2.1** Please use `pollinationEvents`. Github issue number #265 - >
The timestamp when the pollination took place - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossName` (string) - - * Changed property `crossType` (string) - > The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'. - - - * Changed property `crossingProjectDbId` (string) - - * Changed property `crossingProjectName` (string) - - * Changed property `plannedCrossDbId` (string) - - * Changed property `plannedCrossName` (string) - - * Changed property `parent1` (object) - > The identifying information gor the parent material of a cross. - - - * Added property `germplasm` (object) - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Property `accessionNumber` (string) - - * Property `acquisitionDate` (string) - - * Property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Property `biologicalStatusOfAccessionCode` (string) - > MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. - > - > 100) Wild - > 110) Natural - > 120) Semi-natural/wild - > 130) Semi-natural/sown - > 200) Weedy - > 300) Traditional cultivar/landrace - > 400) Breeding/research material - > 410) Breeders line - > 411) Synthetic population - > 412) Hybrid - > 413) Founder stock/base population - > 414) Inbred line (parent of hybrid cultivar) - > 415) Segregating population - > 416) Clonal selection - > 420) Genetic stock - > 421) Mutant (e.g. induced/insertion mutants, tilling populations) - > 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) - > 423) Other genetic stocks (e.g. mapping populations) - > 500) Advanced or improved cultivar (conventional breeding methods) - > 600) GMO (by genetic engineering) - > 999) Other (Elaborate in REMARKS field) - - - Enum values: - - * `100` - * `110` - * `120` - * `130` - * `200` - * `300` - * `400` - * `410` - * `411` - * `412` - * `413` - * `414` - * `415` - * `416` - * `420` - * `421` - * `422` - * `423` - * `500` - * `600` - * `999` - * Property `biologicalStatusOfAccessionDescription` (string) - - * Property `breedingMethodDbId` (string) - - * Property `breedingMethodName` (string) - - * Property `collection` (string) - - * Property `commonCropName` (string) - - * Property `countryOfOriginCode` (string) - - * Property `defaultDisplayName` (string) - - * Property `documentationURL` (string) - - * Property `genus` (string) - - * Property `germplasmName` (string) - - * Property `germplasmPUI` (string) - - * Property `germplasmPreprocessing` (string) - - * Property `instituteCode` (string) - - * Property `instituteName` (string) - - * Property `pedigree` (string) - - * Property `sampleDbIds` (array) - - * Property `seedSource` (string) - - * Property `seedSourceDescription` (string) - - * Property `species` (string) - - * Property `speciesAuthority` (string) - - * Property `subtaxa` (string) - - * Property `subtaxaAuthority` (string) - - * Added property `observationUnitPUI` (string) - - * Deleted property `germplasmDbId` (string) - > the unique identifier for a germplasm - - - * Deleted property `germplasmName` (string) - > the human readable name for a germplasm - - - * Changed property `observationUnitDbId` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `parentType` (string) - > The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. - - - Added enum value: - - * `CLONAL` -##### `PUT` /crosses - -> Update the details for an existing Cross - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `crossDbId` -- `crossDbId` - -* Added property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - -* Added property `crossDbId` (string) - -* Added property `crossName` (string) - -* Added property `crossType` (string) - > The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'. - - - Enum values: - - * `BIPARENTAL` - * `SELF` - * `OPEN_POLLINATED` - * `BULK` - * `BULK_SELFED` - * `BULK_OPEN_POLLINATED` - * `DOUBLE_HAPLOID` -* Added property `crossingProjectDbId` (string) - -* Added property `crossingProjectName` (string) - -* Added property `parent1` (object) - > The identifying information gor the parent material of a cross. - - - * Property `germplasm` (object) - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Property `observationUnitDbId` (string) - - * Property `observationUnitName` (string) - - * Property `observationUnitPUI` (string) - - * Property `parentType` (string) - > The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. - - - Enum values: - - * `MALE` - * `FEMALE` - * `SELF` - * `POPULATION` - * `CLONAL` -* Added property `parent2` (object) - > The identifying information gor the parent material of a cross. - - -* Added property `plannedCrossDbId` (string) - -* Added property `plannedCrossName` (string) - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present. - - - * Deleted property `crossAttributes` (array) - > Set of custom attributes associated with a cross - - - * Deleted property `crossDbId` (string) - > the unique identifier for a cross - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `pollinationEvents` (array) - > The list of pollination events that occurred for this cross - - - * Deleted property `pollinationTimeStamp` (string) - > **Deprecated in v2.1** Please use `pollinationEvents`. Github issue number #265 - >
The timestamp when the pollination took place - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossName` (string) - - * Changed property `crossType` (string) - > The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'. - - - * Changed property `crossingProjectDbId` (string) - - * Changed property `crossingProjectName` (string) - - * Changed property `plannedCrossDbId` (string) - - * Changed property `plannedCrossName` (string) - - * Changed property `parent1` (object) - > The identifying information gor the parent material of a cross. - - - * Added property `germplasm` (object) - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `observationUnitPUI` (string) - - * Deleted property `germplasmDbId` (string) - > the unique identifier for a germplasm - - - * Deleted property `germplasmName` (string) - > the human readable name for a germplasm - - - * Changed property `observationUnitDbId` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `parentType` (string) - > The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. - - - Added enum value: - - * `CLONAL` -##### `POST` /crosses - -> Create new Cross - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present. - - - * Deleted property `crossAttributes` (array) - > Set of custom attributes associated with a cross - - - * Deleted property `crossDbId` (string) - > the unique identifier for a cross - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `pollinationEvents` (array) - > The list of pollination events that occurred for this cross - - - * Deleted property `pollinationTimeStamp` (string) - > **Deprecated in v2.1** Please use `pollinationEvents`. Github issue number #265 - >
The timestamp when the pollination took place - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossName` (string) - - * Changed property `crossType` (string) - > The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'. - - - * Changed property `crossingProjectDbId` (string) - - * Changed property `crossingProjectName` (string) - - * Changed property `plannedCrossDbId` (string) - - * Changed property `plannedCrossName` (string) - - * Changed property `parent1` (object) - > The identifying information gor the parent material of a cross. - - - * Added property `germplasm` (object) - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `observationUnitPUI` (string) - - * Deleted property `germplasmDbId` (string) - > the unique identifier for a germplasm - - - * Deleted property `germplasmName` (string) - > the human readable name for a germplasm - - - * Changed property `observationUnitDbId` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `parentType` (string) - > The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. - - - Added enum value: - - * `CLONAL` -##### `GET` /plannedcrosses - -> Get a filtered list of PlannedCross - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossType` (string) - > The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'. - - - * Changed property `crossingProjectDbId` (string) - - * Changed property `crossingProjectName` (string) - - * Changed property `plannedCrossDbId` (string) - - * Changed property `plannedCrossName` (string) - - * Changed property `status` (string) - > The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED'). - - - * Changed property `parent1` (object) - > The identifying information gor the parent material of a cross. - - - * Added property `germplasm` (object) - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `observationUnitPUI` (string) - - * Deleted property `germplasmDbId` (string) - > the unique identifier for a germplasm - - - * Deleted property `germplasmName` (string) - > the human readable name for a germplasm - - - * Changed property `observationUnitDbId` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `parentType` (string) - > The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. - - - Added enum value: - - * `CLONAL` -##### `PUT` /plannedcrosses - -> Update the details for an existing PlannedCross - - -###### Request: - -Changed content type : `application/json` - -New required properties: -- `plannedCrossDbId` - -* Added property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - -* Added property `crossType` (string) - > The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'. - - -* Added property `crossingProjectDbId` (string) - -* Added property `crossingProjectName` (string) - -* Added property `parent1` (object) - > The identifying information gor the parent material of a cross. - - -* Added property `parent2` (object) - > The identifying information gor the parent material of a cross. - - -* Added property `plannedCrossDbId` (string) - -* Added property `plannedCrossName` (string) - -* Added property `status` (string) - > The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED'). - - - Enum values: - - * `TODO` - * `DONE` - * `SKIPPED` -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossType` (string) - > The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'. - - - * Changed property `crossingProjectDbId` (string) - - * Changed property `crossingProjectName` (string) - - * Changed property `plannedCrossDbId` (string) - - * Changed property `plannedCrossName` (string) - - * Changed property `status` (string) - > The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED'). - - - * Changed property `parent1` (object) - > The identifying information gor the parent material of a cross. - - - * Added property `germplasm` (object) - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `observationUnitPUI` (string) - - * Deleted property `germplasmDbId` (string) - > the unique identifier for a germplasm - - - * Deleted property `germplasmName` (string) - > the human readable name for a germplasm - - - * Changed property `observationUnitDbId` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `parentType` (string) - > The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. - - - Added enum value: - - * `CLONAL` -##### `POST` /plannedcrosses - -> Create new PlannedCross - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field. - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `crossType` (string) - > The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'. - - - * Changed property `crossingProjectDbId` (string) - - * Changed property `crossingProjectName` (string) - - * Changed property `plannedCrossDbId` (string) - - * Changed property `plannedCrossName` (string) - - * Changed property `status` (string) - > The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED'). - - - * Changed property `parent1` (object) - > The identifying information gor the parent material of a cross. - - - * Added property `germplasm` (object) - > The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy. - - - * Added property `observationUnitPUI` (string) - - * Deleted property `germplasmDbId` (string) - > the unique identifier for a germplasm - - - * Deleted property `germplasmName` (string) - > the human readable name for a germplasm - - - * Changed property `observationUnitDbId` (string) - - * Changed property `observationUnitName` (string) - - * Changed property `parentType` (string) - > The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. - - - Added enum value: - - * `CLONAL` -##### `GET` /references - -> Get a filtered list of Reference - - -###### Parameters: - -Added: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -Added: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `externalReferenceID` in `query` -> **Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 ->
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter) - - -Changed: `referenceDbId` in `query` -> A list of IDs which uniquely identify `References` within the given database server - - -Changed: `referenceSetDbId` in `query` -> A list of IDs which uniquely identify `ReferenceSets` within the given database server - - -Changed: `accession` in `query` -> If specified, return the references for which the `accession` matches this string (case-sensitive, exact match). - - -Changed: `isDerived` in `query` -> A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases. - - -Changed: `minLength` in `query` -> The minimum length of this `References` sequence. - - -Changed: `maxLength` in `query` -> The minimum length of this `References` sequence. - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable. - - - * Added property `sourceGermplasmDbIds` (array) - - * Added property `variantDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `sourceAccessions` (array) - > All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`. - - - * Deleted property `sourceGermplasm` (array) - > All known corresponding Germplasm - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `isDerived` (boolean -> boolean) - - * Changed property `length` (integer -> integer) - - * Changed property `md5checksum` (string) - - * Changed property `referenceDbId` (string) - - * Changed property `referenceName` (string) - - * Changed property `referenceSetDbId` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `sourceDivergence` (number -> number) - - * Changed property `sourceURI` (string) - - * Changed property `species` (object) - > A pointer to an ontology used by a genomic reference - - - * Changed property `term` (string) - - * Changed property `termURI` (string) - -##### `GET` /references/{referenceDbId} - -> Get the details of a specific Reference - - -###### Parameters: - -Deleted: `referenceDbId` in `path` -> The ID of the `Reference` to be retrieved. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable. - - - * Added property `sourceGermplasmDbIds` (array) - - * Added property `variantDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `sourceAccessions` (array) - > All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`. - - - * Deleted property `sourceGermplasm` (array) - > All known corresponding Germplasm - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `isDerived` (boolean -> boolean) - - * Changed property `length` (integer -> integer) - - * Changed property `md5checksum` (string) - - * Changed property `referenceDbId` (string) - - * Changed property `referenceName` (string) - - * Changed property `referenceSetDbId` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `sourceDivergence` (number -> number) - - * Changed property `sourceURI` (string) - - * Changed property `species` (object) - > A pointer to an ontology used by a genomic reference - - - * Changed property `term` (string) - - * Changed property `termURI` (string) - -##### `GET` /referencesets - -> Get a filtered list of ReferenceSet - - -###### Parameters: - -Added: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -Added: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `studyName` in `query` -> List of study names to filter search results - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `externalReferenceID` in `query` -> **Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 ->
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter) - - -Changed: `referenceSetDbId` in `query` -> The `ReferenceSets` to search. - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data. - - - * Added property `referenceDbId` (string) - - * Added property `referenceName` (string) - - * Added property `sourceGermplasmDbIds` (array) - - * Added property `variantDbIds` (array) - - * Added property `variantSetDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `referenceSetDbId` (string) - > The unique identifier for a ReferenceSet - - - * Deleted property `sourceAccessions` (array) - > All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`. - - - * Deleted property `sourceGermplasm` (array) - > All known corresponding Germplasm - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `assemblyPUI` (string) - - * Changed property `commonCropName` (string) - - * Changed property `description` (string) - - * Changed property `isDerived` (boolean -> boolean) - - * Changed property `md5checksum` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `sourceURI` (string) - - * Changed property `species` (object) - > A pointer to an ontology used by a genomic reference - - - * Changed property `term` (string) - - * Changed property `termURI` (string) - -##### `GET` /referencesets/{referenceSetDbId} - -> Get the details of a specific ReferenceSet - - -###### Parameters: - -Deleted: `referenceSetDbId` in `path` -> The ID of the `ReferenceSet` to be retrieved. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -New response : **400 Bad Request** -New response : **401 Unauthorized** -New response : **403 Forbidden** -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data. - - - * Added property `referenceDbId` (string) - - * Added property `referenceName` (string) - - * Added property `sourceGermplasmDbIds` (array) - - * Added property `variantDbIds` (array) - - * Added property `variantSetDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `referenceSetDbId` (string) - > The unique identifier for a ReferenceSet - - - * Deleted property `sourceAccessions` (array) - > All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`. - - - * Deleted property `sourceGermplasm` (array) - > All known corresponding Germplasm - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `assemblyPUI` (string) - - * Changed property `commonCropName` (string) - - * Changed property `description` (string) - - * Changed property `isDerived` (boolean -> boolean) - - * Changed property `md5checksum` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `sourceURI` (string) - - * Changed property `species` (object) - > A pointer to an ontology used by a genomic reference - - - * Changed property `term` (string) - - * Changed property `termURI` (string) - -##### `GET` /scales - -> Get a filtered list of Scale - - -###### Parameters: - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `scaleDbId` in `query` -> The unique identifier for a scale. - - -Changed: `observationVariableDbId` in `query` -> The unique identifier for an observation variable. - - -Changed: `ontologyDbId` in `query` -> The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology -> -> Use `GET /ontologies` to find the list of available ontologies on a server. - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Scale describes the units and acceptable values for an ObservationVariable. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `scaleDbId` (string) - > Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `dataType` (string) - >

Class of the scale, entries can be

- >

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

- >

"Date" - The date class is for events expressed in a time format, See ISO 8601

- >

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

- >

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

- >

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

- >

"Ordinal" - Ordinal scales are scales composed of ordered categories

- >

"Text" - A free text is used to express the trait.

- - - * Changed property `decimalPlaces` (integer -> integer) - - * Changed property `scaleName` (string) - - * Changed property `scalePUI` (string) - - * Changed property `units` (string) - - * Changed property `validValues` (object) - > Metadata describing the acceptable values for this Scale - - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Deleted property `categories` (array) - > List of possible values with optional labels - - - * Deleted property `max` (integer) - > **Deprecated in v2.1** Please use `maximumValue`. Github issue number #450 - >
Maximum value for numerical scales. Typically used for data capture control and QC. - - - * Deleted property `min` (integer) - > **Deprecated in v2.1** Please use `minimumValue`. Github issue number #450 - >
Minimum value for numerical scales. Typically used for data capture control and QC. - - - * Changed property `maximumValue` (string) - - * Changed property `minimumValue` (string) - -##### `POST` /scales - -> Create new Scale - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Scale describes the units and acceptable values for an ObservationVariable. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `scaleDbId` (string) - > Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `dataType` (string) - >

Class of the scale, entries can be

- >

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

- >

"Date" - The date class is for events expressed in a time format, See ISO 8601

- >

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

- >

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

- >

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

- >

"Ordinal" - Ordinal scales are scales composed of ordered categories

- >

"Text" - A free text is used to express the trait.

- - - * Changed property `decimalPlaces` (integer -> integer) - - * Changed property `scaleName` (string) - - * Changed property `scalePUI` (string) - - * Changed property `units` (string) - - * Changed property `validValues` (object) - > Metadata describing the acceptable values for this Scale - - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Deleted property `categories` (array) - > List of possible values with optional labels - - - * Deleted property `max` (integer) - > **Deprecated in v2.1** Please use `maximumValue`. Github issue number #450 - >
Maximum value for numerical scales. Typically used for data capture control and QC. - - - * Deleted property `min` (integer) - > **Deprecated in v2.1** Please use `minimumValue`. Github issue number #450 - >
Minimum value for numerical scales. Typically used for data capture control and QC. - - - * Changed property `maximumValue` (string) - - * Changed property `minimumValue` (string) - -##### `GET` /scales/{scaleDbId} - - -###### Parameters: - -Deleted: `scaleDbId` in `path` -> Id of the scale to retrieve details of. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A Scale describes the units and acceptable values for an ObservationVariable. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `scaleDbId` (string) - > Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `dataType` (string) - >

Class of the scale, entries can be

- >

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

- >

"Date" - The date class is for events expressed in a time format, See ISO 8601

- >

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

- >

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

- >

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

- >

"Ordinal" - Ordinal scales are scales composed of ordered categories

- >

"Text" - A free text is used to express the trait.

- - - * Changed property `decimalPlaces` (integer -> integer) - - * Changed property `scaleName` (string) - - * Changed property `scalePUI` (string) - - * Changed property `units` (string) - - * Changed property `validValues` (object) - > Metadata describing the acceptable values for this Scale - - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Deleted property `categories` (array) - > List of possible values with optional labels - - - * Deleted property `max` (integer) - > **Deprecated in v2.1** Please use `maximumValue`. Github issue number #450 - >
Maximum value for numerical scales. Typically used for data capture control and QC. - - - * Deleted property `min` (integer) - > **Deprecated in v2.1** Please use `minimumValue`. Github issue number #450 - >
Minimum value for numerical scales. Typically used for data capture control and QC. - - - * Changed property `maximumValue` (string) - - * Changed property `minimumValue` (string) - -##### `PUT` /scales/{scaleDbId} - -> Update the details for an existing Scale - - -###### Parameters: - -Deleted: `scaleDbId` in `path` -> Id of the scale to retrieve details of. - - -###### Request: - -Changed content type : `application/json` - -###### Return Type: - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - > A Scale describes the units and acceptable values for an ObservationVariable. - >
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". - - - * Added property `ontologyReferenceDbId` (string) - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `ontologyReference` (object) - - * Deleted property `scaleDbId` (string) - > Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID. - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `dataType` (string) - >

Class of the scale, entries can be

- >

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

- >

"Date" - The date class is for events expressed in a time format, See ISO 8601

- >

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

- >

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

- >

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

- >

"Ordinal" - Ordinal scales are scales composed of ordered categories

- >

"Text" - A free text is used to express the trait.

- - - * Changed property `decimalPlaces` (integer -> integer) - - * Changed property `scaleName` (string) - - * Changed property `scalePUI` (string) - - * Changed property `units` (string) - - * Changed property `validValues` (object) - > Metadata describing the acceptable values for this Scale - - - * Added property `scaleDbId` (string) - - * Added property `scaleName` (string) - - * Added property `scalePUI` (string) - - * Deleted property `categories` (array) - > List of possible values with optional labels - - - * Deleted property `max` (integer) - > **Deprecated in v2.1** Please use `maximumValue`. Github issue number #450 - >
Maximum value for numerical scales. Typically used for data capture control and QC. - - - * Deleted property `min` (integer) - > **Deprecated in v2.1** Please use `minimumValue`. Github issue number #450 - >
Minimum value for numerical scales. Typically used for data capture control and QC. - - - * Changed property `maximumValue` (string) - - * Changed property `minimumValue` (string) - -##### `POST` /search/references - -> Submit a search request for `Reference` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable. - - - * Added property `sourceGermplasmDbIds` (array) - - * Added property `variantDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `sourceAccessions` (array) - > All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`. - - - * Deleted property `sourceGermplasm` (array) - > All known corresponding Germplasm - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `isDerived` (boolean -> boolean) - - * Changed property `length` (integer -> integer) - - * Changed property `md5checksum` (string) - - * Changed property `referenceDbId` (string) - - * Changed property `referenceName` (string) - - * Changed property `referenceSetDbId` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `sourceDivergence` (number -> number) - - * Changed property `sourceURI` (string) - - * Changed property `species` (object) - > A pointer to an ontology used by a genomic reference - - - * Changed property `term` (string) - - * Changed property `termURI` (string) - -##### `GET` /search/references/{searchResultsDbId} - -> Submit a search request for `Reference`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/reference/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable. - - - * Added property `sourceGermplasmDbIds` (array) - - * Added property `variantDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `sourceAccessions` (array) - > All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`. - - - * Deleted property `sourceGermplasm` (array) - > All known corresponding Germplasm - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `isDerived` (boolean -> boolean) - - * Changed property `length` (integer -> integer) - - * Changed property `md5checksum` (string) - - * Changed property `referenceDbId` (string) - - * Changed property `referenceName` (string) - - * Changed property `referenceSetDbId` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `sourceDivergence` (number -> number) - - * Changed property `sourceURI` (string) - - * Changed property `species` (object) - > A pointer to an ontology used by a genomic reference - - - * Changed property `term` (string) - - * Changed property `termURI` (string) - -##### `POST` /search/referencesets - -> Submit a search request for `ReferenceSet` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data. - - - * Added property `referenceDbId` (string) - - * Added property `referenceName` (string) - - * Added property `sourceGermplasmDbIds` (array) - - * Added property `variantDbIds` (array) - - * Added property `variantSetDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `referenceSetDbId` (string) - > The unique identifier for a ReferenceSet - - - * Deleted property `sourceAccessions` (array) - > All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`. - - - * Deleted property `sourceGermplasm` (array) - > All known corresponding Germplasm - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `assemblyPUI` (string) - - * Changed property `commonCropName` (string) - - * Changed property `description` (string) - - * Changed property `isDerived` (boolean -> boolean) - - * Changed property `md5checksum` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `sourceURI` (string) - - * Changed property `species` (object) - > A pointer to an ontology used by a genomic reference - - - * Changed property `term` (string) - - * Changed property `termURI` (string) - -##### `GET` /search/referencesets/{searchResultsDbId} - -> Submit a search request for `ReferenceSet`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/referenceSet/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data. - - - * Added property `referenceDbId` (string) - - * Added property `referenceName` (string) - - * Added property `sourceGermplasmDbIds` (array) - - * Added property `variantDbIds` (array) - - * Added property `variantSetDbIds` (array) - - * Deleted property `externalReferences` (object) - - * Deleted property `referenceSetDbId` (string) - > The unique identifier for a ReferenceSet - - - * Deleted property `sourceAccessions` (array) - > All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`. - - - * Deleted property `sourceGermplasm` (array) - > All known corresponding Germplasm - - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `assemblyPUI` (string) - - * Changed property `commonCropName` (string) - - * Changed property `description` (string) - - * Changed property `isDerived` (boolean -> boolean) - - * Changed property `md5checksum` (string) - - * Changed property `referenceSetName` (string) - - * Changed property `sourceURI` (string) - - * Changed property `species` (object) - > A pointer to an ontology used by a genomic reference - - - * Changed property `term` (string) - - * Changed property `termURI` (string) - -##### `POST` /search/studies - -> Submit a search request for `Study` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. - - - * Added property `contactDbIds` (array) - - * Added property `lastUpdateDbId` (string) - - * Added property `observationLevelDbIds` (array) - - * Added property `trialPUI` (string) - - * Deleted property `contacts` (array) - > List of contact entities associated with this study - - - * Deleted property `dataLinks` (array) - > List of links to extra data files associated with this study. Extra data could include notes, images, and reference data. - - - * Deleted property `environmentParameters` (array) - > Environmental parameters that were kept constant throughout the study and did not change between observation units. - > - > MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `lastUpdate` (object) - - * Deleted property `observationLevels` (array) - > Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). - - - * Deleted property `seasons` (array) - > List of seasons over which this study was performed. - - - * Deleted property `studyDbId` (string) - > The ID which uniquely identifies a study within the given database server - > - > MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. - - - * Changed property `active` (boolean) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `culturalPractices` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `endDate` (string -> string) - - * Changed property `license` (string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `observationUnitsDescription` (string) - - * Changed property `observationVariableDbIds` (array) - - * Changed property `startDate` (string -> string) - - * Changed property `studyCode` (string) - - * Changed property `studyDescription` (string) - - * Changed property `studyName` (string) - - * Changed property `studyPUI` (string) - - * Changed property `studyType` (string) - - * Changed property `trialDbId` (string) - - * Changed property `trialName` (string) - - * Changed property `experimentalDesign` (object) - > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology - - - * Added property `studyDbId` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Changed property `PUI` (string) - - * Changed property `description` (string) - - * Changed property `growthFacility` (object) - > Short description of the facility in which the study was carried out. - - - * Added property `studyDbId` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Changed property `PUI` (string) - - * Changed property `description` (string) - -##### `GET` /search/studies/{searchResultsDbId} - -> Submit a search request for `Study`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. - - - * Added property `contactDbIds` (array) - - * Added property `lastUpdateDbId` (string) - - * Added property `observationLevelDbIds` (array) - - * Added property `trialPUI` (string) - - * Deleted property `contacts` (array) - > List of contact entities associated with this study - - - * Deleted property `dataLinks` (array) - > List of links to extra data files associated with this study. Extra data could include notes, images, and reference data. - - - * Deleted property `environmentParameters` (array) - > Environmental parameters that were kept constant throughout the study and did not change between observation units. - > - > MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `lastUpdate` (object) - - * Deleted property `observationLevels` (array) - > Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). - - - * Deleted property `seasons` (array) - > List of seasons over which this study was performed. - - - * Deleted property `studyDbId` (string) - > The ID which uniquely identifies a study within the given database server - > - > MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. - - - * Changed property `active` (boolean) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `culturalPractices` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `endDate` (string -> string) - - * Changed property `license` (string) - - * Changed property `locationDbId` (string) - - * Changed property `locationName` (string) - - * Changed property `observationUnitsDescription` (string) - - * Changed property `observationVariableDbIds` (array) - - * Changed property `startDate` (string -> string) - - * Changed property `studyCode` (string) - - * Changed property `studyDescription` (string) - - * Changed property `studyName` (string) - - * Changed property `studyPUI` (string) - - * Changed property `studyType` (string) - - * Changed property `trialDbId` (string) - - * Changed property `trialName` (string) - - * Changed property `experimentalDesign` (object) - > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology - - - * Added property `studyDbId` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Changed property `PUI` (string) - - * Changed property `description` (string) - - * Changed property `growthFacility` (object) - > Short description of the facility in which the study was carried out. - - - * Added property `studyDbId` (string) - - * Added property `studyName` (string) - - * Added property `studyPUI` (string) - - * Changed property `PUI` (string) - - * Changed property `description` (string) - -##### `POST` /search/trials - -> Submit a search request for `Trial` - - -###### Parameters: - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} +##### `POST` /search/plates ###### Request: -Deleted content type : `application/json` - -###### Return Type: - -Changed response : **202 Accepted** -> Accepted - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. - - - * Added property `studyDbIds` (array) - - * Deleted property `datasetAuthorships` (array) - > License and citation information for the data in this trial - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `publications` (array) - > MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended. - - - * Deleted property `trialDbId` (string) - > The ID which uniquely identifies a trial - > - > MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. - - - * Changed property `active` (boolean) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `endDate` (string -> string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `startDate` (string -> string) - - * Changed property `trialDescription` (string) - - * Changed property `trialName` (string) - - * Changed property `trialPUI` (string) - - * Changed property `contacts` (array) - - Changed items (object): - > A persons contact information - - - * Changed property `contactDbId` (string) - - * Changed property `email` (string) - - * Changed property `instituteName` (string) - - * Changed property `name` (string) - - * Changed property `orcid` (string) - - * Changed property `type` (string) - -##### `GET` /search/trials/{searchResultsDbId} - -> Submit a search request for `Trial`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. - - -###### Parameters: - -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results - - -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - - -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. - - -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Return Type: - -Deleted response : **202 Accepted** -> Accepted - -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. - - - * Added property `studyDbIds` (array) - - * Deleted property `datasetAuthorships` (array) - > License and citation information for the data in this trial - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `publications` (array) - > MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended. - - - * Deleted property `trialDbId` (string) - > The ID which uniquely identifies a trial - > - > MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. - - - * Changed property `active` (boolean) - - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) - - * Changed property `commonCropName` (string) - - * Changed property `documentationURL` (string -> string) - - * Changed property `endDate` (string -> string) - - * Changed property `programDbId` (string) - - * Changed property `programName` (string) - - * Changed property `startDate` (string -> string) - - * Changed property `trialDescription` (string) - - * Changed property `trialName` (string) - - * Changed property `trialPUI` (string) - - * Changed property `contacts` (array) - - Changed items (object): - > A persons contact information - - - * Changed property `contactDbId` (string) - - * Changed property `email` (string) - - * Changed property `instituteName` (string) - - * Changed property `name` (string) - - * Changed property `orcid` (string) - - * Changed property `type` (string) - -##### `GET` /studies - -> Get a filtered list of Study - - -###### Parameters: - -Added: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for - - -Added: `locationName` in `query` -> A human readable names to search for - - -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Added: `trialName` in `query` -> The human readable name of a trial to search for - - -Added: `observationVariableName` in `query` -> The names of Variables to search for - - -Added: `observationVariablePUI` in `query` -> The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI - - -Added: `actife` in `query` -> A flag to indicate if a Study is currently active and ongoing - - -Deleted: `active` in `query` -> A flag to indicate if a Study is currently active and ongoing - - -Deleted: `sortBy` in `query` -> Name of the field to sort by. - - -Deleted: `sortOrder` in `query` -> Sort order direction. Ascending/Descending. - - -Changed: `studyType` in `query` -> The type of study being performed. ex. "Yield Trial", etc - - -Changed: `locationDbId` in `query` -> The location ids to search for - - -Changed: `seasonDbId` in `query` -> The ID which uniquely identifies a season - - -Changed: `studyCode` in `query` -> A short human readable code for a study - - -Changed: `studyPUI` in `query` -> Permanent unique identifier associated with study data. For example, a URI or DOI - - -Changed: `observationVariableDbId` in `query` -> The DbIds of Variables to search for - - -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. - - -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. - - -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for - - -Changed: `studyDbId` in `query` -> List of study identifiers to search for - - -Changed: `studyName` in `query` -> List of study names to filter search results - - -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for - - -###### Return Type: - -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (object): - > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. - - - * Added property `contactDbIds` (array) - - * Added property `lastUpdateDbId` (string) - - * Added property `observationLevelDbIds` (array) - - * Added property `trialPUI` (string) - - * Deleted property `contacts` (array) - > List of contact entities associated with this study - - - * Deleted property `dataLinks` (array) - > List of links to extra data files associated with this study. Extra data could include notes, images, and reference data. - - - * Deleted property `environmentParameters` (array) - > Environmental parameters that were kept constant throughout the study and did not change between observation units. - > - > MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). - - - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - - - * Deleted property `lastUpdate` (object) - - * Deleted property `observationLevels` (array) - > Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). - - - * Deleted property `seasons` (array) - > List of seasons over which this study was performed. - +* Changed content type : `application/json` - * Deleted property `studyDbId` (string) - > The ID which uniquely identifies a study within the given database server - > - > MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + * Changed property `germplasmDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `active` (boolean) + * Changed property `observationUnitDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `plateBarcodes` (array): + - Nullable changed: `true` -> `null` + * Changed property `plateDbIds` (array): + - Nullable changed: `true` -> `null` - * Added property `additionalProperties` (string) + * Changed property `plateNames` (array): + - Nullable changed: `true` -> `null` - * Changed property `commonCropName` (string) + * Changed property `sampleDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `culturalPractices` (string) + * Changed property `sampleGroupDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `documentationURL` (string -> string) + * Changed property `sampleNames` (array): + - Nullable changed: `true` -> `null` - * Changed property `endDate` (string -> string) +##### `GET` /search/plates/{searchResultsDbId} - * Changed property `license` (string) - * Changed property `locationDbId` (string) +###### Return Type: - * Changed property `locationName` (string) +Deleted response : **202** - * Changed property `observationUnitsDescription` (string) +Deleted response : **404** - * Changed property `observationVariableDbIds` (array) +##### `POST` /search/programs - * Changed property `startDate` (string -> string) - * Changed property `studyCode` (string) +###### Request: - * Changed property `studyDescription` (string) +* Changed content type : `application/json` - * Changed property `studyName` (string) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `studyPUI` (string) + * Changed property `abbreviations` (array): + - Nullable changed: `true` -> `null` - * Changed property `studyType` (string) + * Changed property `leadPersonDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `trialDbId` (string) + * Changed property `leadPersonNames` (array): + - Nullable changed: `true` -> `null` - * Changed property `trialName` (string) + * Changed property `objectives` (array): + - Nullable changed: `true` -> `null` - * Changed property `experimentalDesign` (object) - > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + * Changed property `programTypes` (array): + - Nullable changed: `true` -> `null` +##### `GET` /search/programs/{searchResultsDbId} - * Added property `studyDbId` (string) - * Added property `studyName` (string) +###### Return Type: - * Added property `studyPUI` (string) +Deleted response : **202** - * Changed property `PUI` (string) +Deleted response : **404** - * Changed property `description` (string) +##### `POST` /search/referencesets - * Changed property `growthFacility` (object) - > Short description of the facility in which the study was carried out. +###### Request: - * Added property `studyDbId` (string) +* Changed content type : `application/json` - * Added property `studyName` (string) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Added property `studyPUI` (string) + * Changed property `accessions` (array): + - Nullable changed: `true` -> `null` - * Changed property `PUI` (string) + * Changed property `assemblyPUIs` (array): + - Nullable changed: `true` -> `null` - * Changed property `description` (string) + * Changed property `md5checksums` (array): + - Nullable changed: `true` -> `null` -##### `POST` /studies + * Changed property `referenceSetDbIds` (array): + - Nullable changed: `true` -> `null` -> Create new Study +##### `GET` /search/referencesets/{searchResultsDbId} -###### Request: +###### Return Type: -Changed content type : `application/json` +Deleted response : **202** -###### Return Type: +##### `POST` /search/samples -Changed response : **200 OK** -> OK +###### Request: * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + * Changed property `germplasmDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `result` (object) - - * Changed property `data` (array) + * Changed property `observationUnitDbIds` (array): + - Nullable changed: `true` -> `null` - Changed items (object): - > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. + * Changed property `plateDbIds` (array): + - Nullable changed: `true` -> `null` + * Changed property `plateNames` (array): + - Nullable changed: `true` -> `null` - * Added property `contactDbIds` (array) + * Changed property `sampleDbIds` (array): + - Nullable changed: `true` -> `null` - * Added property `lastUpdateDbId` (string) + * Changed property `sampleGroupDbIds` (array): + - Nullable changed: `true` -> `null` - * Added property `observationLevelDbIds` (array) + * Changed property `sampleNames` (array): + - Nullable changed: `true` -> `null` - * Added property `trialPUI` (string) +##### `GET` /search/samples/{searchResultsDbId} - * Deleted property `contacts` (array) - > List of contact entities associated with this study +###### Return Type: - * Deleted property `dataLinks` (array) - > List of links to extra data files associated with this study. Extra data could include notes, images, and reference data. +Deleted response : **202** +Deleted response : **404** - * Deleted property `environmentParameters` (array) - > Environmental parameters that were kept constant throughout the study and did not change between observation units. - > - > MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). +##### `POST` /search/studies - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. +###### Request: +* Changed content type : `application/json` - * Deleted property `lastUpdate` (object) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Deleted property `observationLevels` (array) - > Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). + * Changed property `active` (boolean): + - Nullable changed: `true` -> `null` + * Changed property `seasonDbIds` (array): + - Nullable changed: `true` -> `null` - * Deleted property `seasons` (array) - > List of seasons over which this study was performed. + * Changed property `sortBy` (string): + - Nullable changed: `true` -> `null` + - Removed enum values: [germplasmDbId, observationVariableDbId] + * Changed property `sortOrder` (string): + - Nullable changed: `true` -> `null` + - Added enum values: [asc, desc] - * Deleted property `studyDbId` (string) - > The ID which uniquely identifies a study within the given database server - > - > MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + * Changed property `studyCodes` (array): + - Nullable changed: `true` -> `null` + * Changed property `studyPUIs` (array): + - Nullable changed: `true` -> `null` - * Changed property `active` (boolean) + * Changed property `studyTypes` (array): + - Nullable changed: `true` -> `null` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +##### `GET` /search/studies/{searchResultsDbId} - * Added property `additionalProperties` (string) +###### Return Type: - * Changed property `commonCropName` (string) +Deleted response : **202** - * Changed property `culturalPractices` (string) +Deleted response : **404** - * Changed property `documentationURL` (string -> string) +##### `POST` /search/trials - * Changed property `endDate` (string -> string) - * Changed property `license` (string) +###### Request: - * Changed property `locationDbId` (string) +* Changed content type : `application/json` - * Changed property `locationName` (string) + New properties: `observationVariablePUIs`, `observationVariableNames`, `observationVariableDbIds`, `sortOrder`, `sortBy` - * Changed property `observationUnitsDescription` (string) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `observationVariableDbIds` (array) +##### `GET` /search/trials/{searchResultsDbId} - * Changed property `startDate` (string -> string) - * Changed property `studyCode` (string) +###### Return Type: - * Changed property `studyDescription` (string) +Deleted response : **202** - * Changed property `studyName` (string) +Deleted response : **404** - * Changed property `studyPUI` (string) +##### `POST` /search/variables - * Changed property `studyType` (string) - * Changed property `trialDbId` (string) +###### Request: - * Changed property `trialName` (string) +* Changed content type : `application/json` - * Changed property `experimentalDesign` (object) - > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + * Changed property `studyDbId` (array): + - Deprecated status changed - * Added property `studyDbId` (string) +##### `GET` /search/variables/{searchResultsDbId} - * Added property `studyName` (string) - * Added property `studyPUI` (string) +###### Return Type: - * Changed property `PUI` (string) +Deleted response : **202** - * Changed property `description` (string) +Deleted response : **404** - * Changed property `growthFacility` (object) - > Short description of the facility in which the study was carried out. +##### `GET` /seasons - * Added property `studyDbId` (string) +###### Parameters: - * Added property `studyName` (string) +Changed: `year` in `query`: + - Type changed: `integer` -> `string` - * Added property `studyPUI` (string) +##### `GET` /traits - * Changed property `PUI` (string) - * Changed property `description` (string) +###### Parameters: -##### `GET` /studies/{studyDbId} +Deleted: `externalReferenceID` in `query` -> Get the details of a specific Study +##### `GET` /attributevalues ###### Parameters: -Deleted: `studyDbId` in `path` -> Identifier of the study. Usually a number, could be alphanumeric. - +Deleted: `externalReferenceID` in `query` -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} +##### `POST` /attributevalues -###### Return Type: +###### Request: -Deleted response : **404 Not Found** -> Not Found +* Changed content type : `application/json` -Changed response : **200 OK** -> OK + Changed items (array): + New properties: `attributePUI`, `germplasmPUI` -* Changed content type : `application/json` + * Changed property `attributeDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + * Changed property `attributeName` (string): + - Nullable changed: `true` -> `null` + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `result` (object) - > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array) - * Added property `contactDbIds` (array) + Changed items (array): - * Added property `lastUpdateDbId` (string) + Deleted properties: `referenceID` - * Added property `observationLevelDbIds` (array) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Added property `trialPUI` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Deleted property `contacts` (array) - > List of contact entities associated with this study +##### `PUT` /attributevalues/{attributeValueDbId} - * Deleted property `dataLinks` (array) - > List of links to extra data files associated with this study. Extra data could include notes, images, and reference data. +###### Request: +* Changed content type : `application/json` - * Deleted property `environmentParameters` (array) - > Environmental parameters that were kept constant throughout the study and did not change between observation units. - > - > MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). + New properties: `attributePUI`, `germplasmPUI` + * Changed property `attributeDbId` (string): + - Nullable changed: `true` -> `null` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `attributeName` (string): + - Nullable changed: `true` -> `null` + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` - * Deleted property `lastUpdate` (object) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` - * Deleted property `observationLevels` (array) - > Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). + * Changed property `externalReferences` (array) + Changed items (array): - * Deleted property `seasons` (array) - > List of seasons over which this study was performed. + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Deleted property `studyDbId` (string) - > The ID which uniquely identifies a study within the given database server - > - > MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` +##### `GET` /calls - * Changed property `active` (boolean) - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +###### Return Type: +Changed response : **200** - * Added property `additionalProperties` (string) +* Changed content type : `application/json` - * Changed property `commonCropName` (string) + * Changed property `result` (object) - * Changed property `culturalPractices` (string) + Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` - * Changed property `documentationURL` (string -> string) + * Changed property `data` (array) - * Changed property `endDate` (string -> string) + Changed items (array): - * Changed property `license` (string) + Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - * Changed property `locationDbId` (string) + * Changed property `genotypeValue` (string): + - Nullable changed: `null` -> `true` - * Changed property `locationName` (string) + * Changed property `phaseSet` (string): + - Nullable changed: `null` -> `true` - * Changed property `observationUnitsDescription` (string) + * Changed property `genotypeMetadata` (array): + - Nullable changed: `null` -> `true` - * Changed property `observationVariableDbIds` (array) + Changed items (array): - * Changed property `startDate` (string -> string) + * Changed property `dataType` (string): + - Nullable changed: `null` -> `true` - * Changed property `studyCode` (string) + * Changed property `fieldAbbreviation` (string): + - Nullable changed: `null` -> `true` - * Changed property `studyDescription` (string) + * Changed property `fieldName` (string): + - Nullable changed: `null` -> `true` - * Changed property `studyName` (string) + * Changed property `fieldValue` (string): + - Nullable changed: `null` -> `true` - * Changed property `studyPUI` (string) +##### `GET` /callsets - * Changed property `studyType` (string) - * Changed property `trialDbId` (string) +###### Return Type: - * Changed property `trialName` (string) +Changed response : **200** - * Changed property `experimentalDesign` (object) - > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology +* Changed content type : `application/json` + * Changed property `result` (object) - * Added property `studyDbId` (string) + * Changed property `data` (array) - * Added property `studyName` (string) + Changed items (array): - * Added property `studyPUI` (string) + New properties: `sampleName`, `samplePUI`, `studyName`, `studyPUI` - * Changed property `PUI` (string) + Deleted properties: `variantSetDbIds` - * Changed property `description` (string) + * Changed property `sampleDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `growthFacility` (object) - > Short description of the facility in which the study was carried out. + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Added property `studyDbId` (string) + Changed items (array): - * Added property `studyName` (string) + Deleted properties: `referenceID` - * Added property `studyPUI` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `PUI` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `description` (string) +##### `GET` /callsets/{callSetDbId} -##### `PUT` /studies/{studyDbId} -> Update the details for an existing Study +###### Return Type: +Changed response : **200** -###### Parameters: +* Changed content type : `application/json` -Deleted: `studyDbId` in `path` -> Identifier of the study. Usually a number, could be alphanumeric. + * Changed property `result` (object) + New properties: `sampleName`, `samplePUI`, `studyName`, `studyPUI` -###### Request: + Deleted properties: `variantSetDbIds` -Changed content type : `application/json` + * Changed property `sampleDbId` (string): + - Nullable changed: `true` -> `null` -New required properties: -- `studyDbId` -- `studyDbId` + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` -* Added property `contactDbIds` (array) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` -* Added property `lastUpdateDbId` (string) + Changed items (array): -* Added property `observationLevelDbIds` (array) + Deleted properties: `referenceID` -* Added property `studyDbId` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -* Added property `trialPUI` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -* Deleted property `contacts` (array) - > List of contact entities associated with this study +##### `GET` /callsets/{callSetDbId}/calls -* Deleted property `dataLinks` (array) - > List of links to extra data files associated with this study. Extra data could include notes, images, and reference data. +###### Return Type: +Changed response : **200** -* Deleted property `environmentParameters` (array) - > Environmental parameters that were kept constant throughout the study and did not change between observation units. - > - > MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). +* Changed content type : `application/json` + * Changed property `result` (object) -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` + * Changed property `data` (array) -* Deleted property `lastUpdate` (object) + Changed items (array): -* Deleted property `observationLevels` (array) - > Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). + Deleted properties: `genotype`, `genotype_likelihood`, `variantName` + * Changed property `genotypeValue` (string): + - Nullable changed: `null` -> `true` -* Deleted property `seasons` (array) - > List of seasons over which this study was performed. + * Changed property `phaseSet` (string): + - Nullable changed: `null` -> `true` + * Changed property `genotypeMetadata` (array): + - Nullable changed: `null` -> `true` -* Changed property `active` (boolean) + Changed items (array): -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `dataType` (string): + - Nullable changed: `null` -> `true` + * Changed property `fieldAbbreviation` (string): + - Nullable changed: `null` -> `true` - * Added property `additionalProperties` (string) + * Changed property `fieldName` (string): + - Nullable changed: `null` -> `true` -* Changed property `commonCropName` (string) + * Changed property `fieldValue` (string): + - Nullable changed: `null` -> `true` -* Changed property `culturalPractices` (string) +##### `GET` /crosses -* Changed property `documentationURL` (string -> string) -* Changed property `endDate` (string -> string) +###### Parameters: -* Changed property `license` (string) +Deleted: `externalReferenceID` in `query` -* Changed property `locationDbId` (string) +##### `POST` /crosses -* Changed property `locationName` (string) -* Changed property `observationUnitsDescription` (string) +###### Request: -* Changed property `observationVariableDbIds` (array) +* Changed content type : `application/json` -* Changed property `startDate` (string -> string) + Changed items (array): -* Changed property `studyCode` (string) + Deleted properties: `pollinationTimeStamp` -* Changed property `studyDescription` (string) + * Changed property `crossType` (string): + - Nullable changed: `true` -> `null` -* Changed property `studyName` (string) + * Changed property `crossingProjectDbId` (string): + - Nullable changed: `true` -> `null` -* Changed property `studyPUI` (string) + * Changed property `crossingProjectName` (string): + - Nullable changed: `true` -> `null` -* Changed property `studyType` (string) + * Changed property `plannedCrossDbId` (string): + - Nullable changed: `true` -> `null` -* Changed property `trialDbId` (string) + * Changed property `plannedCrossName` (string): + - Nullable changed: `true` -> `null` -* Changed property `trialName` (string) + * Changed property `crossAttributes` (array) -* Changed property `experimentalDesign` (object) - > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + Changed items (array): + New properties: `crossDbId`, `crossName` - * Added property `studyDbId` (string) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Added property `studyName` (string) + Changed items (array): - * Added property `studyPUI` (string) + Deleted properties: `referenceID` - * Changed property `PUI` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `description` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -* Changed property `growthFacility` (object) - > Short description of the facility in which the study was carried out. + * Changed property `parent1` (object): + - Nullable changed: `true` -> `null` + New properties: `germplasmPUI`, `observationUnitPUI` - * Added property `studyDbId` (string) + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `studyName` (string) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` - * Added property `studyPUI` (string) + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `PUI` (string) + * Changed property `observationUnitName` (string): + - Nullable changed: `true` -> `null` - * Changed property `description` (string) + * Changed property `parentType` (string): + - Added enum values: [CLONAL] -###### Return Type: + * Changed property `pollinationEvents` (array) -Deleted response : **404 Not Found** -> Not Found + Changed items (array): -Changed response : **200 OK** -> OK + New properties: `crossDbId`, `crossName` +##### `GET` /crossingprojects -* Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. +###### Parameters: +Deleted: `externalReferenceID` in `query` - * Changed property `result` (object) - > A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. +##### `POST` /crossingprojects - * Added property `contactDbIds` (array) +###### Request: - * Added property `lastUpdateDbId` (string) +* Changed content type : `application/json` - * Added property `observationLevelDbIds` (array) + Changed items (array): - * Added property `trialPUI` (string) + * Changed property `programDbId` (string): + - Nullable changed: `true` -> `null` - * Deleted property `contacts` (array) - > List of contact entities associated with this study + * Changed property `programName` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array) - * Deleted property `dataLinks` (array) - > List of links to extra data files associated with this study. Extra data could include notes, images, and reference data. + Changed items (array): + Deleted properties: `referenceID` - * Deleted property `environmentParameters` (array) - > Environmental parameters that were kept constant throughout the study and did not change between observation units. - > - > MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `potentialParents` (array) + Changed items (array): - * Deleted property `lastUpdate` (object) + New properties: `germplasmPUI`, `observationUnitPUI` - * Deleted property `observationLevels` (array) - > Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` - * Deleted property `seasons` (array) - > List of seasons over which this study was performed. + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `observationUnitName` (string): + - Nullable changed: `true` -> `null` - * Deleted property `studyDbId` (string) - > The ID which uniquely identifies a study within the given database server - > - > MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + * Changed property `parentType` (string): + - Added enum values: [CLONAL] +##### `PUT` /crossingprojects/{crossingProjectDbId} - * Changed property `active` (boolean) - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +###### Request: +* Changed content type : `application/json` - * Added property `additionalProperties` (string) + * Changed property `programDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `commonCropName` (string) + * Changed property `programName` (string): + - Nullable changed: `true` -> `null` - * Changed property `culturalPractices` (string) + * Changed property `externalReferences` (array) - * Changed property `documentationURL` (string -> string) + Changed items (array): - * Changed property `endDate` (string -> string) + Deleted properties: `referenceID` - * Changed property `license` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `locationDbId` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `locationName` (string) + * Changed property `potentialParents` (array) - * Changed property `observationUnitsDescription` (string) + Changed items (array): - * Changed property `observationVariableDbIds` (array) + New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `startDate` (string -> string) + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `studyCode` (string) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` - * Changed property `studyDescription` (string) + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `studyName` (string) + * Changed property `observationUnitName` (string): + - Nullable changed: `true` -> `null` - * Changed property `studyPUI` (string) + * Changed property `parentType` (string): + - Added enum values: [CLONAL] - * Changed property `studyType` (string) +##### `GET` /events - * Changed property `trialDbId` (string) - * Changed property `trialName` (string) +###### Return Type: - * Changed property `experimentalDesign` (object) - > The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology +Changed response : **200** +* Changed content type : `application/json` - * Added property `studyDbId` (string) + * Changed property `result` (object) - * Added property `studyName` (string) + * Changed property `data` (array) - * Added property `studyPUI` (string) + Changed items (array): - * Changed property `PUI` (string) + New properties: `studyPUI` - * Changed property `description` (string) + Deleted properties: `date`, `observationUnitDbIds` - * Changed property `growthFacility` (object) - > Short description of the facility in which the study was carried out. + * Changed property `eventDateRange` (object -> array): + - Type changed: `object` -> `array` + * Changed property `eventType` (string): + - Nullable changed: `null` -> `true` - * Added property `studyDbId` (string) + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `studyName` (string) + * Changed property `studyName` (string): + - Nullable changed: `true` -> `null` - * Added property `studyPUI` (string) + * Changed property `eventParameters` (array) - * Changed property `PUI` (string) + Changed items (array): - * Changed property `description` (string) + New properties: `eventDbId` -##### `GET` /trials + Deleted properties: `key`, `rdfValue` -> Get a filtered list of Trial +##### `GET` /germplasm ###### Parameters: -Added: `locationName` in `query` -> A human readable names to search for +Deleted: `externalReferenceID` in `query` +##### `POST` /germplasm -Added: `observationVariableDbId` in `query` -> The DbIds of Variables to search for +###### Request: -Added: `observationVariableName` in `query` -> The names of Variables to search for +* Changed content type : `application/json` + Changed items (array): -Added: `observationVariablePUI` in `query` -> The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI + New properties: `sampleDbIds` + * Changed property `breedingMethodDbId` (string): + - Nullable changed: `true` -> `null` -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. + * Changed property `breedingMethodName` (string): + - Nullable changed: `true` -> `null` + * Changed property `donors` (array) -Added: `studyName` in `query` -> List of study names to filter search results + Changed items (array): + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` -Added: `actife` in `query` -> A flag to indicate if a Trial is currently active and ongoing + * Changed property `externalReferences` (array) + Changed items (array): -Deleted: `active` in `query` -> A flag to indicate if a Trial is currently active and ongoing + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -Deleted: `sortBy` in `query` -> Sort order. Name of the field to sort by. + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` + * Changed property `germplasmOrigin` (array) -Deleted: `sortOrder` in `query` -> Sort order direction: asc/desc + Changed items (array): + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` -Changed: `contactDbId` in `query` -> List of contact entities associated with this trial + * Changed property `coordinates` (object -> array): + - Type changed: `object` -> `array` + * Changed property `storageTypes` (array) -Changed: `locationDbId` in `query` -> The location ids to search for + Changed items (array): + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` -Changed: `searchDateRangeStart` in `query` -> The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`. -> -> Return a Trial entity if any of the following cases are true -> -> - `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null -> -> - `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate` -> -> - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null -> -> - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate` + * Changed property `synonyms` (array) + Changed items (array): -Changed: `searchDateRangeEnd` in `query` -> The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`. -> -> Return a Trial entity if any of the following cases are true -> -> - `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null -> -> - `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate` -> -> - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null -> -> - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate` + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + * Changed property `taxonIds` (array) -Changed: `trialPUI` in `query` -> A permanent identifier for a trial. Could be DOI or other URI formatted identifier. + Changed items (array): + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. +##### `PUT` /germplasm/{germplasmDbId} -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. +###### Request: +* Changed content type : `application/json` -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for + New properties: `sampleDbIds` + * Changed property `breedingMethodDbId` (string): + - Nullable changed: `true` -> `null` -Changed: `trialName` in `query` -> The human readable name of a trial to search for + * Changed property `breedingMethodName` (string): + - Nullable changed: `true` -> `null` + * Changed property `donors` (array) -Changed: `studyDbId` in `query` -> List of study identifiers to search for + Changed items (array): + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` -###### Return Type: + * Changed property `externalReferences` (array) -Changed response : **200 OK** -> OK + Changed items (array): + Deleted properties: `referenceID` -* Changed content type : `application/json` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` + * Changed property `germplasmOrigin` (array) - * Changed property `result` (object) + Changed items (array): - * Changed property `data` (array) + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - Changed items (object): - > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. + * Changed property `coordinates` (object -> array): + - Type changed: `object` -> `array` + * Changed property `storageTypes` (array) - * Added property `studyDbIds` (array) + Changed items (array): - * Deleted property `datasetAuthorships` (array) - > License and citation information for the data in this trial + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + * Changed property `synonyms` (array) - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + Changed items (array): + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - * Deleted property `publications` (array) - > MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended. + * Changed property `taxonIds` (array) + Changed items (array): - * Deleted property `trialDbId` (string) - > The ID which uniquely identifies a trial - > - > MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` +##### `GET` /germplasm/{germplasmDbId}/mcpd - * Changed property `active` (boolean) - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +###### Return Type: +Changed response : **200** - * Added property `additionalProperties` (string) +* Changed content type : `application/json` - * Changed property `commonCropName` (string) + * Changed property `result` (object) - * Changed property `documentationURL` (string -> string) + New properties: `germplasmName` - * Changed property `endDate` (string -> string) + New required properties: + - `commonCropName` + - `germplasmDbId` + - `germplasmName` + - `germplasmPUI` - * Changed property `programDbId` (string) + * Changed property `germplasmPUI` (string): + - Nullable changed: `true` -> `null` - * Changed property `programName` (string) + * Changed property `breedingInstitutes` (array) - * Changed property `startDate` (string -> string) + Changed items (array): - * Changed property `trialDescription` (string) + New properties: `instituteAddress` - * Changed property `trialName` (string) +##### `GET` /lists - * Changed property `trialPUI` (string) - * Changed property `contacts` (array) +###### Parameters: - Changed items (object): - > A persons contact information +Deleted: `externalReferenceID` in `query` +##### `POST` /lists - * Changed property `contactDbId` (string) - * Changed property `email` (string) +###### Request: - * Changed property `instituteName` (string) +* Changed content type : `application/json` - * Changed property `name` (string) + Changed items (array): - * Changed property `orcid` (string) + New properties: `personDbId` - * Changed property `type` (string) + Deleted properties: `listOwnerPersonDbId` -##### `POST` /trials + * Changed property `externalReferences` (array) -> Create new Trial + Changed items (array): + Deleted properties: `referenceID` -###### Request: + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -Changed content type : `application/json` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -###### Return Type: +##### `PUT` /lists/{listDbId} -Changed response : **200 OK** -> OK +###### Request: * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - + New properties: `personDbId` - * Changed property `result` (object) + Deleted properties: `listOwnerPersonDbId` - * Changed property `data` (array) + * Changed property `externalReferences` (array) - Changed items (object): - > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. + Changed items (array): + Deleted properties: `referenceID` - * Added property `studyDbIds` (array) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Deleted property `datasetAuthorships` (array) - > License and citation information for the data in this trial + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` +##### `GET` /observationunits - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. +###### Parameters: - * Deleted property `publications` (array) - > MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended. +Deleted: `externalReferenceID` in `query` +##### `POST` /observationunits - * Deleted property `trialDbId` (string) - > The ID which uniquely identifies a trial - > - > MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. +###### Request: - * Changed property `active` (boolean) +* Changed content type : `application/json` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + Changed items (array): + New properties: `germplasmPUI`, `studyPUI`, `trialPUI` - * Added property `additionalProperties` (string) + * Changed property `crossDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `commonCropName` (string) + * Changed property `crossName` (string): + - Nullable changed: `true` -> `null` - * Changed property `documentationURL` (string -> string) + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `endDate` (string -> string) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` - * Changed property `programDbId` (string) + * Changed property `locationDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `programName` (string) + * Changed property `locationName` (string): + - Nullable changed: `true` -> `null` - * Changed property `startDate` (string -> string) + * Changed property `observationUnitPosition` (object -> array): + - Type changed: `object` -> `array` - * Changed property `trialDescription` (string) + * Changed property `programDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `trialName` (string) + * Changed property `programName` (string): + - Nullable changed: `true` -> `null` - * Changed property `trialPUI` (string) + * Changed property `seedLotDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `contacts` (array) + * Changed property `seedLotName` (string): + - Nullable changed: `true` -> `null` - Changed items (object): - > A persons contact information + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `studyName` (string): + - Nullable changed: `true` -> `null` - * Changed property `contactDbId` (string) + * Changed property `trialDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `email` (string) + * Changed property `trialName` (string): + - Nullable changed: `true` -> `null` - * Changed property `instituteName` (string) + * Changed property `externalReferences` (array) - * Changed property `name` (string) + Changed items (array): - * Changed property `orcid` (string) + Deleted properties: `referenceID` - * Changed property `type` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -##### `GET` /trials/{trialDbId} + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` + * Changed property `treatments` (array) -###### Parameters: + Changed items (array): -Deleted: `trialDbId` in `path` -> The internal trialDbId + New properties: `observationUnitDbId`, `observationUnitName`, `observationUnitPUI` +##### `GET` /people -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} +###### Parameters: -###### Return Type: +Deleted: `externalReferenceID` in `query` -Deleted response : **404 Not Found** -> Not Found +##### `POST` /people -Changed response : **200 OK** -> OK +###### Request: * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + Changed items (array): + * Changed property `externalReferences` (array) - * Changed property `result` (object) - > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. + Changed items (array): + Deleted properties: `referenceID` - * Added property `studyDbIds` (array) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Deleted property `datasetAuthorships` (array) - > License and citation information for the data in this trial + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` +##### `PUT` /people/{personDbId} - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. +###### Request: - * Deleted property `publications` (array) - > MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended. +* Changed content type : `application/json` + * Changed property `externalReferences` (array) - * Deleted property `trialDbId` (string) - > The ID which uniquely identifies a trial - > - > MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + Changed items (array): + Deleted properties: `referenceID` - * Changed property `active` (boolean) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` +##### `GET` /plannedcrosses - * Added property `additionalProperties` (string) - * Changed property `commonCropName` (string) +###### Parameters: - * Changed property `documentationURL` (string -> string) +Deleted: `externalReferenceID` in `query` - * Changed property `endDate` (string -> string) +###### Return Type: - * Changed property `programDbId` (string) +Changed response : **200** - * Changed property `programName` (string) +* Changed content type : `application/json` - * Changed property `startDate` (string -> string) + * Changed property `result` (object) - * Changed property `trialDescription` (string) + * Changed property `data` (array) - * Changed property `trialName` (string) + Changed items (array): - * Changed property `trialPUI` (string) + * Changed property `crossType` (string): + - Nullable changed: `true` -> `null` - * Changed property `contacts` (array) + * Changed property `crossingProjectDbId` (string): + - Nullable changed: `true` -> `null` - Changed items (object): - > A persons contact information + * Changed property `crossingProjectName` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array) - * Changed property `contactDbId` (string) + Changed items (array): - * Changed property `email` (string) + Deleted properties: `referenceID` - * Changed property `instituteName` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `name` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `orcid` (string) + * Changed property `parent1` (object): + - Nullable changed: `true` -> `null` - * Changed property `type` (string) + New properties: `germplasmPUI`, `observationUnitPUI` -##### `PUT` /trials/{trialDbId} + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` -> Update the details for an existing Trial + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` -###### Parameters: + * Changed property `observationUnitName` (string): + - Nullable changed: `true` -> `null` -Deleted: `trialDbId` in `path` -> The internal trialDbId + * Changed property `parentType` (string): + - Added enum values: [CLONAL] +##### `PUT` /plannedcrosses -###### Request: -Changed content type : `application/json` +###### Return Type: -New required properties: -- `trialDbId` -- `trialDbId` +Changed response : **200** -* Added property `studyDbIds` (array) +* Changed content type : `application/json` -* Added property `trialDbId` (string) + * Changed property `result` (object) -* Deleted property `datasetAuthorships` (array) - > License and citation information for the data in this trial + * Changed property `data` (array) + Changed items (array): -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `crossType` (string): + - Nullable changed: `true` -> `null` + * Changed property `crossingProjectDbId` (string): + - Nullable changed: `true` -> `null` -* Deleted property `publications` (array) - > MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended. + * Changed property `crossingProjectName` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array) -* Changed property `active` (boolean) + Changed items (array): -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Added property `additionalProperties` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -* Changed property `commonCropName` (string) + * Changed property `parent1` (object): + - Nullable changed: `true` -> `null` -* Changed property `documentationURL` (string -> string) + New properties: `germplasmPUI`, `observationUnitPUI` -* Changed property `endDate` (string -> string) + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` -* Changed property `programDbId` (string) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` -* Changed property `programName` (string) + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` -* Changed property `startDate` (string -> string) + * Changed property `observationUnitName` (string): + - Nullable changed: `true` -> `null` -* Changed property `trialDescription` (string) + * Changed property `parentType` (string): + - Added enum values: [CLONAL] -* Changed property `trialName` (string) +##### `POST` /plannedcrosses -* Changed property `trialPUI` (string) -* Changed property `contacts` (array) +###### Request: - Changed items (object): - > A persons contact information +* Changed content type : `application/json` + Changed items (array): - * Changed property `contactDbId` (string) + New properties: `plannedCrossDbId` - * Changed property `email` (string) + New required properties: + - `plannedCrossDbId` - * Changed property `instituteName` (string) + * Changed property `crossType` (string): + - Nullable changed: `true` -> `null` - * Changed property `name` (string) + * Changed property `crossingProjectDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `orcid` (string) + * Changed property `crossingProjectName` (string): + - Nullable changed: `true` -> `null` - * Changed property `type` (string) + * Changed property `externalReferences` (array) -###### Return Type: + Changed items (array): -Deleted response : **404 Not Found** -> Not Found + Deleted properties: `referenceID` -Changed response : **200 OK** -> OK + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -* Changed content type : `application/json` + * Changed property `parent1` (object): + - Nullable changed: `true` -> `null` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + New properties: `germplasmPUI`, `observationUnitPUI` + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `result` (object) - > A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing. + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `studyDbIds` (array) + * Changed property `observationUnitName` (string): + - Nullable changed: `true` -> `null` - * Deleted property `datasetAuthorships` (array) - > License and citation information for the data in this trial + * Changed property `parentType` (string): + - Added enum values: [CLONAL] + +###### Return Type: +Changed response : **200** - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. +* Changed content type : `application/json` + * Changed property `result` (object) - * Deleted property `publications` (array) - > MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended. + * Changed property `data` (array) + Changed items (array): - * Deleted property `trialDbId` (string) - > The ID which uniquely identifies a trial - > - > MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + * Changed property `crossType` (string): + - Nullable changed: `true` -> `null` + * Changed property `crossingProjectDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `active` (boolean) + * Changed property `crossingProjectName` (string): + - Nullable changed: `true` -> `null` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `externalReferences` (array) + Changed items (array): - * Added property `additionalProperties` (string) + Deleted properties: `referenceID` - * Changed property `commonCropName` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `documentationURL` (string -> string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `endDate` (string -> string) + * Changed property `parent1` (object): + - Nullable changed: `true` -> `null` - * Changed property `programDbId` (string) + New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `programName` (string) + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `startDate` (string -> string) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` - * Changed property `trialDescription` (string) + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `trialName` (string) + * Changed property `observationUnitName` (string): + - Nullable changed: `true` -> `null` - * Changed property `trialPUI` (string) + * Changed property `parentType` (string): + - Added enum values: [CLONAL] - * Changed property `contacts` (array) +##### `GET` /plates - Changed items (object): - > A persons contact information +###### Parameters: - * Changed property `contactDbId` (string) +Deleted: `externalReferenceID` in `query` - * Changed property `email` (string) +##### `POST` /plates - * Changed property `instituteName` (string) - * Changed property `name` (string) +###### Request: - * Changed property `orcid` (string) +* Changed content type : `application/json` - * Changed property `type` (string) + Changed items (array): -##### `GET` /images + New properties: `programName`, `studyName`, `studyPUI`, `trialName`, `trialPUI` -> Get a filtered list of Image + * Changed property `programDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` -###### Parameters: + * Changed property `trialDbId` (string): + - Nullable changed: `true` -> `null` -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. + * Changed property `externalReferences` (array) + Changed items (array): -Added: `imageFileName` in `query` -> Image file names to search for. + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -Added: `imageFileSizeMax` in `query` -> A maximum image file size to search for. + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` +##### `GET` /programs -Added: `imageFileSizeMin` in `query` -> A minimum image file size to search for. +###### Parameters: -Added: `imageHeightMax` in `query` -> A maximum image height to search for. +Deleted: `externalReferenceID` in `query` +Changed: `programType` in `query`: + - Added enum values: [STANDARD] + - Removed enum values: [STANARD] -Added: `imageHeightMin` in `query` -> A minimum image height to search for. +##### `POST` /programs -Added: `imageLocation` in `query` +###### Request: -Added: `imageTimeStampRangeEnd` in `query` -> The latest timestamp to search for. +* Changed content type : `application/json` + Changed items (array): -Added: `imageTimeStampRangeStart` in `query` -> The earliest timestamp to search for. + New properties: `personDbId` + Deleted properties: `leadPersonDbId`, `leadPersonName` -Added: `imageWidthMax` in `query` -> A maximum image width to search for. + * Changed property `programType` (string): + - Nullable changed: `null` -> `true` + * Changed property `externalReferences` (array) -Added: `imageWidthMin` in `query` -> A minimum image width to search for. + Changed items (array): + Deleted properties: `referenceID` -Added: `mimeType` in `query` -> A set of image file types to search for. + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -Changed: `imageDbId` in `query` -> A list of image Ids to search for +##### `PUT` /programs/{programDbId} -Changed: `imageName` in `query` -> Human readable names to search for. +###### Request: +* Changed content type : `application/json` -Changed: `observationUnitDbId` in `query` -> A set of observation unit identifiers to search for. + New properties: `personDbId` + Deleted properties: `leadPersonDbId`, `leadPersonName` -Changed: `observationDbId` in `query` -> A list of observation Ids this image is associated with to search for + * Changed property `programType` (string): + - Nullable changed: `null` -> `true` + * Changed property `externalReferences` (array) -Changed: `descriptiveOntologyTerm` in `query` -> A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL. + Changed items (array): + Deleted properties: `referenceID` -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. +##### `GET` /references ###### Return Type: -Changed response : **200 OK** -> OK - +Changed response : **200** * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - * Changed property `result` (object) * Changed property `data` (array) - Changed items (object): - > The metadata for an image file that is connected to some phenotypic observation data. - - - * Added property `observationUnitName` (string) + Changed items (array): - * Added property `observationUnitPUI` (string) + New properties: `sourceGermplasmDbIds`, `variantDbIds` - * Deleted property `descriptiveOntologyTerms` (array) - > A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL. + Deleted properties: `sourceGermplasm` + * Changed property `referenceSetDbId` (string): + - Nullable changed: `true` -> `null` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `referenceSetName` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Deleted property `imageDbId` (string) - > The unique identifier of an image + Changed items (array): + Deleted properties: `referenceID` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Added property `additionalProperties` (string) - - * Changed property `copyright` (string) +##### `GET` /references/{referenceDbId} - * Changed property `description` (string) - * Changed property `imageFileName` (string) +###### Return Type: - * Changed property `imageFileSize` (integer -> integer) +Changed response : **200** - * Changed property `imageHeight` (integer -> integer) +* Changed content type : `application/json` - * Changed property `imageName` (string) + * Changed property `result` (object) - * Changed property `imageTimeStamp` (string -> string) + New properties: `sourceGermplasmDbIds`, `variantDbIds` - * Changed property `imageURL` (string) + Deleted properties: `sourceGermplasm` - * Changed property `imageWidth` (integer -> integer) + * Changed property `referenceSetDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `mimeType` (string) + * Changed property `referenceSetName` (string): + - Nullable changed: `true` -> `null` - * Changed property `observationDbIds` (array) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Changed property `observationUnitDbId` (string) + Changed items (array): - * Changed property `imageLocation` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `type` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `geometry` (object -> object) +##### `GET` /samples -##### `POST` /images -> Create new Image +###### Parameters: +Deleted: `externalReferenceID` in `query` -###### Request: +##### `PUT` /samples -Changed content type : `application/json` ###### Return Type: -Changed response : **200 OK** -> OK - - -* Changed content type : `application/json` - - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. +Deleted response : **404** +##### `POST` /samples - * Changed property `result` (object) - - * Changed property `data` (array) - Changed items (object): - > The metadata for an image file that is connected to some phenotypic observation data. +###### Request: +* Changed content type : `application/json` - * Added property `observationUnitName` (string) + Changed items (array): - * Added property `observationUnitPUI` (string) + New properties: `callSetDbIds`, `germplasmName`, `germplasmPUI`, `observationUnitName`, `observationUnitPUI`, `programName`, `sampleGroupId`, `studyName`, `studyPUI`, `trialName`, `trialPUI` - * Deleted property `descriptiveOntologyTerms` (array) - > A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL. + Deleted properties: `sampleGroupDbId` + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `plateDbId` (string): + - Nullable changed: `true` -> `null` - * Deleted property `imageDbId` (string) - > The unique identifier of an image + * Changed property `plateName` (string): + - Nullable changed: `true` -> `null` + * Changed property `programDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `trialDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `additionalProperties` (string) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Changed property `copyright` (string) + Changed items (array): - * Changed property `description` (string) + Deleted properties: `referenceID` - * Changed property `imageFileName` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `imageFileSize` (integer -> integer) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `imageHeight` (integer -> integer) +##### `POST` /search/calls - * Changed property `imageName` (string) - * Changed property `imageTimeStamp` (string -> string) +###### Request: - * Changed property `imageURL` (string) +* Changed content type : `application/json` - * Changed property `imageWidth` (integer -> integer) + Deleted properties: `page`, `pageSize`, `pageToken` - * Changed property `mimeType` (string) + * Changed property `callSetDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `observationDbIds` (array) + * Changed property `expandHomozygotes` (boolean): + - Nullable changed: `true` -> `null` - * Changed property `observationUnitDbId` (string) + * Changed property `sepPhased` (string): + - Nullable changed: `true` -> `null` - * Changed property `imageLocation` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + * Changed property `sepUnphased` (string): + - Nullable changed: `true` -> `null` + * Changed property `unknownString` (string): + - Nullable changed: `true` -> `null` - * Changed property `type` (string) + * Changed property `variantDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `geometry` (object -> object) + * Changed property `variantSetDbIds` (array): + - Nullable changed: `true` -> `null` -##### `GET` /images/{imageDbId} +###### Return Type: -> Get the details of a specific Image +Changed response : **200** +* Changed content type : `application/json` -###### Parameters: + * Changed property `result` (object) -Deleted: `imageDbId` in `path` -> The unique identifier for a image + Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` + * Changed property `data` (array) -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} + Changed items (array): + Deleted properties: `genotype`, `genotype_likelihood`, `variantName` -###### Return Type: + * Changed property `genotypeValue` (string): + - Nullable changed: `null` -> `true` -Deleted response : **404 Not Found** -> Not Found + * Changed property `phaseSet` (string): + - Nullable changed: `null` -> `true` -Changed response : **200 OK** -> OK + * Changed property `genotypeMetadata` (array): + - Nullable changed: `null` -> `true` + Changed items (array): -* Changed content type : `application/json` + * Changed property `dataType` (string): + - Nullable changed: `null` -> `true` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + * Changed property `fieldAbbreviation` (string): + - Nullable changed: `null` -> `true` + * Changed property `fieldName` (string): + - Nullable changed: `null` -> `true` - * Changed property `result` (object) - > The metadata for an image file that is connected to some phenotypic observation data. + * Changed property `fieldValue` (string): + - Nullable changed: `null` -> `true` +##### `GET` /search/calls/{searchResultsDbId} - * Added property `observationUnitName` (string) - * Added property `observationUnitPUI` (string) +###### Parameters: - * Deleted property `descriptiveOntologyTerms` (array) - > A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL. +Deleted: `pageToken` in `query` +###### Return Type: - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. +Deleted response : **202** +Changed response : **200** - * Deleted property `imageDbId` (string) - > The unique identifier of an image +* Changed content type : `application/json` + * Changed property `result` (object) - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` + * Changed property `data` (array) - * Added property `additionalProperties` (string) + Changed items (array): - * Changed property `copyright` (string) + Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - * Changed property `description` (string) + * Changed property `genotypeValue` (string): + - Nullable changed: `null` -> `true` - * Changed property `imageFileName` (string) + * Changed property `phaseSet` (string): + - Nullable changed: `null` -> `true` - * Changed property `imageFileSize` (integer -> integer) + * Changed property `genotypeMetadata` (array): + - Nullable changed: `null` -> `true` - * Changed property `imageHeight` (integer -> integer) + Changed items (array): - * Changed property `imageName` (string) + * Changed property `dataType` (string): + - Nullable changed: `null` -> `true` - * Changed property `imageTimeStamp` (string -> string) + * Changed property `fieldAbbreviation` (string): + - Nullable changed: `null` -> `true` - * Changed property `imageURL` (string) + * Changed property `fieldName` (string): + - Nullable changed: `null` -> `true` - * Changed property `imageWidth` (integer -> integer) + * Changed property `fieldValue` (string): + - Nullable changed: `null` -> `true` - * Changed property `mimeType` (string) +##### `POST` /search/callsets - * Changed property `observationDbIds` (array) - * Changed property `observationUnitDbId` (string) +###### Request: - * Changed property `imageLocation` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +* Changed content type : `application/json` + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `type` (string) + * Changed property `callSetDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `geometry` (object -> object) + * Changed property `callSetNames` (array): + - Nullable changed: `true` -> `null` -##### `PUT` /images/{imageDbId} + * Changed property `sampleDbIds` (array): + - Nullable changed: `true` -> `null` -> Update the details for an existing Image + * Changed property `sampleNames` (array): + - Nullable changed: `true` -> `null` + * Changed property `variantSetDbIds` (array): + - Nullable changed: `true` -> `null` -###### Parameters: +###### Return Type: -Deleted: `imageDbId` in `path` -> The unique identifier for a image +Changed response : **200** +* Changed content type : `application/json` -###### Request: + * Changed property `result` (object) -Changed content type : `application/json` + * Changed property `data` (array) -New required properties: -- `imageDbId` -- `imageDbId` + Changed items (array): -* Added property `imageDbId` (string) + New properties: `sampleName`, `samplePUI`, `studyName`, `studyPUI` -* Added property `observationUnitName` (string) + Deleted properties: `variantSetDbIds` -* Added property `observationUnitPUI` (string) + * Changed property `sampleDbId` (string): + - Nullable changed: `true` -> `null` -* Deleted property `descriptiveOntologyTerms` (array) - > A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL. + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + Changed items (array): + Deleted properties: `referenceID` -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Added property `additionalProperties` (string) +##### `GET` /search/callsets/{searchResultsDbId} -* Changed property `copyright` (string) -* Changed property `description` (string) +###### Return Type: -* Changed property `imageFileName` (string) +Deleted response : **202** -* Changed property `imageFileSize` (integer -> integer) +Changed response : **200** -* Changed property `imageHeight` (integer -> integer) +* Changed content type : `application/json` -* Changed property `imageName` (string) + * Changed property `result` (object) -* Changed property `imageTimeStamp` (string -> string) + * Changed property `data` (array) -* Changed property `imageURL` (string) + Changed items (array): -* Changed property `imageWidth` (integer -> integer) + New properties: `sampleName`, `samplePUI`, `studyName`, `studyPUI` -* Changed property `mimeType` (string) + Deleted properties: `variantSetDbIds` -* Changed property `observationDbIds` (array) + * Changed property `sampleDbId` (string): + - Nullable changed: `true` -> `null` -* Changed property `observationUnitDbId` (string) + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` -* Changed property `imageLocation` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` + Changed items (array): - * Changed property `type` (string) + Deleted properties: `referenceID` - * Changed property `geometry` (object -> object) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -###### Return Type: + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -Deleted response : **404 Not Found** -> Not Found +##### `POST` /search/observations -Changed response : **200 OK** -> OK +###### Request: * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + * Changed property `observationDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `result` (object) - > The metadata for an image file that is connected to some phenotypic observation data. + * Changed property `observationTimeStampRangeEnd` (string): + - Nullable changed: `true` -> `null` + * Changed property `observationTimeStampRangeStart` (string): + - Nullable changed: `true` -> `null` - * Added property `observationUnitName` (string) + * Changed property `observationUnitDbIds` (array): + - Nullable changed: `true` -> `null` - * Added property `observationUnitPUI` (string) + * Changed property `seasonDbIds` (array): + - Nullable changed: `true` -> `null` - * Deleted property `descriptiveOntologyTerms` (array) - > A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL. + * Changed property `observationLevelRelationships` (array): + - Nullable changed: `true` -> `null` + Changed items (array): - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + New properties: `observationUnitName`, `observationUnitPUI` + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` - * Deleted property `imageDbId` (string) - > The unique identifier of an image + * Changed property `observationLevels` (array): + - Nullable changed: `true` -> `null` +##### `POST` /search/observationunits - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +###### Request: - * Added property `additionalProperties` (string) +* Changed content type : `application/json` - * Changed property `copyright` (string) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `description` (string) + * Changed property `includeObservations` (boolean): + - Nullable changed: `true` -> `null` - * Changed property `imageFileName` (string) + * Changed property `observationUnitDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `imageFileSize` (integer -> integer) + * Changed property `observationUnitNames` (array): + - Nullable changed: `true` -> `null` - * Changed property `imageHeight` (integer -> integer) + * Changed property `seasonDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `imageName` (string) + * Changed property `observationLevelRelationships` (array): + - Nullable changed: `true` -> `null` - * Changed property `imageTimeStamp` (string -> string) + Changed items (array): - * Changed property `imageURL` (string) + New properties: `observationUnitName`, `observationUnitPUI` - * Changed property `imageWidth` (integer -> integer) + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `mimeType` (string) + * Changed property `observationLevels` (array): + - Nullable changed: `true` -> `null` - * Changed property `observationDbIds` (array) +##### `POST` /search/references - * Changed property `observationUnitDbId` (string) - * Changed property `imageLocation` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +###### Request: +* Changed content type : `application/json` - * Changed property `type` (string) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `geometry` (object -> object) + * Changed property `accessions` (array): + - Nullable changed: `true` -> `null` -##### `GET` /locations + * Changed property `isDerived` (boolean): + - Nullable changed: `true` -> `null` -> Get a filtered list of Location + * Changed property `md5checksums` (array): + - Nullable changed: `true` -> `null` + * Changed property `referenceDbIds` (array): + - Nullable changed: `true` -> `null` -###### Parameters: + * Changed property `referenceSetDbIds` (array): + - Nullable changed: `true` -> `null` -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. +###### Return Type: +Changed response : **200** -Added: `abbreviation` in `query` -> A list of shortened human readable names for a set of Locations +* Changed content type : `application/json` + * Changed property `result` (object) -Added: `altitudeMin` in `query` -> The minimum altitude to search for + * Changed property `data` (array) + Changed items (array): -Added: `altitudeMax` in `query` -> The maximum altitude to search for + New properties: `sourceGermplasmDbIds`, `variantDbIds` + Deleted properties: `sourceGermplasm` -Added: `countryCode` in `query` -> [ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec + * Changed property `referenceSetDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `referenceSetName` (string): + - Nullable changed: `true` -> `null` -Added: `countryName` in `query` -> The full name of the country to search for + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` + Changed items (array): -Added: `coordinate` in `query` + Deleted properties: `referenceID` -Added: `instituteAddress` in `query` -> The street address of the institute to search for + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -Added: `instituteName` in `query` -> The name of the institute to search for +##### `GET` /search/references/{searchResultsDbId} -Changed: `locationType` in `query` -> The type of location this represents (ex. Breeding Location, Storage Location, etc) +###### Return Type: +Deleted response : **202** -Changed: `locationDbId` in `query` -> The location ids to search for +Changed response : **200** +* Changed content type : `application/json` -Changed: `locationName` in `query` -> A human readable names to search for + * Changed property `result` (object) + * Changed property `data` (array) -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. + Changed items (array): + New properties: `sourceGermplasmDbIds`, `variantDbIds` -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. + Deleted properties: `sourceGermplasm` + * Changed property `referenceSetDbId` (string): + - Nullable changed: `true` -> `null` -###### Return Type: + * Changed property `referenceSetName` (string): + - Nullable changed: `true` -> `null` -Changed response : **200 OK** -> OK + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` + Changed items (array): -* Changed content type : `application/json` + Deleted properties: `referenceID` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `result` (object) +##### `POST` /search/variants - * Changed property `data` (array) - Changed items (object): - > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. +###### Request: +* Changed content type : `application/json` - * Added property `childLocationDbIds` (array) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize`, `pageToken` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `callSetDbIds` (array): + - Nullable changed: `true` -> `null` + - Deprecated status changed + * Changed property `referenceDbId` (string): + - Nullable changed: `true` -> `null` + - Deprecated status changed - * Deleted property `parentLocationDbId` (string) - > The unique identifier for a Location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + * Changed property `referenceDbIds` (array): + - Nullable changed: `true` -> `null` + * Changed property `referenceSetDbIds` (array): + - Nullable changed: `true` -> `null` - * Deleted property `parentLocationName` (string) - > A human readable name for a location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + * Changed property `variantDbIds` (array): + - Nullable changed: `true` -> `null` + * Changed property `variantSetDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `abbreviation` (string) +###### Return Type: - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +Changed response : **200** +* Changed content type : `application/json` - * Added property `additionalProperties` (string) + * Changed property `result` (object) - * Changed property `coordinateDescription` (string) + * Changed property `data` (array) - * Changed property `coordinateUncertainty` (string) + Changed items (array): - * Changed property `countryCode` (string) + New properties: `analysis`, `variantSetName` - * Changed property `countryName` (string) + Deleted properties: `alternateBases`, `alternate_bases` - * Changed property `documentationURL` (string -> string) + * Changed property `referenceDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `environmentType` (string) + * Changed property `referenceName` (string): + - Nullable changed: `true` -> `null` - * Changed property `exposure` (string) + * Changed property `referenceSetDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `instituteAddress` (string) + * Changed property `referenceSetName` (string): + - Nullable changed: `true` -> `null` - * Changed property `instituteName` (string) + * Changed property `variantDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `locationDbId` (string) + * Changed property `variantSetDbId` (array -> string): + - Type changed: `array` -> `string` - * Changed property `locationName` (string) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Changed property `locationType` (string) + Changed items (array): - * Changed property `siteStatus` (string) + Deleted properties: `referenceID` - * Changed property `slope` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `topography` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `coordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +##### `GET` /search/variants/{searchResultsDbId} - * Changed property `type` (string) +###### Parameters: - * Changed property `geometry` (object -> object) +Deleted: `pageToken` in `query` -##### `POST` /locations +###### Return Type: -> Create new Location +Deleted response : **202** +Changed response : **200** -###### Request: +* Changed content type : `application/json` -Changed content type : `application/json` + * Changed property `result` (object) -###### Return Type: + * Changed property `data` (array) -Changed response : **200 OK** -> OK + Changed items (array): + New properties: `analysis`, `variantSetName` -* Changed content type : `application/json` + Deleted properties: `alternateBases`, `alternate_bases` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + * Changed property `referenceDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `referenceName` (string): + - Nullable changed: `true` -> `null` - * Changed property `result` (object) + * Changed property `referenceSetDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `data` (array) + * Changed property `referenceSetName` (string): + - Nullable changed: `true` -> `null` - Changed items (object): - > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + * Changed property `variantDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `variantSetDbId` (array -> string): + - Type changed: `array` -> `string` - * Added property `childLocationDbIds` (array) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + Changed items (array): + Deleted properties: `referenceID` - * Deleted property `parentLocationDbId` (string) - > The unique identifier for a Location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Deleted property `parentLocationName` (string) - > A human readable name for a location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. +##### `POST` /search/variantsets - * Changed property `abbreviation` (string) +###### Request: - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +* Changed content type : `application/json` + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Added property `additionalProperties` (string) +###### Return Type: - * Changed property `coordinateDescription` (string) +Changed response : **200** - * Changed property `coordinateUncertainty` (string) +* Changed content type : `application/json` - * Changed property `countryCode` (string) + * Changed property `result` (object) - * Changed property `countryName` (string) + * Changed property `data` (array) - * Changed property `documentationURL` (string -> string) + Changed items (array): - * Changed property `environmentType` (string) + New properties: `referenceSetName`, `studyName`, `studyPUI` - * Changed property `exposure` (string) + Deleted properties: `availableFormats` - * Changed property `instituteAddress` (string) + * Changed property `referenceSetDbId` (string): + - Nullable changed: `false` -> `null` - * Changed property `instituteName` (string) + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `locationDbId` (string) + * Changed property `analysis` (array) - * Changed property `locationName` (string) + Changed items (array): - * Changed property `locationType` (string) + New properties: `variantSetDbId`, `variantSetName` - * Changed property `siteStatus` (string) + New required properties: + - `analysisDbId` - * Changed property `slope` (string) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Changed property `topography` (string) + Changed items (array): - * Changed property `coordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `type` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `geometry` (object -> object) + * Changed property `metadataFields` (array) -##### `GET` /locations/{locationDbId} + Changed items (array): + New properties: `variantSetDbId`, `variantSetName` -###### Parameters: + * Changed property `dataType` (string): + - Nullable changed: `null` -> `true` -Deleted: `locationDbId` in `path` -> The internal DB id for a location + * Changed property `fieldAbbreviation` (string): + - Nullable changed: `null` -> `true` + * Changed property `fieldName` (string): + - Nullable changed: `null` -> `true` -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} +##### `GET` /search/variantsets/{searchResultsDbId} ###### Return Type: -Deleted response : **404 Not Found** -> Not Found - -Changed response : **200 OK** -> OK +Deleted response : **202** +Changed response : **200** * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + * Changed property `result` (object) + * Changed property `data` (array) - * Changed property `result` (object) - > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + Changed items (array): + New properties: `referenceSetName`, `studyName`, `studyPUI` - * Added property `childLocationDbIds` (array) + Deleted properties: `availableFormats` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `referenceSetDbId` (string): + - Nullable changed: `false` -> `null` + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` - * Deleted property `parentLocationDbId` (string) - > The unique identifier for a Location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + * Changed property `analysis` (array) + Changed items (array): - * Deleted property `parentLocationName` (string) - > A human readable name for a location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + New properties: `variantSetDbId`, `variantSetName` + New required properties: + - `analysisDbId` - * Changed property `abbreviation` (string) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + Changed items (array): + Deleted properties: `referenceID` - * Added property `additionalProperties` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `coordinateDescription` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `coordinateUncertainty` (string) + * Changed property `metadataFields` (array) - * Changed property `countryCode` (string) + Changed items (array): - * Changed property `countryName` (string) + New properties: `variantSetDbId`, `variantSetName` - * Changed property `documentationURL` (string -> string) + * Changed property `dataType` (string): + - Nullable changed: `null` -> `true` - * Changed property `environmentType` (string) + * Changed property `fieldAbbreviation` (string): + - Nullable changed: `null` -> `true` - * Changed property `exposure` (string) + * Changed property `fieldName` (string): + - Nullable changed: `null` -> `true` - * Changed property `instituteAddress` (string) +##### `GET` /seedlots - * Changed property `instituteName` (string) - * Changed property `locationDbId` (string) +###### Parameters: - * Changed property `locationName` (string) +Deleted: `externalReferenceID` in `query` - * Changed property `locationType` (string) +##### `POST` /seedlots - * Changed property `siteStatus` (string) - * Changed property `slope` (string) +###### Request: - * Changed property `topography` (string) +* Changed content type : `application/json` - * Changed property `coordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + Changed items (array): + New properties: `transactions` - * Changed property `type` (string) + * Changed property `locationDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `geometry` (object -> object) + * Changed property `locationName` (string): + - Nullable changed: `true` -> `null` -##### `PUT` /locations/{locationDbId} + * Changed property `programDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `programName` (string): + - Nullable changed: `true` -> `null` -###### Parameters: + * Changed property `contentMixture` (array) -Deleted: `locationDbId` in `path` -> The internal DB id for a location + Changed items (array): + New properties: `germplasmPUI`, `seedLotDbId`, `seedLotName` -###### Request: + * Changed property `crossDbId` (string): + - Nullable changed: `true` -> `null` -Changed content type : `application/json` + * Changed property `crossName` (string): + - Nullable changed: `true` -> `null` -New required properties: -- `locationDbId` -- `locationDbId` + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` -* Added property `childLocationDbIds` (array) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` -* Added property `locationDbId` (string) + * Changed property `externalReferences` (array) -* Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + Changed items (array): + Deleted properties: `referenceID` -* Deleted property `parentLocationDbId` (string) - > The unique identifier for a Location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -* Deleted property `parentLocationName` (string) - > A human readable name for a location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. +##### `PUT` /seedlots/{seedLotDbId} -* Changed property `abbreviation` (string) +###### Request: -* Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +* Changed content type : `application/json` + New properties: `transactions` - * Added property `additionalProperties` (string) + * Changed property `locationDbId` (string): + - Nullable changed: `true` -> `null` -* Changed property `coordinateDescription` (string) + * Changed property `locationName` (string): + - Nullable changed: `true` -> `null` -* Changed property `coordinateUncertainty` (string) + * Changed property `programDbId` (string): + - Nullable changed: `true` -> `null` -* Changed property `countryCode` (string) + * Changed property `programName` (string): + - Nullable changed: `true` -> `null` -* Changed property `countryName` (string) + * Changed property `contentMixture` (array) -* Changed property `documentationURL` (string -> string) + Changed items (array): -* Changed property `environmentType` (string) + New properties: `germplasmPUI`, `seedLotDbId`, `seedLotName` -* Changed property `exposure` (string) + * Changed property `crossDbId` (string): + - Nullable changed: `true` -> `null` -* Changed property `instituteAddress` (string) + * Changed property `crossName` (string): + - Nullable changed: `true` -> `null` -* Changed property `instituteName` (string) + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` -* Changed property `locationName` (string) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` -* Changed property `locationType` (string) + * Changed property `externalReferences` (array) -* Changed property `siteStatus` (string) + Changed items (array): -* Changed property `slope` (string) + Deleted properties: `referenceID` -* Changed property `topography` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -* Changed property `coordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` +##### `GET` /studies - * Changed property `type` (string) - * Changed property `geometry` (object -> object) +###### Parameters: -###### Return Type: +Deleted: `externalReferenceID` in `query` -Deleted response : **404 Not Found** -> Not Found +##### `POST` /studies -Changed response : **200 OK** -> OK +###### Request: * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + Changed items (array): + New properties: `trialPUI` - * Changed property `result` (object) - > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + Deleted properties: `contacts`, `observationVariableDbIds` + * Changed property `locationDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `childLocationDbIds` (array) + * Changed property `locationName` (string): + - Nullable changed: `true` -> `null` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `studyDescription` (string): + - Nullable changed: `null` -> `true` + * Changed property `studyName` (string): + - Nullable changed: `true` -> `null` - * Deleted property `parentLocationDbId` (string) - > The unique identifier for a Location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + * Changed property `environmentParameters` (array) + Changed items (array): - * Deleted property `parentLocationName` (string) - > A human readable name for a location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + New properties: `environmentParametersDbId`, `studyDbId`, `studyName`, `studyPUI` + New required properties: + - `environmentParametersDbId` - * Changed property `abbreviation` (string) + * Changed property `experimentalDesign` (object): + - Nullable changed: `true` -> `null` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + New properties: `studyDbId`, `studyName`, `studyPUI` + * Changed property `externalReferences` (array) - * Added property `additionalProperties` (string) + Changed items (array): - * Changed property `coordinateDescription` (string) + Deleted properties: `referenceID` - * Changed property `coordinateUncertainty` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `countryCode` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `countryName` (string) + * Changed property `growthFacility` (object): + - Nullable changed: `true` -> `null` - * Changed property `documentationURL` (string -> string) + * Changed property `PUI` (string): + - Nullable changed: `null` -> `true` - * Changed property `environmentType` (string) + * Changed property `lastUpdate` (object): + - Nullable changed: `true` -> `null` - * Changed property `exposure` (string) + New properties: `lastUpdateDbId`, `studyDbId`, `studyName`, `studyPUI` - * Changed property `instituteAddress` (string) + New required properties: + - `lastUpdateDbId` - * Changed property `instituteName` (string) +##### `PUT` /studies/{studyDbId} - * Changed property `locationDbId` (string) - * Changed property `locationName` (string) +###### Request: - * Changed property `locationType` (string) +* Changed content type : `application/json` - * Changed property `siteStatus` (string) + New properties: `trialPUI` - * Changed property `slope` (string) + Deleted properties: `contacts`, `observationVariableDbIds` - * Changed property `topography` (string) + * Changed property `locationDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `coordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + * Changed property `locationName` (string): + - Nullable changed: `true` -> `null` + * Changed property `studyDescription` (string): + - Nullable changed: `null` -> `true` - * Changed property `type` (string) + * Changed property `studyName` (string): + - Nullable changed: `true` -> `null` - * Changed property `geometry` (object -> object) + * Changed property `environmentParameters` (array) -##### `GET` /observations + Changed items (array): -> Get a filtered list of Observation + New properties: `environmentParametersDbId`, `studyDbId`, `studyName`, `studyPUI` + New required properties: + - `environmentParametersDbId` -###### Parameters: + * Changed property `experimentalDesign` (object): + - Nullable changed: `true` -> `null` -Added: `germplasmName` in `query` -> List of human readable names to identify germplasm to search for + New properties: `studyDbId`, `studyName`, `studyPUI` + * Changed property `externalReferences` (array) -Added: `locationName` in `query` -> A human readable names to search for + Changed items (array): + Deleted properties: `referenceID` -Added: `observationVariableName` in `query` -> The names of Variables to search for + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -Added: `observationVariablePUI` in `query` -> The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI + * Changed property `growthFacility` (object): + - Nullable changed: `true` -> `null` + * Changed property `PUI` (string): + - Nullable changed: `null` -> `true` -Added: `programName` in `query` -> Use this parameter to only return results associated with the given program names. Program names are not required to be unique. -> -> Use `GET /programs` to find the list of available programs on a server. + * Changed property `lastUpdate` (object): + - Nullable changed: `true` -> `null` + New properties: `lastUpdateDbId`, `studyDbId`, `studyName`, `studyPUI` -Added: `studyName` in `query` -> List of study names to filter search results + New required properties: + - `lastUpdateDbId` +##### `GET` /trials -Added: `trialName` in `query` -> The human readable name of a trial to search for +###### Parameters: -Added: `observationLevel` in `query` -> Searches for values in ObservationUnit->observationUnitPosition->observationLevel +Deleted: `externalReferenceID` in `query` +##### `POST` /trials -Added: `observationLevelRelationship` in `query` -> Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships +###### Request: -Deleted: `observationUnitLevelName` in `query` -> The Observation Unit Level. Returns only the observation unit of the specified Level. ->
References ObservationUnit->observationUnitPosition->observationLevel->levelName ->
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ->
For more information on Observation Levels, please review the Observation Levels documentation. +* Changed content type : `application/json` + Changed items (array): -Deleted: `observationUnitLevelOrder` in `query` -> The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. -> References ObservationUnit->observationUnitPosition->observationLevel->levelOrder ->
For more information on Observation Levels, please review the Observation Levels documentation. + New properties: `studyDbIds` + * Changed property `programDbId` (string): + - Nullable changed: `true` -> `null` -Deleted: `observationUnitLevelCode` in `query` -> The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` -> or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode ->
For more information on Observation Levels, please review the Observation Levels documentation. + * Changed property `programName` (string): + - Nullable changed: `true` -> `null` + * Changed property `datasetAuthorships` (array) -Deleted: `observationUnitLevelRelationshipName` in `query` -> The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. ->
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. ->
Use this parameter to identify groups of observation units that share a relationship level. ->
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ->
For more information on Observation Levels, please review the Observation Levels documentation. + Changed items (array): + New properties: `trialDbId`, `trialName`, `trialPUI` -Deleted: `observationUnitLevelRelationshipOrder` in `query` -> The Observation Unit Level Order Number. ->
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder ->
For more information on Observation Levels, please review the Observation Levels documentation. + * Changed property `externalReferences` (array) + Changed items (array): -Deleted: `observationUnitLevelRelationshipCode` in `query` -> The Observation Unit Level Code. ->
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode ->
For more information on Observation Levels, please review the Observation Levels documentation. + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -Deleted: `observationUnitLevelRelationshipDbId` in `query` -> The observationUnitDbId associated with a particular level and code. ->
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId ->
For more information on Observation Levels, please review the Observation Levels documentation. + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` + * Changed property `publications` (array) -Changed: `observationDbId` in `query` -> The unique id of an Observation + Changed items (array): + New properties: `trialDbId`, `trialName`, `trialPUI` -Changed: `observationUnitDbId` in `query` -> The unique id of an Observation Unit +##### `PUT` /trials/{trialDbId} -Changed: `observationVariableDbId` in `query` -> The DbIds of Variables to search for +###### Request: +* Changed content type : `application/json` -Changed: `locationDbId` in `query` -> The location ids to search for + New properties: `studyDbIds` + * Changed property `programDbId` (string): + - Nullable changed: `true` -> `null` -Changed: `observationTimeStampRangeStart` in `query` -> Timestamp range start + * Changed property `programName` (string): + - Nullable changed: `true` -> `null` + * Changed property `datasetAuthorships` (array) -Changed: `observationTimeStampRangeEnd` in `query` -> Timestamp range end + Changed items (array): + New properties: `trialDbId`, `trialName`, `trialPUI` -Changed: `commonCropName` in `query` -> The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. -> -> Use this parameter to only return results associated with the given crops. -> -> Use `GET /commoncropnames` to find the list of available crops on a server. + * Changed property `externalReferences` (array) + Changed items (array): -Changed: `programDbId` in `query` -> A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. -> -> Use this parameter to only return results associated with the given programs. -> -> Use `GET /programs` to find the list of available programs on a server. + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -Changed: `trialDbId` in `query` -> The ID which uniquely identifies a trial to search for + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` + * Changed property `publications` (array) -Changed: `studyDbId` in `query` -> List of study identifiers to search for + Changed items (array): + New properties: `trialDbId`, `trialName`, `trialPUI` -Changed: `germplasmDbId` in `query` -> List of IDs which uniquely identify germplasm to search for +##### `GET` /variants ###### Return Type: -Changed response : **200 OK** -> OK - +Changed response : **200** * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - - * Changed property `result` (object) * Changed property `data` (array) - Changed items (object): - > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + Changed items (array): + New properties: `analysis`, `variantSetName` - * Added property `germplasmPUI` (string) + Deleted properties: `alternateBases`, `alternate_bases` - * Added property `observationUnitPUI` (string) + * Changed property `referenceDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `observationVariablePUI` (string) + * Changed property `referenceName` (string): + - Nullable changed: `true` -> `null` - * Added property `seasonDbId` (string) + * Changed property `referenceSetDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `seasonName` (string) + * Changed property `referenceSetName` (string): + - Nullable changed: `true` -> `null` - * Added property `studyName` (string) + * Changed property `variantDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `studyPUI` (string) + * Changed property `variantSetDbId` (array -> string): + - Type changed: `array` -> `string` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` + Changed items (array): - * Deleted property `observationDbId` (string) - > The ID which uniquely identifies an observation + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Deleted property `season` (object) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. - - - * Added property `additionalProperties` (string) +##### `GET` /variants/{variantDbId} - * Changed property `collector` (string) - * Changed property `germplasmDbId` (string) +###### Return Type: - * Changed property `germplasmName` (string) +Changed response : **200** - * Changed property `observationTimeStamp` (string -> string) +* Changed content type : `application/json` - * Changed property `observationUnitDbId` (string) + * Changed property `result` (object) - * Changed property `observationUnitName` (string) + New properties: `analysis`, `variantSetName` - * Changed property `observationVariableDbId` (string) + Deleted properties: `alternateBases`, `alternate_bases` - * Changed property `observationVariableName` (string) + * Changed property `referenceDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `studyDbId` (string) + * Changed property `referenceName` (string): + - Nullable changed: `true` -> `null` - * Changed property `uploadedBy` (string) + * Changed property `referenceSetDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `value` (string) + * Changed property `referenceSetName` (string): + - Nullable changed: `true` -> `null` - * Changed property `geoCoordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + * Changed property `variantDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `variantSetDbId` (array -> string): + - Type changed: `array` -> `string` - * Changed property `type` (string) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Changed property `geometry` (object -> object) + Changed items (array): -##### `PUT` /observations + Deleted properties: `referenceID` -> Update the details for an existing Observation + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -###### Request: +##### `GET` /variants/{variantDbId}/calls -Changed content type : `application/json` -New required properties: -- `observationDbId` -- `observationDbId` +###### Return Type: -* Added property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +Changed response : **200** +* Changed content type : `application/json` -* Added property `collector` (string) + * Changed property `result` (object) -* Added property `geoCoordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` + * Changed property `data` (array) - * Property `geometry` (object) + Changed items (array): - One of: + Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - * Property `coordinates` (array) + * Changed property `genotypeValue` (string): + - Nullable changed: `null` -> `true` - Items (number): + * Changed property `phaseSet` (string): + - Nullable changed: `null` -> `true` - * Property `type` (string) + * Changed property `genotypeMetadata` (array): + - Nullable changed: `null` -> `true` - * Property `coordinates` (array) + Changed items (array): - Items (array): + * Changed property `dataType` (string): + - Nullable changed: `null` -> `true` - Items (array): + * Changed property `fieldAbbreviation` (string): + - Nullable changed: `null` -> `true` - * Property `type` (string) + * Changed property `fieldName` (string): + - Nullable changed: `null` -> `true` - * Property `type` (string) + * Changed property `fieldValue` (string): + - Nullable changed: `null` -> `true` -* Added property `germplasmDbId` (string) +##### `GET` /variantsets -* Added property `germplasmName` (string) -* Added property `germplasmPUI` (string) +###### Return Type: -* Added property `observationDbId` (string) +Changed response : **200** -* Added property `observationTimeStamp` (string) +* Changed content type : `application/json` -* Added property `observationUnitDbId` (string) + * Changed property `result` (object) -* Added property `observationUnitName` (string) + * Changed property `data` (array) -* Added property `observationUnitPUI` (string) + Changed items (array): -* Added property `observationVariableDbId` (string) + New properties: `referenceSetName`, `studyName`, `studyPUI` -* Added property `observationVariableName` (string) + Deleted properties: `availableFormats` -* Added property `observationVariablePUI` (string) + * Changed property `referenceSetDbId` (string): + - Nullable changed: `false` -> `null` -* Added property `seasonDbId` (string) + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` -* Added property `seasonName` (string) + * Changed property `analysis` (array) -* Added property `studyDbId` (string) + Changed items (array): -* Added property `studyName` (string) + New properties: `variantSetDbId`, `variantSetName` -* Added property `studyPUI` (string) + New required properties: + - `analysisDbId` -* Added property `uploadedBy` (string) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` -* Added property `value` (string) + Changed items (array): -###### Return Type: + Deleted properties: `referenceID` -Deleted response : **404 Not Found** -> Not Found + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -Changed response : **200 OK** -> OK + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` + * Changed property `metadataFields` (array) -* Changed content type : `application/json` + Changed items (array): - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + New properties: `variantSetDbId`, `variantSetName` + * Changed property `dataType` (string): + - Nullable changed: `null` -> `true` - * Changed property `result` (object) + * Changed property `fieldAbbreviation` (string): + - Nullable changed: `null` -> `true` - * Changed property `data` (array) + * Changed property `fieldName` (string): + - Nullable changed: `null` -> `true` - Changed items (object): - > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. +##### `GET` /variantsets/{variantSetDbId} - * Added property `germplasmPUI` (string) +###### Return Type: - * Added property `observationUnitPUI` (string) +Changed response : **200** - * Added property `observationVariablePUI` (string) +* Changed content type : `application/json` - * Added property `seasonDbId` (string) + * Changed property `result` (object) - * Added property `seasonName` (string) + New properties: `referenceSetName`, `studyName`, `studyPUI` - * Added property `studyName` (string) + Deleted properties: `availableFormats` - * Added property `studyPUI` (string) + * Changed property `referenceSetDbId` (string): + - Nullable changed: `false` -> `null` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `analysis` (array) - * Deleted property `observationDbId` (string) - > The ID which uniquely identifies an observation + Changed items (array): + New properties: `variantSetDbId`, `variantSetName` - * Deleted property `season` (object) + New required properties: + - `analysisDbId` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` + Changed items (array): - * Added property `additionalProperties` (string) + Deleted properties: `referenceID` - * Changed property `collector` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `germplasmDbId` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `germplasmName` (string) + * Changed property `metadataFields` (array) - * Changed property `observationTimeStamp` (string -> string) + Changed items (array): - * Changed property `observationUnitDbId` (string) + New properties: `variantSetDbId`, `variantSetName` - * Changed property `observationUnitName` (string) + * Changed property `dataType` (string): + - Nullable changed: `null` -> `true` - * Changed property `observationVariableDbId` (string) + * Changed property `fieldAbbreviation` (string): + - Nullable changed: `null` -> `true` - * Changed property `observationVariableName` (string) + * Changed property `fieldName` (string): + - Nullable changed: `null` -> `true` - * Changed property `studyDbId` (string) +##### `GET` /variantsets/{variantSetDbId}/calls - * Changed property `uploadedBy` (string) - * Changed property `value` (string) +###### Return Type: - * Changed property `geoCoordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +Changed response : **200** +* Changed content type : `application/json` - * Changed property `type` (string) + * Changed property `result` (object) - * Changed property `geometry` (object -> object) + Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` -##### `POST` /observations + * Changed property `data` (array) -> Create new Observation + Changed items (array): + Deleted properties: `genotype`, `genotype_likelihood`, `variantName` -###### Request: + * Changed property `genotypeValue` (string): + - Nullable changed: `null` -> `true` -Changed content type : `application/json` + * Changed property `phaseSet` (string): + - Nullable changed: `null` -> `true` -###### Return Type: + * Changed property `genotypeMetadata` (array): + - Nullable changed: `null` -> `true` -Deleted response : **404 Not Found** -> Not Found + Changed items (array): -Changed response : **200 OK** -> OK + * Changed property `dataType` (string): + - Nullable changed: `null` -> `true` + * Changed property `fieldAbbreviation` (string): + - Nullable changed: `null` -> `true` -* Changed content type : `application/json` + * Changed property `fieldName` (string): + - Nullable changed: `null` -> `true` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + * Changed property `fieldValue` (string): + - Nullable changed: `null` -> `true` +##### `GET` /variantsets/{variantSetDbId}/callsets - * Changed property `result` (object) - * Changed property `data` (array) +###### Return Type: - Changed items (object): - > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. +New response : **404** +Changed response : **200** - * Added property `germplasmPUI` (string) +* Changed content type : `application/json` - * Added property `observationUnitPUI` (string) + * Changed property `result` (object) - * Added property `observationVariablePUI` (string) + * Changed property `data` (array) - * Added property `seasonDbId` (string) + Changed items (array): - * Added property `seasonName` (string) + New properties: `sampleName`, `samplePUI`, `studyName`, `studyPUI` - * Added property `studyName` (string) + Deleted properties: `variantSetDbIds` - * Added property `studyPUI` (string) + * Changed property `sampleDbId` (string): + - Nullable changed: `true` -> `null` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Deleted property `observationDbId` (string) - > The ID which uniquely identifies an observation + Changed items (array): + Deleted properties: `referenceID` - * Deleted property `season` (object) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` +##### `GET` /variantsets/{variantSetDbId}/variants - * Added property `additionalProperties` (string) - * Changed property `collector` (string) +###### Return Type: - * Changed property `germplasmDbId` (string) +New response : **404** - * Changed property `germplasmName` (string) +Changed response : **200** - * Changed property `observationTimeStamp` (string -> string) +* Changed content type : `application/json` - * Changed property `observationUnitDbId` (string) + * Changed property `result` (object) - * Changed property `observationUnitName` (string) + * Changed property `data` (array) - * Changed property `observationVariableDbId` (string) + Changed items (array): - * Changed property `observationVariableName` (string) + New properties: `analysis`, `variantSetName` - * Changed property `studyDbId` (string) + Deleted properties: `alternateBases`, `alternate_bases` - * Changed property `uploadedBy` (string) + * Changed property `referenceDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `value` (string) + * Changed property `referenceName` (string): + - Nullable changed: `true` -> `null` - * Changed property `geoCoordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + * Changed property `referenceSetDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `referenceSetName` (string): + - Nullable changed: `true` -> `null` - * Changed property `type` (string) + * Changed property `variantDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `geometry` (object -> object) + * Changed property `variantSetDbId` (array -> string): + - Type changed: `array` -> `string` -##### `GET` /observations/{observationDbId} + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` -> Get the details of a specific Observation + Changed items (array): + Deleted properties: `referenceID` -###### Parameters: + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -Deleted: `observationDbId` in `path` -> The unique ID of an observation + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` +##### `GET` /attributes -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} +###### Parameters: -###### Return Type: +Deleted: `externalReferenceID` in `query` -Deleted response : **404 Not Found** -> Not Found +##### `POST` /attributes -Changed response : **200 OK** -> OK +###### Request: * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + Changed items (array): + New properties: `attributeValueDbIds`, `methodDbId`, `methodName`, `methodPUI`, `scaleDbId`, `scaleName`, `scalePUI`, `traitDbId`, `traitName`, `traitPUI` - * Changed property `result` (object) - > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + Deleted properties: `method`, `scale`, `trait` + New required properties: + - `methodDbId` + - `methodName` + - `scaleDbId` + - `scaleName` + - `traitName` - * Added property `germplasmPUI` (string) + Removed required properties: + - `method` + - `scale` + - `trait` - * Added property `observationUnitPUI` (string) + * Changed property `externalReferences` (array) - * Added property `observationVariablePUI` (string) + Changed items (array): - * Added property `seasonDbId` (string) + Deleted properties: `referenceID` - * Added property `seasonName` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Added property `studyName` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Added property `studyPUI` (string) + * Changed property `ontologyReference` (object): + - Nullable changed: `true` -> `null` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + New properties: `ontologyReferenceDbId` + * Changed property `documentationLinks` (array) - * Deleted property `observationDbId` (string) - > The ID which uniquely identifies an observation + Changed items (array): + * Changed property `URL` (string): + - Nullable changed: `null` -> `true` - * Deleted property `season` (object) + * Changed property `type` (string): + - Nullable changed: `null` -> `true` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +##### `PUT` /attributes/{attributeDbId} - * Added property `additionalProperties` (string) +###### Request: - * Changed property `collector` (string) +* Changed content type : `application/json` - * Changed property `germplasmDbId` (string) + New properties: `attributeValueDbIds`, `methodDbId`, `methodName`, `methodPUI`, `scaleDbId`, `scaleName`, `scalePUI`, `traitDbId`, `traitName`, `traitPUI` - * Changed property `germplasmName` (string) + Deleted properties: `method`, `scale`, `trait` - * Changed property `observationTimeStamp` (string -> string) + New required properties: + - `methodDbId` + - `methodName` + - `scaleDbId` + - `scaleName` + - `traitName` - * Changed property `observationUnitDbId` (string) + Removed required properties: + - `method` + - `scale` + - `trait` - * Changed property `observationUnitName` (string) + * Changed property `externalReferences` (array) - * Changed property `observationVariableDbId` (string) + Changed items (array): - * Changed property `observationVariableName` (string) + Deleted properties: `referenceID` - * Changed property `studyDbId` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `uploadedBy` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `value` (string) + * Changed property `ontologyReference` (object): + - Nullable changed: `true` -> `null` - * Changed property `geoCoordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + New properties: `ontologyReferenceDbId` + * Changed property `documentationLinks` (array) - * Changed property `type` (string) + Changed items (array): - * Changed property `geometry` (object -> object) + * Changed property `URL` (string): + - Nullable changed: `null` -> `true` -##### `POST` /search/images + * Changed property `type` (string): + - Nullable changed: `null` -> `true` -> Submit a search request for `Image` +##### `GET` /images ###### Parameters: -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} - - -###### Request: - -Deleted content type : `application/json` +Deleted: `externalReferenceID` in `query` -###### Return Type: +##### `POST` /images -Changed response : **202 Accepted** -> Accepted +###### Request: * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. - + Changed items (array): -Changed response : **200 OK** -> OK + New properties: `imageContent`, `observationUnitName`, `observationUnitPUI` + Deleted properties: `observationDbIds` -* Changed content type : `application/json` + * Changed property `mimeType` (string): + - Pattern changed: `image/.*` -> `null` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Changed property `result` (object) + Changed items (array): - * Changed property `data` (array) + Deleted properties: `referenceID` - Changed items (object): - > The metadata for an image file that is connected to some phenotypic observation data. + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Added property `observationUnitName` (string) + * Changed property `imageLocation` (object): + - Nullable changed: `true` -> `null` - * Added property `observationUnitPUI` (string) + * Changed property `type` (string): + - Default changed: `Feature` -> `none` - * Deleted property `descriptiveOntologyTerms` (array) - > A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL. + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` +##### `PUT` /images/{imageDbId} - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. +###### Request: - * Deleted property `imageDbId` (string) - > The unique identifier of an image +* Changed content type : `application/json` + New properties: `imageContent`, `observationUnitName`, `observationUnitPUI` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + Deleted properties: `observationDbIds` + * Changed property `mimeType` (string): + - Pattern changed: `image/.*` -> `null` - * Added property `additionalProperties` (string) + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `copyright` (string) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Changed property `description` (string) + Changed items (array): - * Changed property `imageFileName` (string) + Deleted properties: `referenceID` - * Changed property `imageFileSize` (integer -> integer) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `imageHeight` (integer -> integer) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `imageName` (string) + * Changed property `imageLocation` (object): + - Nullable changed: `true` -> `null` - * Changed property `imageTimeStamp` (string -> string) + * Changed property `type` (string): + - Default changed: `Feature` -> `none` - * Changed property `imageURL` (string) + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` - * Changed property `imageWidth` (integer -> integer) +##### `GET` /locations - * Changed property `mimeType` (string) - * Changed property `observationDbIds` (array) +###### Parameters: - * Changed property `observationUnitDbId` (string) +Deleted: `externalReferenceID` in `query` - * Changed property `imageLocation` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +##### `POST` /locations - * Changed property `type` (string) +###### Request: - * Changed property `geometry` (object -> object) +* Changed content type : `application/json` -##### `GET` /search/images/{searchResultsDbId} + Changed items (array): -> Submit a search request for `Image`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. + New properties: `childLocationDbIds`, `locationDbId` + Deleted properties: `parentLocationDbId`, `parentLocationName` -###### Parameters: + * Changed property `externalReferences` (array) -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results + Changed items (array): + Deleted properties: `referenceID` -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. + * Changed property `coordinates` (object): + - Nullable changed: `true` -> `null` + * Changed property `type` (string): + - Default changed: `Feature` -> `none` -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` +##### `PUT` /locations/{locationDbId} -###### Return Type: -Deleted response : **202 Accepted** -> Accepted +###### Request: -Deleted response : **404 Not Found** -> Not Found +* Changed content type : `application/json` -Changed response : **200 OK** -> OK + New properties: `childLocationDbIds`, `locationDbId` + Deleted properties: `parentLocationDbId`, `parentLocationName` -* Changed content type : `application/json` + * Changed property `externalReferences` (array) - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + Changed items (array): + Deleted properties: `referenceID` - * Changed property `result` (object) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `data` (array) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - Changed items (object): - > The metadata for an image file that is connected to some phenotypic observation data. + * Changed property `coordinates` (object): + - Nullable changed: `true` -> `null` + * Changed property `type` (string): + - Default changed: `Feature` -> `none` - * Added property `observationUnitName` (string) + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` - * Added property `observationUnitPUI` (string) +##### `GET` /observations - * Deleted property `descriptiveOntologyTerms` (array) - > A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL. +###### Parameters: - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. +Deleted: `externalReferenceID` in `query` +##### `PUT` /observations - * Deleted property `imageDbId` (string) - > The unique identifier of an image +###### Return Type: - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +Deleted response : **404** +##### `POST` /observations - * Added property `additionalProperties` (string) - * Changed property `copyright` (string) +###### Request: - * Changed property `description` (string) +* Changed content type : `application/json` - * Changed property `imageFileName` (string) + Changed items (array): - * Changed property `imageFileSize` (integer -> integer) + New properties: `germplasmPUI`, `observationUnitPUI`, `observationVariablePUI`, `seasonDbId`, `seasonName`, `studyName`, `studyPUI` - * Changed property `imageHeight` (integer -> integer) + Deleted properties: `season` - * Changed property `imageName` (string) + * Changed property `germplasmDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `imageTimeStamp` (string -> string) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` - * Changed property `imageURL` (string) + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `imageWidth` (integer -> integer) + * Changed property `observationUnitName` (string): + - Nullable changed: `true` -> `null` - * Changed property `mimeType` (string) + * Changed property `observationVariableDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `observationDbIds` (array) + * Changed property `observationVariableName` (string): + - Nullable changed: `true` -> `null` - * Changed property `observationUnitDbId` (string) + * Changed property `studyDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `imageLocation` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + * Changed property `externalReferences` (array) + Changed items (array): - * Changed property `type` (string) + Deleted properties: `referenceID` - * Changed property `geometry` (object -> object) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` -##### `POST` /search/locations + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -> Submit a search request for `Location` + * Changed property `geoCoordinates` (object): + - Nullable changed: `true` -> `null` + * Changed property `type` (string): + - Default changed: `Feature` -> `none` -###### Parameters: + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} +###### Return Type: +Deleted response : **404** -###### Request: +##### `GET` /pedigree -Deleted content type : `application/json` ###### Return Type: -Changed response : **202 Accepted** -> Accepted +Deleted response : **404** +Changed response : **200** * Changed content type : `application/json` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + * Changed property `result` (object) + * Changed property `data` (array) -Changed response : **200 OK** -> OK + Changed items (array): + New properties: `crossingProjectName`, `pedigreeNodeDbId`, `siblingDbIds` -* Changed content type : `application/json` + Deleted properties: `siblings` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + New required properties: + - `germplasmPUI` + - `pedigreeNodeDbId` + * Changed property `breedingMethodDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `result` (object) + * Changed property `breedingMethodName` (string): + - Nullable changed: `true` -> `null` - * Changed property `data` (array) + * Changed property `crossingProjectDbId` (string): + - Nullable changed: `true` -> `null` - Changed items (object): - > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + * Changed property `germplasmPUI` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Added property `childLocationDbIds` (array) + Changed items (array): - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Deleted property `parentLocationDbId` (string) - > The unique identifier for a Location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` + * Changed property `parents` (array) - * Deleted property `parentLocationName` (string) - > A human readable name for a location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + Changed items (array): + New properties: `germplasmPUI`, `pedigreeNodeDbId` - * Changed property `abbreviation` (string) + New required properties: + - `germplasmName` + - `germplasmPUI` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` +##### `POST` /pedigree - * Added property `additionalProperties` (string) - * Changed property `coordinateDescription` (string) +###### Request: - * Changed property `coordinateUncertainty` (string) +* Changed content type : `application/json` - * Changed property `countryCode` (string) + Changed items (array): - * Changed property `countryName` (string) + New properties: `crossingProjectName`, `pedigreeNodeDbId`, `siblingDbIds` - * Changed property `documentationURL` (string -> string) + Deleted properties: `siblings` - * Changed property `environmentType` (string) + New required properties: + - `germplasmPUI` + - `pedigreeNodeDbId` - * Changed property `exposure` (string) + * Changed property `breedingMethodDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `instituteAddress` (string) + * Changed property `breedingMethodName` (string): + - Nullable changed: `true` -> `null` - * Changed property `instituteName` (string) + * Changed property `crossingProjectDbId` (string): + - Nullable changed: `true` -> `null` - * Changed property `locationDbId` (string) + * Changed property `germplasmPUI` (string): + - Nullable changed: `true` -> `null` - * Changed property `locationName` (string) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Changed property `locationType` (string) + Changed items (array): - * Changed property `siteStatus` (string) + Deleted properties: `referenceID` - * Changed property `slope` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `topography` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `coordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + * Changed property `parents` (array) + Changed items (array): - * Changed property `type` (string) + New properties: `germplasmPUI`, `pedigreeNodeDbId` - * Changed property `geometry` (object -> object) + New required properties: + - `germplasmName` + - `germplasmPUI` -##### `GET` /search/locations/{searchResultsDbId} + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` -> Submit a search request for `Location`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/location/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. +###### Return Type: +Deleted response : **404** -###### Parameters: +Changed response : **200** -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results +* Changed content type : `application/json` + * Changed property `result` (object) -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. + * Changed property `data` (array) + Changed items (array): -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. + New properties: `crossingProjectName`, `pedigreeNodeDbId`, `siblingDbIds` + Deleted properties: `siblings` -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} + New required properties: + - `germplasmPUI` + - `pedigreeNodeDbId` + * Changed property `breedingMethodDbId` (string): + - Nullable changed: `true` -> `null` -###### Return Type: + * Changed property `breedingMethodName` (string): + - Nullable changed: `true` -> `null` -Deleted response : **202 Accepted** -> Accepted + * Changed property `crossingProjectDbId` (string): + - Nullable changed: `true` -> `null` -Changed response : **200 OK** -> OK + * Changed property `germplasmPUI` (string): + - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` -* Changed content type : `application/json` + Changed items (array): - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + Deleted properties: `referenceID` + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `result` (object) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `data` (array) + * Changed property `parents` (array) + + Changed items (array): - Changed items (object): - > A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc. + New properties: `germplasmPUI`, `pedigreeNodeDbId` + New required properties: + - `germplasmName` + - `germplasmPUI` - * Added property `childLocationDbIds` (array) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. +##### `POST` /search/images - * Deleted property `parentLocationDbId` (string) - > The unique identifier for a Location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. +###### Request: +* Changed content type : `application/json` - * Deleted property `parentLocationName` (string) - > A human readable name for a location - >
The Parent Location defines the encompassing Location that a smaller Location belongs to. - > For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + * Changed property `imageLocation` (object) - * Changed property `abbreviation` (string) + New properties: `germplasmOrigin`, `imageDbId`, `imageName`, `observationDbId`, `observationUnit` - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + * Changed property `type` (string): + - Default changed: `Feature` -> `none` + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` - * Added property `additionalProperties` (string) +##### `POST` /search/locations - * Changed property `coordinateDescription` (string) - * Changed property `coordinateUncertainty` (string) +###### Request: - * Changed property `countryCode` (string) +* Changed content type : `application/json` - * Changed property `countryName` (string) + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `documentationURL` (string -> string) + * Changed property `abbreviations` (array): + - Nullable changed: `true` -> `null` - * Changed property `environmentType` (string) + * Changed property `altitudeMax` (number): + - Nullable changed: `true` -> `null` - * Changed property `exposure` (string) + * Changed property `altitudeMin` (number): + - Nullable changed: `true` -> `null` - * Changed property `instituteAddress` (string) + * Changed property `countryCodes` (array): + - Nullable changed: `true` -> `null` - * Changed property `instituteName` (string) + * Changed property `countryNames` (array): + - Nullable changed: `true` -> `null` - * Changed property `locationDbId` (string) + * Changed property `instituteAddresses` (array): + - Nullable changed: `true` -> `null` - * Changed property `locationName` (string) + * Changed property `instituteNames` (array): + - Nullable changed: `true` -> `null` - * Changed property `locationType` (string) + * Changed property `locationTypes` (array): + - Nullable changed: `true` -> `null` - * Changed property `siteStatus` (string) + * Changed property `parentLocationDbIds` (array): + - Nullable changed: `true` -> `null` - * Changed property `slope` (string) + * Changed property `parentLocationNames` (array): + - Nullable changed: `true` -> `null` - * Changed property `topography` (string) + * Changed property `coordinates` (object): + - Nullable changed: `true` -> `null` - * Changed property `coordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + New properties: `germplasmOrigin`, `imageDbId`, `imageName`, `observationDbId`, `observationUnit` + * Changed property `type` (string): + - Default changed: `Feature` -> `none` - * Changed property `type` (string) + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` - * Changed property `geometry` (object -> object) +##### `POST` /search/pedigree -##### `POST` /search/observations -> Submit a search request for `Observation` +###### Request: +* Changed content type : `application/json` -###### Parameters: + Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} + * Changed property `accessionNumbers` (array): + - Nullable changed: `true` -> `null` + * Changed property `binomialNames` (array): + - Nullable changed: `true` -> `null` -###### Request: + * Changed property `collections` (array): + - Nullable changed: `true` -> `null` -Deleted content type : `application/json` + * Changed property `familyCodes` (array): + - Nullable changed: `true` -> `null` -###### Return Type: + * Changed property `genus` (array): + - Nullable changed: `true` -> `null` -Changed response : **202 Accepted** -> Accepted + * Changed property `germplasmPUIs` (array): + - Nullable changed: `true` -> `null` + * Changed property `includeFullTree` (boolean): + - Nullable changed: `true` -> `null` -* Changed content type : `application/json` + * Changed property `includeParents` (boolean): + - Nullable changed: `true` -> `null` - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. + * Changed property `includeProgeny` (boolean): + - Nullable changed: `true` -> `null` + * Changed property `includeSiblings` (boolean): + - Nullable changed: `true` -> `null` -Changed response : **200 OK** -> OK + * Changed property `instituteCodes` (array): + - Nullable changed: `true` -> `null` + * Changed property `species` (array): + - Nullable changed: `true` -> `null` -* Changed content type : `application/json` + * Changed property `synonyms` (array): + - Nullable changed: `true` -> `null` + +###### Return Type: - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. +Changed response : **200** +* Changed content type : `application/json` * Changed property `result` (object) * Changed property `data` (array) - Changed items (object): - > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + Changed items (array): + New properties: `crossingProjectName`, `pedigreeNodeDbId`, `siblingDbIds` - * Added property `germplasmPUI` (string) + Deleted properties: `siblings` - * Added property `observationUnitPUI` (string) + New required properties: + - `germplasmPUI` + - `pedigreeNodeDbId` - * Added property `observationVariablePUI` (string) + * Changed property `breedingMethodDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `seasonDbId` (string) + * Changed property `breedingMethodName` (string): + - Nullable changed: `true` -> `null` - * Added property `seasonName` (string) + * Changed property `crossingProjectDbId` (string): + - Nullable changed: `true` -> `null` - * Added property `studyName` (string) + * Changed property `germplasmPUI` (string): + - Nullable changed: `true` -> `null` - * Added property `studyPUI` (string) + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + Changed items (array): + Deleted properties: `referenceID` - * Deleted property `observationDbId` (string) - > The ID which uniquely identifies an observation + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Deleted property `season` (object) + * Changed property `parents` (array) - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. + Changed items (array): + New properties: `germplasmPUI`, `pedigreeNodeDbId` - * Added property `additionalProperties` (string) + New required properties: + - `germplasmName` + - `germplasmPUI` - * Changed property `collector` (string) + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` - * Changed property `germplasmDbId` (string) +##### `GET` /search/pedigree/{searchResultsDbId} - * Changed property `germplasmName` (string) - * Changed property `observationTimeStamp` (string -> string) +###### Return Type: - * Changed property `observationUnitDbId` (string) +Deleted response : **202** - * Changed property `observationUnitName` (string) +Deleted response : **404** - * Changed property `observationVariableDbId` (string) +Changed response : **200** - * Changed property `observationVariableName` (string) +* Changed content type : `application/json` - * Changed property `studyDbId` (string) + * Changed property `result` (object) - * Changed property `uploadedBy` (string) + * Changed property `data` (array) - * Changed property `value` (string) + Changed items (array): - * Changed property `geoCoordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + New properties: `crossingProjectName`, `pedigreeNodeDbId`, `siblingDbIds` + Deleted properties: `siblings` - * Changed property `type` (string) + New required properties: + - `germplasmPUI` + - `pedigreeNodeDbId` - * Changed property `geometry` (object -> object) + * Changed property `breedingMethodDbId` (string): + - Nullable changed: `true` -> `null` -##### `GET` /search/observations/{searchResultsDbId} + * Changed property `breedingMethodName` (string): + - Nullable changed: `true` -> `null` -> Submit a search request for `Observation`
-> Search requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. -> If a server needs more time to process the request, it might respond with a `searchResultsDbId`. -> Use the corresponding `GET /search/observation/{searchResultsDbId}` to retrieve the results of the search.
-> Review the Search Services documentation for additional implementation details. + * Changed property `crossingProjectDbId` (string): + - Nullable changed: `true` -> `null` + * Changed property `germplasmPUI` (string): + - Nullable changed: `true` -> `null` -###### Parameters: + * Changed property `externalReferences` (array): + - Nullable changed: `null` -> `true` -Deleted: `Accept` in `header` -> A standard HTTP request header that is used to request a specific content type (JSON, CSV, etc) which is "acceptable" to the client and should be returned by the server + Changed items (array): + Deleted properties: `referenceID` -Deleted: `Authorization` in `header` -> HTTP HEADER - Token used for Authorization -> -> Bearer {token_string} + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` -Deleted: `searchResultsDbId` in `path` -> Unique identifier which references the search results + * Changed property `parents` (array) + Changed items (array): -Deleted: `page` in `query` -> Used to request a specific page of data to be returned. -> -> The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. + New properties: `germplasmPUI`, `pedigreeNodeDbId` + New required properties: + - `germplasmName` + - `germplasmPUI` -Deleted: `pageSize` in `query` -> The size of the pages to be returned. Default is `1000`. + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` +##### `GET` /variables -###### Return Type: -Deleted response : **202 Accepted** -> Accepted +###### Parameters: + +Deleted: `externalReferenceID` in `query` -Changed response : **200 OK** -> OK +##### `POST` /variables -* Changed content type : `application/json` +###### Request: - * Changed property `metadata` (object -> object) - > An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information. +* Changed content type : `application/json` + Changed items (array): - * Changed property `result` (object) + New properties: `methodDbId`, `methodName`, `methodPUI`, `scaleDbId`, `scaleName`, `scalePUI`, `traitDbId`, `traitName`, `traitPUI` - * Changed property `data` (array) + Deleted properties: `method`, `scale`, `trait` - Changed items (object): - > A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + New required properties: + - `methodDbId` + - `methodName` + - `scaleDbId` + - `scaleName` + - `traitName` + Removed required properties: + - `method` + - `scale` + - `trait` - * Added property `germplasmPUI` (string) + * Changed property `externalReferences` (array) - * Added property `observationUnitPUI` (string) + Changed items (array): - * Added property `observationVariablePUI` (string) + Deleted properties: `referenceID` - * Added property `seasonDbId` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Added property `seasonName` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Added property `studyName` (string) + * Changed property `ontologyReference` (object): + - Nullable changed: `true` -> `null` - * Added property `studyPUI` (string) + New properties: `ontologyReferenceDbId` - * Deleted property `externalReferences` (array) - > An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. + * Changed property `documentationLinks` (array) + Changed items (array): - * Deleted property `observationDbId` (string) - > The ID which uniquely identifies an observation + * Changed property `URL` (string): + - Nullable changed: `null` -> `true` + * Changed property `type` (string): + - Nullable changed: `null` -> `true` - * Deleted property `season` (object) +##### `PUT` /variables/{observationVariableDbId} - * Changed property `additionalInfo` (object) - > A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification. +###### Request: - * Added property `additionalProperties` (string) +* Changed content type : `application/json` - * Changed property `collector` (string) + New properties: `methodDbId`, `methodName`, `methodPUI`, `scaleDbId`, `scaleName`, `scalePUI`, `traitDbId`, `traitName`, `traitPUI` - * Changed property `germplasmDbId` (string) + Deleted properties: `method`, `scale`, `trait` - * Changed property `germplasmName` (string) + New required properties: + - `methodDbId` + - `methodName` + - `scaleDbId` + - `scaleName` + - `traitName` - * Changed property `observationTimeStamp` (string -> string) + Removed required properties: + - `method` + - `scale` + - `trait` - * Changed property `observationUnitDbId` (string) + * Changed property `externalReferences` (array) - * Changed property `observationUnitName` (string) + Changed items (array): - * Changed property `observationVariableDbId` (string) + Deleted properties: `referenceID` - * Changed property `observationVariableName` (string) + * Changed property `referenceId` (string): + - Nullable changed: `null` -> `true` - * Changed property `studyDbId` (string) + * Changed property `referenceSource` (string): + - Nullable changed: `null` -> `true` - * Changed property `uploadedBy` (string) + * Changed property `ontologyReference` (object): + - Nullable changed: `true` -> `null` - * Changed property `value` (string) + New properties: `ontologyReferenceDbId` - * Changed property `geoCoordinates` (object) - > One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - > - > Copied from RFC 7946 Section 3.1.1 - > - > A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - > easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + * Changed property `documentationLinks` (array) + Changed items (array): - * Changed property `type` (string) + * Changed property `URL` (string): + - Nullable changed: `null` -> `true` - * Changed property `geometry` (object -> object) + * Changed property `type` (string): + - Nullable changed: `null` -> `true` From 7acb116eb7ba13b9f026f32b647642a698362b6c Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Thu, 30 Apr 2026 13:21:31 +1200 Subject: [PATCH 24/62] Fix compareOpenAPI to use correct OpenAPI-Components directory - Changed -c parameter from 'Specification/Components' to 'Specification/OpenAPI-Components' - This ensures consistency with generateOpenAPI and generateOpenAPIJSON tasks - Fixes discrepancy between local and CI-generated comparison files --- generator/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/generator/build.gradle b/generator/build.gradle index 479990ab..a13c9f88 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -128,7 +128,7 @@ tasks.register("compareOpenAPI", JavaExec) { '-l', 'OPEN_API', '-f', filename, '-w', 'MARKDOWN', - '-c', 'Specification/Components', + '-c', 'Specification/OpenAPI-Components', '-x', '-t', '-r'] From 059084c067876509ad91e003db6a229b9e006107 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 1 May 2026 20:22:03 +1200 Subject: [PATCH 25/62] Update JSON schema and Gradle tasks for improved validation and response handling --- .../ObservationUnits_ObservationUnitDbId_GET_PUT.yaml | 4 ++++ .../BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json | 5 ++++- .../BrAPI-Schema/BrAPI-Phenotyping/Ontology.json | 5 ++++- generator/build.gradle | 10 +++++++++- 4 files changed, 21 insertions(+), 3 deletions(-) diff --git a/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_ObservationUnitDbId_GET_PUT.yaml b/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_ObservationUnitDbId_GET_PUT.yaml index 5a387139..2dc817fd 100644 --- a/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_ObservationUnitDbId_GET_PUT.yaml +++ b/Specification/BrAPI-Phenotyping/ObservationUnits/ObservationUnits_ObservationUnitDbId_GET_PUT.yaml @@ -24,6 +24,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Observation Units put: @@ -51,6 +53,8 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Observation Units components: diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json index 5504eaa2..246e0168 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/MarkerPosition.json @@ -15,7 +15,10 @@ ] }, "map": { - "$ref": "GenomeMap.json#/$defs/GenomeMap", + "anyOf": [ + {"$ref": "GenomeMap.json#/$defs/GenomeMap"}, + {"type": "null"} + ], "description": "The ID which uniquely identifies a `GenomeMap`", "referencedAttribute": "markerPositions", "relationshipType": "many-to-one" diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json index 0471380b..de3e6ccf 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json @@ -49,7 +49,10 @@ }, "ontologyName": { "description": "Ontology name", - "type": "string" + "type": [ + "null", + "string" + ] }, "version": { "description": "Ontology version (no specific format)", diff --git a/generator/build.gradle b/generator/build.gradle index a13c9f88..b326a4e0 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.64.0' + brapiSchemaToolsVersion = '0.65.0' } repositories { @@ -118,6 +118,8 @@ tasks.register("generateAll") { tasks.register("compareOpenAPI", JavaExec) { group = 'BrAPI' description = 'Compare the compiled OpenAPI schema from the YAML files with the one generated from the Json Schema' + dependsOn copyOpenApi + dependsOn generateOpenAPIJSON classpath = sourceSets.main.runtimeClasspath mainClass = javaMainClass workingDir = '../' @@ -136,4 +138,10 @@ tasks.register("compareOpenAPI", JavaExec) { tasks.register("compareAll") { dependsOn compareOpenAPI + mustRunAfter generateAll +} + +tasks.register("runAll") { + dependsOn generateAll + dependsOn compareAll } From 1cda315db6d479a23cafa9953a5cbede1b185a36 Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Fri, 1 May 2026 09:49:13 +0000 Subject: [PATCH 26/62] Generate specifications (manually triggered) --- Specification/Generated/brapi_generated.ttl | 1012 +++++++++---------- 1 file changed, 506 insertions(+), 506 deletions(-) diff --git a/Specification/Generated/brapi_generated.ttl b/Specification/Generated/brapi_generated.ttl index d9d17179..c20350f8 100644 --- a/Specification/Generated/brapi_generated.ttl +++ b/Specification/Generated/brapi_generated.ttl @@ -10,6 +10,13 @@ PREFIX xsd: rdfs:label "language"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Specifies a FASTA format file/string."@en; + rdfs:domain ; + rdfs:label "sourceURI"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes."@en; @@ -25,13 +32,6 @@ PREFIX xsd: rdfs:label "sourceName"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Specifies a FASTA format file/string."@en; - rdfs:domain ; - rdfs:label "sourceURI"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Describes the approximate slope (height/distance) of a Location."@en; @@ -128,9 +128,12 @@ PREFIX xsd: rdfs:label "analysis"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -139,13 +142,6 @@ PREFIX xsd: rdfs:label "seedLot"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "The unique DbId of the breeding program this Seed Lot belongs to"@en; @@ -235,13 +231,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`."@en; - rdfs:domain ; - rdfs:label "sequence"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)"@en; @@ -249,12 +238,12 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`."@en; + rdfs:domain ; + rdfs:label "sequence"@en; + rdfs:range xsd:string . rdf:type owl:NamedIndividual , . @@ -266,13 +255,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "The child germplasm"@en; - rdfs:domain ; - rdfs:label "childGermplasm"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "Zero or more filters that failed for this variant. VCF column 7 \"FILTER\" shared across all alleles in the same VCF record."@en; @@ -285,6 +267,20 @@ PREFIX xsd: rdfs:comment "Links to various ontology documentation"@en; rdfs:label "DocumentationLink"@en . + + rdf:type owl:ObjectProperty; + rdfs:comment "The child germplasm"@en; + rdfs:domain ; + rdfs:label "childGermplasm"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The name or identifier of the entity which took the `Sample` from the field"@en; @@ -311,16 +307,16 @@ PREFIX xsd: rdfs:comment "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended."@en; rdfs:label "Publication"@en . - - rdf:type owl:Class; - rdfs:comment "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"."@en; - rdfs:label "Season"@en . - rdf:type owl:Class; rdfs:comment "The type of documentation, which can be OBO Foundry, an RDF term or a webpage."@en; rdfs:label "DocumentationLinkType"@en . + + rdf:type owl:Class; + rdfs:comment "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"."@en; + rdfs:label "Season"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "The version of the update."@en; @@ -458,6 +454,10 @@ PREFIX xsd: rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; rdfs:label "GermplasmOrigin"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -486,10 +486,6 @@ PREFIX xsd: rdfs:label "unknownString"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The ID which uniquely identifies a CallSet within the given database server"@en; @@ -533,6 +529,13 @@ PREFIX xsd: rdfs:label "positionCoordinateYType"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "the value of a cross attribute"@en; + rdfs:domain ; + rdfs:label "crossAttributeValue"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study"@en; @@ -540,11 +543,11 @@ PREFIX xsd: rdfs:label "studyDescription"@en; rdfs:range xsd:string . - + rdf:type owl:DatatypeProperty; - rdfs:comment "the value of a cross attribute"@en; - rdfs:domain ; - rdfs:label "crossAttributeValue"@en; + rdfs:comment "Common name for the crop"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; rdfs:range xsd:string . @@ -554,12 +557,9 @@ PREFIX xsd: rdfs:label "program"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -603,12 +603,9 @@ PREFIX xsd: rdfs:label "email"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The full name of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; - rdfs:domain ; - rdfs:label "instituteName"@en; - rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -622,6 +619,13 @@ PREFIX xsd: rdfs:comment "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample"@en; rdfs:label "CallSet"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The full name of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; + rdfs:domain ; + rdfs:label "instituteName"@en; + rdfs:range xsd:string . + rdf:type owl:NamedIndividual , . @@ -645,13 +649,6 @@ PREFIX xsd: rdfs:label "attributeValues"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The timestamp for the last update to this Seed Lot (including transactions)"@en; - rdfs:domain ; - rdfs:label "lastUpdated"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The array of DbIds of the BrAPI objects contained in a List"@en; @@ -659,6 +656,13 @@ PREFIX xsd: rdfs:label "data"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The timestamp for the last update to this Seed Lot (including transactions)"@en; + rdfs:domain ; + rdfs:label "lastUpdated"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "The record of an event where material was moved in or out of a particular SeedLot"@en; @@ -842,11 +846,6 @@ PREFIX xsd: rdfs:comment "The techniques and protocol used to produce a Cross or Germplasm"@en; rdfs:label "BreedingMethod"@en . - - rdf:type owl:Class; - rdfs:comment "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit."@en; - rdfs:label "Observation"@en . - rdf:type owl:ObjectProperty; rdfs:comment "associated pedigreeNode"@en; @@ -854,12 +853,10 @@ PREFIX xsd: rdfs:label "pedigreeNode"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . + + rdf:type owl:Class; + rdfs:comment "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit."@en; + rdfs:label "Observation"@en . rdf:type owl:DatatypeProperty; @@ -868,12 +865,12 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975)."@en; - rdfs:domain ; - rdfs:label "latitudeDecimal"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -882,6 +879,13 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975)."@en; + rdfs:domain ; + rdfs:label "latitudeDecimal"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The human readable name for a crossing project"@en; @@ -1090,13 +1094,6 @@ PREFIX xsd: rdfs:comment "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\""@en; rdfs:label "EntryType"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology database unique identifier"@en; - rdfs:domain ; - rdfs:label "ontologyDbId"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "A string representation of the `Reference` base alleles."@en; @@ -1109,6 +1106,13 @@ PREFIX xsd: rdfs:label "institution"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology database unique identifier"@en; + rdfs:domain ; + rdfs:label "ontologyDbId"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The human readable name of an image. Might be the same as 'imageFileName', but could be different."@en; @@ -1202,9 +1206,12 @@ PREFIX xsd: rdfs:comment "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances."@en; rdfs:label "PedigreeNode"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology licence"@en; + rdfs:domain ; + rdfs:label "licence"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -1213,13 +1220,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology licence"@en; - rdfs:domain ; - rdfs:label "licence"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The Y position coordinate for an observation unit. Different systems may use different coordinate systems."@en; @@ -1255,6 +1255,10 @@ PREFIX xsd: rdfs:label "referenceSet"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; @@ -1345,12 +1349,12 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:NamedIndividual , . + + rdf:type owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . @@ -1480,10 +1484,6 @@ PREFIX xsd: rdfs:label "attributeDescription"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The date the study ends\n\nMIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended"@en; @@ -1510,10 +1510,6 @@ PREFIX xsd: rdfs:label "taxonIds"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The germplasm using in this content mixture"@en; @@ -1688,13 +1684,6 @@ PREFIX xsd: rdfs:label "germplasmDbId"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. "@en; - rdfs:domain ; - rdfs:label "parentType"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -1702,12 +1691,12 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - + rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . + rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. "@en; + rdfs:domain ; + rdfs:label "parentType"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -1716,11 +1705,6 @@ PREFIX xsd: rdfs:label "observationVariable"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit"@en; - rdfs:label "GermplasmAttribute"@en . - rdf:type owl:ObjectProperty; rdfs:comment "siblingPedigreeNodes"@en; @@ -1728,12 +1712,24 @@ PREFIX xsd: rdfs:label "siblingPedigreeNodes"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "observations"@en; - rdfs:domain ; - rdfs:label "observations"@en; - rdfs:range . + + rdf:type owl:Class; + rdfs:comment "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit"@en; + rdfs:label "GermplasmAttribute"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observations"@en; + rdfs:domain ; + rdfs:label "observations"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -1815,9 +1811,6 @@ PREFIX xsd: rdfs:label "coordinates"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "associated observation Unit"@en; @@ -1825,6 +1818,9 @@ PREFIX xsd: rdfs:label "observationUnit"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; @@ -1832,17 +1828,17 @@ PREFIX xsd: rdfs:label "scale"@en; rdfs:range . - + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; + rdfs:domain ; rdfs:label "additionalInfo"@en; rdfs:range . - + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; + rdfs:domain ; rdfs:label "additionalInfo"@en; rdfs:range . @@ -1853,17 +1849,6 @@ PREFIX xsd: rdfs:label "observationUnits"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a Location"@en; - rdfs:domain ; - rdfs:label "locationDbId"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "physical address of this person"@en; @@ -1887,6 +1872,13 @@ PREFIX xsd: rdfs:label "phaseSet"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a Location"@en; + rdfs:domain ; + rdfs:label "locationDbId"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard "@en; @@ -1911,6 +1903,13 @@ PREFIX xsd: rdfs:label "crosses"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a separator for unphased allele calls."@en; + rdfs:domain ; + rdfs:label "sepUnphased"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "the description for a crossing project"@en; @@ -1918,12 +1917,9 @@ PREFIX xsd: rdfs:label "crossingProjectDescription"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a separator for unphased allele calls."@en; - rdfs:domain ; - rdfs:label "sepUnphased"@en; - rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -1966,6 +1962,13 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date this trial ends"@en; + rdfs:domain ; + rdfs:label "endDate"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "A descriptive classification for this synonym"@en; @@ -1973,12 +1976,12 @@ PREFIX xsd: rdfs:label "type"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date this trial ends"@en; - rdfs:domain ; - rdfs:label "endDate"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "Analysis associated with a variant set"@en; + rdfs:domain ; + rdfs:label "variantSet"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -1994,13 +1997,6 @@ PREFIX xsd: rdfs:label "variantSets"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "Analysis associated with a variant set"@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "The ID of the reference set that describes the sequences used by the variants in this set."@en; @@ -2068,13 +2064,6 @@ PREFIX xsd: rdfs:label "progenyPedigreeNodes"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of elements in a List"@en; - rdfs:domain ; - rdfs:label "listSize"@en; - rdfs:range xsd:integer . - rdf:type owl:DatatypeProperty; rdfs:comment "True if all filters for this variant passed. VCF column 7 \"FILTER\" value PASS."@en; @@ -2082,6 +2071,13 @@ PREFIX xsd: rdfs:label "filtersPassed"@en; rdfs:range xsd:boolean . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of elements in a List"@en; + rdfs:domain ; + rdfs:label "listSize"@en; + rdfs:range xsd:integer . + rdf:type owl:DatatypeProperty; rdfs:comment "A unique identifier physically attached to the `Sample`"@en; @@ -2254,10 +2250,6 @@ PREFIX xsd: rdfs:label "observationTimeStamp"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -2310,20 +2302,6 @@ PREFIX xsd: rdfs:label "mcpd"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "observations"@en; - rdfs:domain ; - rdfs:label "observations"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of scientist submitting the variable."@en; - rdfs:domain ; - rdfs:label "scientist"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; @@ -2338,6 +2316,13 @@ PREFIX xsd: rdfs:label "species"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "observations"@en; + rdfs:domain ; + rdfs:label "observations"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described."@en; @@ -2345,12 +2330,12 @@ PREFIX xsd: rdfs:label "publicReleaseDate"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "Information about the location where the sample was collected"@en; - rdfs:domain ; - rdfs:label "collectingSite"@en; - rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of scientist submitting the variable."@en; + rdfs:domain ; + rdfs:label "scientist"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -2366,6 +2351,13 @@ PREFIX xsd: rdfs:label "callSets"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "Information about the location where the sample was collected"@en; + rdfs:domain ; + rdfs:label "collectingSite"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . @@ -2428,12 +2420,9 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . - - rdf:type owl:ObjectProperty; - rdfs:comment "The mixture of germplasm present in the seed lot.\n
\nIf this seed lot only contains a single germplasm, the response should contain the name \nand DbId of that germplasm with a mixturePercentage value of 100\n
\nIf the seed lot contains a mixture of different germplasm, the response should contain \nthe name and DbId every germplasm present. The mixturePercentage field should contain \nthe ratio of each germplasm in the total mixture. All of the mixturePercentage values \nin this array should sum to equal 100."@en; - rdfs:domain ; - rdfs:label "contentMixture"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -2442,6 +2431,17 @@ PREFIX xsd: rdfs:label "taxonId"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The mixture of germplasm present in the seed lot.\n
\nIf this seed lot only contains a single germplasm, the response should contain the name \nand DbId of that germplasm with a mixturePercentage value of 100\n
\nIf the seed lot contains a mixture of different germplasm, the response should contain \nthe name and DbId every germplasm present. The mixturePercentage field should contain \nthe ratio of each germplasm in the total mixture. All of the mixturePercentage values \nin this array should sum to equal 100."@en; + rdfs:domain ; + rdfs:label "contentMixture"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "the maximum number of elements per page in this dimension of the matrix"@en; @@ -2565,6 +2565,13 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "the human readable name of a cross attribute"@en; + rdfs:domain ; + rdfs:label "crossAttributeName"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; @@ -2575,13 +2582,6 @@ PREFIX xsd: rdfs:comment "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; rdfs:label "GeoJSONPoint"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "the human readable name of a cross attribute"@en; - rdfs:domain ; - rdfs:label "crossAttributeName"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required."@en; @@ -2645,10 +2645,6 @@ PREFIX xsd: rdfs:label "trait"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -2710,6 +2706,9 @@ PREFIX xsd: rdfs:label "georeferencingMethod"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "the requested page number (zero indexed)"@en; @@ -2717,9 +2716,6 @@ PREFIX xsd: rdfs:label "page"@en; rdfs:range xsd:integer . - - rdf:type owl:NamedIndividual , . - rdf:type owl:NamedIndividual , . @@ -2863,20 +2859,6 @@ PREFIX xsd: rdfs:label "documentationURL"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated \nby `start + referenceBases.length`."@en; @@ -2884,6 +2866,13 @@ PREFIX xsd: rdfs:label "end"@en; rdfs:range xsd:integer . + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "phone number of this person"@en; @@ -2898,6 +2887,13 @@ PREFIX xsd: rdfs:label "license"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "variants"@en; @@ -2976,10 +2972,6 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "observationUnits"@en; @@ -3095,13 +3087,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)"@en; - rdfs:domain ; - rdfs:label "topography"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "A description of the things being transferred between SeedLots in a transaction (seeds, bulbs, kg, etc)"@en; @@ -3123,15 +3108,18 @@ PREFIX xsd: rdfs:label "dataMatrixAbbreviation"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)"@en; + rdfs:domain ; + rdfs:label "topography"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; rdfs:label "GeoJSON"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "plates"@en; @@ -3160,6 +3148,13 @@ PREFIX xsd: rdfs:label "sampleDescription"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . @@ -3184,13 +3179,6 @@ PREFIX xsd: rdfs:label "crossingProjectDbId"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3532,6 +3520,11 @@ PREFIX xsd: rdfs:label "created"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "If the Scale is a categorical type, these objects define the valid options"@en; + rdfs:label "ValidValuesCategory"@en . + rdf:type owl:ObjectProperty; rdfs:comment "The `GenomeMap` to which this `LinkageGroup` belongs "@en; @@ -3539,10 +3532,9 @@ PREFIX xsd: rdfs:label "genomeMap"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "If the Scale is a categorical type, these objects define the valid options"@en; - rdfs:label "ValidValuesCategory"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -3575,6 +3567,10 @@ PREFIX xsd: rdfs:label "institution"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "List of links to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; @@ -3632,6 +3628,10 @@ PREFIX xsd: rdfs:comment "The dimension of the matrix being paginated"@en; rdfs:label "Dimension"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "the human readable identifier for this breeding method"@en; @@ -3646,13 +3646,6 @@ PREFIX xsd: rdfs:label "version"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "Set of custom attributes associated with a cross"@en; - rdfs:domain ; - rdfs:label "crossAttributes"@en; - rdfs:range . - rdf:type owl:NamedIndividual , . @@ -3663,11 +3656,12 @@ PREFIX xsd: rdfs:label "studyType"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:domain ; - rdfs:label "validValues"@en; - rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "Set of custom attributes associated with a cross"@en; + rdfs:domain ; + rdfs:label "crossAttributes"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -3676,6 +3670,12 @@ PREFIX xsd: rdfs:label "scientificType"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:domain ; + rdfs:label "validValues"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "The list of pollination events that occurred for this cross."@en; @@ -3690,20 +3690,6 @@ PREFIX xsd: rdfs:label "traitDescription"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "Genotype Metadata are additional layers of metadata associated with each genotype."@en; - rdfs:domain ; - rdfs:label "genotypeMetadata"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology's list of authors (no specific format)"@en; - rdfs:domain ; - rdfs:label "authors"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; @@ -3711,30 +3697,38 @@ PREFIX xsd: rdfs:label "biologicalStatusOfAccessionCode"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The value of this attribute for a given germplasm"@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . rdf:type owl:Class; rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; rdfs:label "StorageTypeCode"@en . - + rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . + rdfs:comment "Genotype Metadata are additional layers of metadata associated with each genotype."@en; + rdfs:domain ; + rdfs:label "genotypeMetadata"@en; + rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:domain ; - rdfs:label "safetyDuplicateInstitutes"@en; - rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The value of this attribute for a given germplasm"@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology's list of authors (no specific format)"@en; + rdfs:domain ; + rdfs:label "authors"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -3743,6 +3737,12 @@ PREFIX xsd: rdfs:label "collectingInstitutes"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:domain ; + rdfs:label "safetyDuplicateInstitutes"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The date this call set was created"@en; @@ -3821,9 +3821,6 @@ PREFIX xsd: rdfs:label "md5checksum"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3831,9 +3828,8 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:NamedIndividual , . rdf:type owl:DatatypeProperty; @@ -3903,13 +3899,6 @@ PREFIX xsd: rdfs:label "callSets"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Siblings share at least one parent with the given germplasm. \n
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response."@en; - rdfs:domain ; - rdfs:label "siblings"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "associated scale"@en; @@ -3917,6 +3906,13 @@ PREFIX xsd: rdfs:label "scale"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Siblings share at least one parent with the given germplasm. \n
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response."@en; + rdfs:domain ; + rdfs:label "siblings"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3929,10 +3925,6 @@ PREFIX xsd: rdfs:comment "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100."@en; rdfs:label "ContentMixture"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123)."@en; @@ -3940,6 +3932,10 @@ PREFIX xsd: rdfs:label "longitudeDecimal"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The human readable identifier for a `GenomeMap`"@en; @@ -3990,13 +3986,6 @@ PREFIX xsd: rdfs:label "observationUnit"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a trial"@en; - rdfs:domain ; - rdfs:label "trial"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "The unique identifier for a List Owner. (usually a user or person)"@en; @@ -4004,6 +3993,13 @@ PREFIX xsd: rdfs:label "listOwnerPerson"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a trial"@en; + rdfs:domain ; + rdfs:label "trial"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; @@ -4077,10 +4073,6 @@ PREFIX xsd: rdfs:label "observationVariables"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -4102,13 +4094,6 @@ PREFIX xsd: rdfs:comment "Information about the collection of a germplasm"@en; rdfs:label "CollectingInfo"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "List of contact entities associated with this trial"@en; @@ -4116,6 +4101,13 @@ PREFIX xsd: rdfs:label "contacts"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "For numerical, number of decimal places to be reported"@en; @@ -4133,6 +4125,11 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:Class; + rdfs:comment "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)"@en; + rdfs:label "AcquisitionSourceCode"@en . + rdf:type owl:ObjectProperty; rdfs:comment "samples"@en; @@ -4140,11 +4137,6 @@ PREFIX xsd: rdfs:label "samples"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)"@en; - rdfs:label "AcquisitionSourceCode"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'."@en; @@ -4159,6 +4151,13 @@ PREFIX xsd: rdfs:label "abbreviation"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The percentage of the given germplasm in the seed lot mixture."@en; + rdfs:domain ; + rdfs:label "mixturePercentage"@en; + rdfs:range xsd:integer . + rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers\" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\"."@en; @@ -4173,12 +4172,9 @@ PREFIX xsd: rdfs:label "coordinateDescription"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The percentage of the given germplasm in the seed lot mixture."@en; - rdfs:domain ; - rdfs:label "mixturePercentage"@en; - rdfs:range xsd:integer . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -4201,10 +4197,6 @@ PREFIX xsd: rdfs:label "study"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows."@en; @@ -4303,6 +4295,10 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing."@en; @@ -4313,13 +4309,6 @@ PREFIX xsd: rdfs:comment "The metadata for an image file that is connected to some phenotypic observation data."@en; rdfs:label "Image"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The number of CallSets included in this VariantSet"@en; @@ -4334,18 +4323,18 @@ PREFIX xsd: rdfs:label "unit"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "A persons contact information"@en; rdfs:label "Contact"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of Variants included in this VariantSet"@en; - rdfs:domain ; - rdfs:label "variantCount"@en; - rdfs:range xsd:integer . - rdf:type owl:ObjectProperty; rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; @@ -4353,6 +4342,13 @@ PREFIX xsd: rdfs:label "method"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of Variants included in this VariantSet"@en; + rdfs:domain ; + rdfs:label "variantCount"@en; + rdfs:range xsd:integer . + rdf:type owl:ObjectProperty; rdfs:comment "the first parent used in the cross"@en; @@ -4400,6 +4396,10 @@ PREFIX xsd: rdfs:label "attributeValueDbId"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "The type of documentation, which can be OBO Foundry, an RDF term or a webpage."@en; @@ -4436,10 +4436,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -4590,13 +4586,6 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date this study started\n\nMIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started"@en; - rdfs:domain ; - rdfs:label "startDate"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "A single position"@en; @@ -4604,6 +4593,13 @@ PREFIX xsd: rdfs:label "coordinates"@en; rdfs:range xsd:double . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date this study started\n\nMIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started"@en; + rdfs:domain ; + rdfs:label "startDate"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum."@en; @@ -4618,14 +4614,14 @@ PREFIX xsd: rdfs:label "type"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:Class; rdfs:comment "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other."@en; rdfs:label "AvailableFormat"@en . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; @@ -4633,13 +4629,6 @@ PREFIX xsd: rdfs:label "defaultValue"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; - rdfs:domain ; - rdfs:label "donorAccessionNumber"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The full name of this contact person\n\nMIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications)"@en; @@ -4647,6 +4636,13 @@ PREFIX xsd: rdfs:label "name"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; + rdfs:domain ; + rdfs:label "donorAccessionNumber"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study."@en; @@ -4701,10 +4697,6 @@ PREFIX xsd: rdfs:label "collectingNumber"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "samples"@en; @@ -4743,6 +4735,13 @@ PREFIX xsd: rdfs:comment "An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. \n
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other"@en; rdfs:label "Event"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard."@en; + rdfs:domain ; + rdfs:label "fieldName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The ID which uniquely identifies a `Variant`"@en; @@ -4794,11 +4793,11 @@ PREFIX xsd: rdfs:label "potentialParents"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard."@en; - rdfs:domain ; - rdfs:label "fieldName"@en; + rdfs:comment "The human readable name which identifies a germplasm within the given database server"@en; + rdfs:domain ; + rdfs:label "callSetName"@en; rdfs:range xsd:string . @@ -4862,12 +4861,12 @@ PREFIX xsd: rdfs:label "levelOrder"@en; rdfs:range xsd:integer . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name which identifies a germplasm within the given database server"@en; - rdfs:domain ; - rdfs:label "callSetName"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "images"@en; + rdfs:domain ; + rdfs:label "images"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -4876,13 +4875,6 @@ PREFIX xsd: rdfs:label "elevation"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "images"@en; - rdfs:domain ; - rdfs:label "images"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "Unique identifier for this analysis description"@en; @@ -4959,6 +4951,10 @@ PREFIX xsd: rdfs:label "parent2"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The number of markers present in a `GenomeMap`"@en; @@ -4997,6 +4993,10 @@ PREFIX xsd: rdfs:comment "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology"@en; rdfs:label "ExperimentalDesign"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "Information about an accession donor"@en; @@ -5096,6 +5096,10 @@ PREFIX xsd: rdfs:label "updated"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation"@en; @@ -5187,6 +5191,13 @@ PREFIX xsd: rdfs:label "samplePUI"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "The season for this Observation"@en; @@ -5222,12 +5233,9 @@ PREFIX xsd: rdfs:label "toSeedLot"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -5241,10 +5249,6 @@ PREFIX xsd: rdfs:comment "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding "@en; rdfs:label "ProgramType"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Name of institution submitting the variable"@en; @@ -5325,16 +5329,16 @@ PREFIX xsd: rdfs:comment "The type of positional coordinate. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; rdfs:label "PositionCoordinateType"@en . - - rdf:type owl:Class; - rdfs:comment "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented."@en; - rdfs:label "CrossingProject"@en . - rdf:type owl:Class; rdfs:comment "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)"@en; rdfs:label "EventDateRange"@en . + + rdf:type owl:Class; + rdfs:comment "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented."@en; + rdfs:label "CrossingProject"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "The ID which uniquely identifies an observation"@en; @@ -5353,10 +5357,6 @@ PREFIX xsd: rdf:type owl:Class; rdfs:label "ExternalReference"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The time at which this call set was last updated"@en; @@ -5413,13 +5413,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a study within the given database server\n\nMIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution."@en; - rdfs:domain ; - rdfs:label "studyDbId"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -5427,6 +5420,13 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a study within the given database server\n\nMIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution."@en; + rdfs:domain ; + rdfs:label "studyDbId"@en; + rdfs:range xsd:string . + rdf:type owl:NamedIndividual , . @@ -5494,13 +5494,6 @@ PREFIX xsd: rdfs:label "term"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The DOI or other permanent unique identifier for this published dataset"@en; - rdfs:domain ; - rdfs:label "datasetPUI"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; @@ -5508,6 +5501,13 @@ PREFIX xsd: rdfs:label "growthStage"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The DOI or other permanent unique identifier for this published dataset"@en; + rdfs:domain ; + rdfs:label "datasetPUI"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies an `ObservationUnit`"@en; @@ -5525,13 +5525,6 @@ PREFIX xsd: rdfs:comment "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present."@en; rdfs:label "Cross"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Timestamp when the entity was last updated"@en; - rdfs:domain ; - rdfs:label "dateModified"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Human readable name used for display purposes"@en; @@ -5539,6 +5532,13 @@ PREFIX xsd: rdfs:label "defaultDisplayName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Timestamp when the entity was last updated"@en; + rdfs:domain ; + rdfs:label "dateModified"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level."@en; @@ -5648,6 +5648,13 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."@en; + rdfs:domain ; + rdfs:label "orcid"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. "@en; @@ -5683,13 +5690,6 @@ PREFIX xsd: rdfs:label "accessionNumber"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."@en; - rdfs:domain ; - rdfs:label "orcid"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Method unique identifier"@en; @@ -5772,10 +5772,6 @@ PREFIX xsd: rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; rdfs:label "ObservationUnitHierarchyLevel"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation"@en; @@ -5856,10 +5852,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a `Program` within the given database server"@en; @@ -5902,10 +5894,6 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -5934,10 +5922,6 @@ PREFIX xsd: rdfs:label "instituteCode"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -6020,13 +6004,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The description of the source where this material was originally collected (wild, nursery, etc)"@en; - rdfs:domain ; - rdfs:label "sourceCollection"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The URL or URI to the documentation"@en; @@ -6034,6 +6011,13 @@ PREFIX xsd: rdfs:label "URL"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The description of the source where this material was originally collected (wild, nursery, etc)"@en; + rdfs:domain ; + rdfs:label "sourceCollection"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space."@en; @@ -6062,10 +6046,6 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this attribute"@en; @@ -6127,9 +6107,12 @@ PREFIX xsd: rdfs:label "software"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -6150,12 +6133,9 @@ PREFIX xsd: rdfs:label "discreteDates"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -6199,6 +6179,14 @@ PREFIX xsd: rdfs:label "samples"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "Description of a List"@en; @@ -6275,6 +6263,10 @@ PREFIX xsd: rdfs:comment "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap."@en; rdfs:label "MarkerPosition"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "URI pointing to an ontology class for the parameter"@en; @@ -6282,13 +6274,6 @@ PREFIX xsd: rdfs:label "parameterPUI"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "mapDbId"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group."@en; @@ -6315,6 +6300,13 @@ PREFIX xsd: rdfs:label "defaultDisplayName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "mapDbId"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; @@ -6520,6 +6512,10 @@ PREFIX xsd: rdfs:label "filtersApplied"@en; rdfs:range xsd:boolean . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples."@en; @@ -6633,6 +6629,13 @@ PREFIX xsd: rdfs:label "row"@en; rdfs:range xsd:string . + + rdf:type , owl:NamedIndividual , . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "List of treatments applied to an observation unit.\n\nMIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit."@en; @@ -6640,9 +6643,6 @@ PREFIX xsd: rdfs:label "treatments"@en; rdfs:range . - - rdf:type , owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment ""@en; From bcc17dc68dbc6ea5c06903d777bfd5e122538a8d Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Sat, 2 May 2026 06:47:29 +0000 Subject: [PATCH 27/62] Generate specifications (manually triggered) --- Specification/Generated/BrAPI-Core.yaml | 6 + Specification/Generated/BrAPI-Genotyping.yaml | 12 +- Specification/Generated/BrAPI-Germplasm.yaml | 14 + .../Generated/BrAPI-Phenotyping.yaml | 8 + Specification/Generated/brapi_generated.json | 117 +- Specification/Generated/brapi_generated.ttl | 1040 ++++++++--------- Specification/Generated/brapi_openapi.json | 22 + .../Generated/brapi_openapi_comparison.md | 309 +---- 8 files changed, 706 insertions(+), 822 deletions(-) diff --git a/Specification/Generated/BrAPI-Core.yaml b/Specification/Generated/BrAPI-Core.yaml index b5230fe1..c3a5dce1 100644 --- a/Specification/Generated/BrAPI-Core.yaml +++ b/Specification/Generated/BrAPI-Core.yaml @@ -125,6 +125,7 @@ paths: schema: $ref: "#/components/schemas/ListType" - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -228,6 +229,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -319,6 +321,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -415,6 +418,7 @@ paths: - STANDARD - PROJECT - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -646,6 +650,7 @@ paths: - desc - DESC - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -810,6 +815,7 @@ paths: - desc - DESC - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" diff --git a/Specification/Generated/BrAPI-Genotyping.yaml b/Specification/Generated/BrAPI-Genotyping.yaml index c45f621c..52293db9 100644 --- a/Specification/Generated/BrAPI-Genotyping.yaml +++ b/Specification/Generated/BrAPI-Genotyping.yaml @@ -110,6 +110,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -338,6 +339,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -469,6 +471,7 @@ paths: type: integer format: int32 - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -551,6 +554,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -648,6 +652,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -753,6 +758,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/pageToken" - $ref: "#/components/parameters/page" @@ -833,6 +839,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -4240,10 +4247,10 @@ components: nullable: true mapDbId: type: string + nullable: true mapName: type: string - mapPUI: - type: string + nullable: true position: type: integer description: The position of a marker or variant within a `LinkageGroup` @@ -4251,6 +4258,7 @@ components: nullable: true variantDbId: type: string + nullable: true description: A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap. diff --git a/Specification/Generated/BrAPI-Germplasm.yaml b/Specification/Generated/BrAPI-Germplasm.yaml index ca169260..a1ada153 100644 --- a/Specification/Generated/BrAPI-Germplasm.yaml +++ b/Specification/Generated/BrAPI-Germplasm.yaml @@ -76,6 +76,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -192,6 +193,7 @@ paths: schema: type: boolean - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -342,6 +344,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -502,6 +505,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -592,6 +596,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -780,6 +785,7 @@ paths: type: integer format: int32 - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -882,6 +888,7 @@ paths: - DONE - SKIPPED - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -1008,6 +1015,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -2486,16 +2494,22 @@ components: properties: germplasmDbId: type: string + nullable: true germplasmName: type: string + nullable: true germplasmPUI: type: string + nullable: true observationUnitDbId: type: string + nullable: true observationUnitName: type: string + nullable: true observationUnitPUI: type: string + nullable: true parentType: $ref: "#/components/schemas/ParentType" description: The identifying information gor the parent material of a cross. diff --git a/Specification/Generated/BrAPI-Phenotyping.yaml b/Specification/Generated/BrAPI-Phenotyping.yaml index b5a49dee..73af2c46 100644 --- a/Specification/Generated/BrAPI-Phenotyping.yaml +++ b/Specification/Generated/BrAPI-Phenotyping.yaml @@ -123,6 +123,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -209,6 +210,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -417,6 +419,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -646,6 +649,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -851,6 +855,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -993,6 +998,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -1079,6 +1085,7 @@ paths: schema: type: string - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -5394,6 +5401,7 @@ components: ontologyName: type: string description: Ontology name + nullable: true version: type: string description: Ontology version (no specific format) diff --git a/Specification/Generated/brapi_generated.json b/Specification/Generated/brapi_generated.json index 2ac94fcd..acde9b4b 100644 --- a/Specification/Generated/brapi_generated.json +++ b/Specification/Generated/brapi_generated.json @@ -195,6 +195,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -289,6 +292,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -451,6 +457,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -860,6 +869,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -1082,6 +1094,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -1214,6 +1229,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -1355,6 +1373,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -1486,6 +1507,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -1627,6 +1651,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -1831,6 +1858,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -2082,6 +2112,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -2352,6 +2385,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -2631,6 +2667,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -2981,6 +3020,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -3113,6 +3155,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -3259,6 +3304,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -3475,6 +3523,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -3603,6 +3654,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -3783,6 +3837,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -3895,6 +3952,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -4034,6 +4094,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -4196,6 +4259,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -4445,6 +4511,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -4677,6 +4746,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -4800,6 +4872,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -5014,6 +5089,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -5128,6 +5206,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -5243,6 +5324,9 @@ { "$ref" : "#/components/parameters/externalReferenceId" }, + { + "$ref" : "#/components/parameters/externalReferenceID" + }, { "$ref" : "#/components/parameters/externalReferenceSource" }, @@ -11412,22 +11496,28 @@ "type" : "object", "properties" : { "germplasmDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "parentType" : { "$ref" : "#/components/schemas/ParentType" @@ -15417,13 +15507,12 @@ "nullable" : true }, "mapDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "mapName" : { - "type" : "string" - }, - "mapPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "position" : { "type" : "integer", @@ -15432,7 +15521,8 @@ "nullable" : true }, "variantDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true } }, "description" : "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." @@ -17349,7 +17439,8 @@ }, "ontologyName" : { "type" : "string", - "description" : "Ontology name" + "description" : "Ontology name", + "nullable" : true }, "version" : { "type" : "string", diff --git a/Specification/Generated/brapi_generated.ttl b/Specification/Generated/brapi_generated.ttl index c20350f8..fc2b3bde 100644 --- a/Specification/Generated/brapi_generated.ttl +++ b/Specification/Generated/brapi_generated.ttl @@ -231,6 +231,13 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`."@en; + rdfs:domain ; + rdfs:label "sequence"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)"@en; @@ -238,12 +245,12 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`."@en; - rdfs:domain ; - rdfs:label "sequence"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . rdf:type owl:NamedIndividual , . @@ -255,6 +262,13 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "The child germplasm"@en; + rdfs:domain ; + rdfs:label "childGermplasm"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "Zero or more filters that failed for this variant. VCF column 7 \"FILTER\" shared across all alleles in the same VCF record."@en; @@ -267,20 +281,6 @@ PREFIX xsd: rdfs:comment "Links to various ontology documentation"@en; rdfs:label "DocumentationLink"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "The child germplasm"@en; - rdfs:domain ; - rdfs:label "childGermplasm"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The name or identifier of the entity which took the `Sample` from the field"@en; @@ -338,6 +338,10 @@ PREFIX xsd: rdfs:label "instituteCode"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; @@ -454,10 +458,6 @@ PREFIX xsd: rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; rdfs:label "GermplasmOrigin"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -529,13 +529,6 @@ PREFIX xsd: rdfs:label "positionCoordinateYType"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "the value of a cross attribute"@en; - rdfs:domain ; - rdfs:label "crossAttributeValue"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study"@en; @@ -543,6 +536,13 @@ PREFIX xsd: rdfs:label "studyDescription"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "the value of a cross attribute"@en; + rdfs:domain ; + rdfs:label "crossAttributeValue"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Common name for the crop"@en; @@ -557,10 +557,6 @@ PREFIX xsd: rdfs:label "program"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; @@ -603,9 +599,12 @@ PREFIX xsd: rdfs:label "email"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The full name of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; + rdfs:domain ; + rdfs:label "instituteName"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -619,13 +618,6 @@ PREFIX xsd: rdfs:comment "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample"@en; rdfs:label "CallSet"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The full name of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; - rdfs:domain ; - rdfs:label "instituteName"@en; - rdfs:range xsd:string . - rdf:type owl:NamedIndividual , . @@ -649,13 +641,6 @@ PREFIX xsd: rdfs:label "attributeValues"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The array of DbIds of the BrAPI objects contained in a List"@en; - rdfs:domain ; - rdfs:label "data"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The timestamp for the last update to this Seed Lot (including transactions)"@en; @@ -663,6 +648,13 @@ PREFIX xsd: rdfs:label "lastUpdated"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The array of DbIds of the BrAPI objects contained in a List"@en; + rdfs:domain ; + rdfs:label "data"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "The record of an event where material was moved in or out of a particular SeedLot"@en; @@ -692,6 +684,10 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type , owl:NamedIndividual , . @@ -748,6 +744,9 @@ PREFIX xsd: rdfs:label "programType"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "Environment parameters associated with a study"@en; @@ -755,9 +754,6 @@ PREFIX xsd: rdfs:label "study"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The start position at which this variant occurs (0-based). This corresponds to the first base of the string \nof reference bases. Genomic positions are non-negative integers less than reference length. Variants spanning \nthe join of circular genomes are represented as two variants one on each side of the join (position 0)."@en; @@ -858,6 +854,13 @@ PREFIX xsd: rdfs:comment "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit."@en; rdfs:label "Observation"@en . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; @@ -865,12 +868,12 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975)."@en; + rdfs:domain ; + rdfs:label "latitudeDecimal"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -879,11 +882,11 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975)."@en; - rdfs:domain ; - rdfs:label "latitudeDecimal"@en; + rdfs:comment "The reference bases for this variant. They start at the given start position."@en; + rdfs:domain ; + rdfs:label "referenceBases"@en; rdfs:range xsd:string . @@ -893,13 +896,6 @@ PREFIX xsd: rdfs:label "crossingProjectName"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The reference bases for this variant. They start at the given start position."@en; - rdfs:domain ; - rdfs:label "referenceBases"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The literal string \"Point\""@en; @@ -1094,6 +1090,13 @@ PREFIX xsd: rdfs:comment "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\""@en; rdfs:label "EntryType"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology database unique identifier"@en; + rdfs:domain ; + rdfs:label "ontologyDbId"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "A string representation of the `Reference` base alleles."@en; @@ -1106,13 +1109,6 @@ PREFIX xsd: rdfs:label "institution"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology database unique identifier"@en; - rdfs:domain ; - rdfs:label "ontologyDbId"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The human readable name of an image. Might be the same as 'imageFileName', but could be different."@en; @@ -1127,13 +1123,6 @@ PREFIX xsd: rdfs:label "abbreviation"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The description of where a List originated from"@en; - rdfs:domain ; - rdfs:label "listSource"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The name of the institute that maintains the material"@en; @@ -1141,6 +1130,13 @@ PREFIX xsd: rdfs:label "instituteName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The description of where a List originated from"@en; + rdfs:domain ; + rdfs:label "listSource"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076"@en; @@ -1255,10 +1251,6 @@ PREFIX xsd: rdfs:label "referenceSet"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; @@ -1349,12 +1341,12 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:NamedIndividual , . + + rdf:type owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . @@ -1593,6 +1585,10 @@ PREFIX xsd: rdfs:comment "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc."@en; rdfs:label "Location"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The string representation of the pedigree for this germplasm in PURDY notation"@en; @@ -1684,6 +1680,13 @@ PREFIX xsd: rdfs:label "germplasmDbId"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. "@en; + rdfs:domain ; + rdfs:label "parentType"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -1691,12 +1694,12 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - + rdf:type owl:ObjectProperty; - rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. "@en; - rdfs:domain ; - rdfs:label "parentType"@en; - rdfs:range . + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -1717,13 +1720,6 @@ PREFIX xsd: rdfs:comment "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit"@en; rdfs:label "GermplasmAttribute"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "observations"@en; @@ -1804,12 +1800,8 @@ PREFIX xsd: rdfs:label "breedingMethod"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:domain ; - rdfs:label "coordinates"@en; - rdfs:range . + + rdf:type owl:NamedIndividual , . rdf:type owl:ObjectProperty; @@ -1818,8 +1810,12 @@ PREFIX xsd: rdfs:label "observationUnit"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . + + rdf:type owl:ObjectProperty; + rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:domain ; + rdfs:label "coordinates"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -1849,6 +1845,13 @@ PREFIX xsd: rdfs:label "observationUnits"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a Location"@en; + rdfs:domain ; + rdfs:label "locationDbId"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "physical address of this person"@en; @@ -1872,13 +1875,6 @@ PREFIX xsd: rdfs:label "phaseSet"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a Location"@en; - rdfs:domain ; - rdfs:label "locationDbId"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard "@en; @@ -1917,10 +1913,6 @@ PREFIX xsd: rdfs:label "crossingProjectDescription"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The time stamp for when this seed lot was created"@en; @@ -1962,6 +1954,13 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A descriptive classification for this synonym"@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The date this trial ends"@en; @@ -1969,25 +1968,11 @@ PREFIX xsd: rdfs:label "endDate"@en; rdfs:range xsd:string . - + rdf:type owl:DatatypeProperty; - rdfs:comment "A descriptive classification for this synonym"@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Analysis associated with a variant set"@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology copyright"@en; - rdfs:domain ; - rdfs:label "copyright"@en; + rdfs:comment "Ontology copyright"@en; + rdfs:domain ; + rdfs:label "copyright"@en; rdfs:range xsd:string . @@ -1997,6 +1982,13 @@ PREFIX xsd: rdfs:label "variantSets"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "Analysis associated with a variant set"@en; + rdfs:domain ; + rdfs:label "variantSet"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "The ID of the reference set that describes the sequences used by the variants in this set."@en; @@ -2064,13 +2056,6 @@ PREFIX xsd: rdfs:label "progenyPedigreeNodes"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "True if all filters for this variant passed. VCF column 7 \"FILTER\" value PASS."@en; - rdfs:domain ; - rdfs:label "filtersPassed"@en; - rdfs:range xsd:boolean . - rdf:type owl:DatatypeProperty; rdfs:comment "The number of elements in a List"@en; @@ -2078,6 +2063,13 @@ PREFIX xsd: rdfs:label "listSize"@en; rdfs:range xsd:integer . + + rdf:type owl:DatatypeProperty; + rdfs:comment "True if all filters for this variant passed. VCF column 7 \"FILTER\" value PASS."@en; + rdfs:domain ; + rdfs:label "filtersPassed"@en; + rdfs:range xsd:boolean . + rdf:type owl:DatatypeProperty; rdfs:comment "A unique identifier physically attached to the `Sample`"@en; @@ -2085,6 +2077,10 @@ PREFIX xsd: rdfs:label "sampleBarcode"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "Identifier assigned to an accession by the material donor."@en; @@ -2137,6 +2133,10 @@ PREFIX xsd: rdfs:label "variantNames"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "parentPedigreeNodes"@en; @@ -2189,6 +2189,10 @@ PREFIX xsd: rdfs:label "variants"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -2229,13 +2233,6 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Description the storage location"@en; - rdfs:domain ; - rdfs:label "storageLocation"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Information describing the grant or funding source for this program"@en; @@ -2250,6 +2247,13 @@ PREFIX xsd: rdfs:label "observationTimeStamp"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Description the storage location"@en; + rdfs:domain ; + rdfs:label "storageLocation"@en; + rdfs:range xsd:string . + rdf:type owl:NamedIndividual , . @@ -2302,6 +2306,20 @@ PREFIX xsd: rdfs:label "mcpd"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "observations"@en; + rdfs:domain ; + rdfs:label "observations"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of scientist submitting the variable."@en; + rdfs:domain ; + rdfs:label "scientist"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; @@ -2316,13 +2334,6 @@ PREFIX xsd: rdfs:label "species"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "observations"@en; - rdfs:domain ; - rdfs:label "observations"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described."@en; @@ -2330,12 +2341,12 @@ PREFIX xsd: rdfs:label "publicReleaseDate"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of scientist submitting the variable."@en; - rdfs:domain ; - rdfs:label "scientist"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "Information about the location where the sample was collected"@en; + rdfs:domain ; + rdfs:label "collectingSite"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -2351,13 +2362,6 @@ PREFIX xsd: rdfs:label "callSets"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "Information about the location where the sample was collected"@en; - rdfs:domain ; - rdfs:label "collectingSite"@en; - rdfs:range . - rdf:type owl:NamedIndividual , . @@ -2420,10 +2424,6 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The identifier (name, ID, URI) of a particular taxonomy within the source provider"@en; @@ -2438,10 +2438,6 @@ PREFIX xsd: rdfs:label "contentMixture"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "the maximum number of elements per page in this dimension of the matrix"@en; @@ -2541,13 +2537,6 @@ PREFIX xsd: rdfs:comment "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'."@en; rdfs:label "CrossType"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "True if the pollination was successful"@en; - rdfs:domain ; - rdfs:label "pollinationSuccessful"@en; - rdfs:range xsd:boolean . - rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this analysis"@en; @@ -2555,6 +2544,13 @@ PREFIX xsd: rdfs:label "analysisName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "True if the pollination was successful"@en; + rdfs:domain ; + rdfs:label "pollinationSuccessful"@en; + rdfs:range xsd:boolean . + rdf:type , owl:NamedIndividual , . @@ -2589,6 +2585,10 @@ PREFIX xsd: rdfs:label "genus"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "Persons last name"@en; @@ -2678,13 +2678,6 @@ PREFIX xsd: rdfs:label "submissionTimestamp"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:domain ; - rdfs:label "imageLocation"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -2692,6 +2685,13 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:domain ; + rdfs:label "imageLocation"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -2706,9 +2706,6 @@ PREFIX xsd: rdfs:label "georeferencingMethod"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "the requested page number (zero indexed)"@en; @@ -2716,6 +2713,13 @@ PREFIX xsd: rdfs:label "page"@en; rdfs:range xsd:integer . + + rdf:type owl:NamedIndividual , . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -2840,6 +2844,10 @@ PREFIX xsd: rdfs:label "plate"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "The Cross associated with this Pollination Event"@en; @@ -2859,13 +2867,6 @@ PREFIX xsd: rdfs:label "documentationURL"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated \nby `start + referenceBases.length`."@en; - rdfs:domain ; - rdfs:label "end"@en; - rdfs:range xsd:integer . - rdf:type owl:ObjectProperty; rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; @@ -2873,6 +2874,13 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated \nby `start + referenceBases.length`."@en; + rdfs:domain ; + rdfs:label "end"@en; + rdfs:range xsd:integer . + rdf:type owl:DatatypeProperty; rdfs:comment "phone number of this person"@en; @@ -2887,13 +2895,6 @@ PREFIX xsd: rdfs:label "license"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "variants"@en; @@ -2901,6 +2902,13 @@ PREFIX xsd: rdfs:label "variants"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; @@ -3087,6 +3095,13 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)"@en; + rdfs:domain ; + rdfs:label "topography"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "A description of the things being transferred between SeedLots in a transaction (seeds, bulbs, kg, etc)"@en; @@ -3108,13 +3123,6 @@ PREFIX xsd: rdfs:label "dataMatrixAbbreviation"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)"@en; - rdfs:domain ; - rdfs:label "topography"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; @@ -3254,6 +3262,10 @@ PREFIX xsd: rdfs:comment "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended."@en; rdfs:label "TaxonId"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The literal string \"Feature\""@en; @@ -3490,12 +3502,7 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The timestamp when the pollination took place"@en; - rdfs:domain ; - rdfs:label "pollinationTimeStamp"@en; - rdfs:range xsd:string . + rdf:type owl:Ontology . rdf:type owl:DatatypeProperty; @@ -3504,7 +3511,19 @@ PREFIX xsd: rdfs:label "pollinationNumber"@en; rdfs:range xsd:string . - rdf:type owl:Ontology . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The time at which this record was created, in ISO 8601 format."@en; + rdfs:domain ; + rdfs:label "created"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The timestamp when the pollination took place"@en; + rdfs:domain ; + rdfs:label "pollinationTimeStamp"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -3513,13 +3532,6 @@ PREFIX xsd: rdfs:label "commonCropName"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The time at which this record was created, in ISO 8601 format."@en; - rdfs:domain ; - rdfs:label "created"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "If the Scale is a categorical type, these objects define the valid options"@en; @@ -3532,10 +3544,6 @@ PREFIX xsd: rdfs:label "genomeMap"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'."@en; @@ -3567,10 +3575,6 @@ PREFIX xsd: rdfs:label "institution"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "List of links to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; @@ -3628,10 +3632,6 @@ PREFIX xsd: rdfs:comment "The dimension of the matrix being paginated"@en; rdfs:label "Dimension"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "the human readable identifier for this breeding method"@en; @@ -3646,6 +3646,13 @@ PREFIX xsd: rdfs:label "version"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "Set of custom attributes associated with a cross"@en; + rdfs:domain ; + rdfs:label "crossAttributes"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . @@ -3656,26 +3663,19 @@ PREFIX xsd: rdfs:label "studyType"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "Set of custom attributes associated with a cross"@en; - rdfs:domain ; - rdfs:label "crossAttributes"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc"@en; - rdfs:domain ; - rdfs:label "scientificType"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:domain ; rdfs:label "validValues"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc"@en; + rdfs:domain ; + rdfs:label "scientificType"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "The list of pollination events that occurred for this cross."@en; @@ -3690,6 +3690,20 @@ PREFIX xsd: rdfs:label "traitDescription"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "Genotype Metadata are additional layers of metadata associated with each genotype."@en; + rdfs:domain ; + rdfs:label "genotypeMetadata"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology's list of authors (no specific format)"@en; + rdfs:domain ; + rdfs:label "authors"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; @@ -3697,6 +3711,13 @@ PREFIX xsd: rdfs:label "biologicalStatusOfAccessionCode"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The value of this attribute for a given germplasm"@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3709,26 +3730,11 @@ PREFIX xsd: rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; rdfs:label "StorageTypeCode"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "Genotype Metadata are additional layers of metadata associated with each genotype."@en; - rdfs:domain ; - rdfs:label "genotypeMetadata"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The value of this attribute for a given germplasm"@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology's list of authors (no specific format)"@en; - rdfs:domain ; - rdfs:label "authors"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:domain ; + rdfs:label "safetyDuplicateInstitutes"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -3737,12 +3743,6 @@ PREFIX xsd: rdfs:label "collectingInstitutes"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:domain ; - rdfs:label "safetyDuplicateInstitutes"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The date this call set was created"@en; @@ -3750,13 +3750,6 @@ PREFIX xsd: rdfs:label "created"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Other variable names"@en; @@ -3767,6 +3760,13 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Common name for the crop"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3831,6 +3831,10 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The type of analysis."@en; @@ -3899,13 +3903,6 @@ PREFIX xsd: rdfs:label "callSets"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "associated scale"@en; - rdfs:domain ; - rdfs:label "scale"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Siblings share at least one parent with the given germplasm. \n
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response."@en; @@ -3913,6 +3910,13 @@ PREFIX xsd: rdfs:label "siblings"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "associated scale"@en; + rdfs:domain ; + rdfs:label "scale"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3932,10 +3936,6 @@ PREFIX xsd: rdfs:label "longitudeDecimal"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The human readable identifier for a `GenomeMap`"@en; @@ -3943,9 +3943,6 @@ PREFIX xsd: rdfs:label "mapName"@en; rdfs:range xsd:string . - - rdf:type , owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a location, associated with this study"@en; @@ -3953,6 +3950,9 @@ PREFIX xsd: rdfs:label "location"@en; rdfs:range . + + rdf:type , owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "The end of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event."@en; @@ -3965,6 +3965,10 @@ PREFIX xsd: rdfs:comment "The identifying information gor the parent material of a cross."@en; rdfs:label "CrossParent"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for a `Plate`"@en; @@ -3986,13 +3990,6 @@ PREFIX xsd: rdfs:label "observationUnit"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a List Owner. (usually a user or person)"@en; - rdfs:domain ; - rdfs:label "listOwnerPerson"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a trial"@en; @@ -4000,6 +3997,13 @@ PREFIX xsd: rdfs:label "trial"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a List Owner. (usually a user or person)"@en; + rdfs:domain ; + rdfs:label "listOwnerPerson"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; @@ -4094,13 +4098,6 @@ PREFIX xsd: rdfs:comment "Information about the collection of a germplasm"@en; rdfs:label "CollectingInfo"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "List of contact entities associated with this trial"@en; - rdfs:domain ; - rdfs:label "contacts"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -4108,6 +4105,13 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "List of contact entities associated with this trial"@en; + rdfs:domain ; + rdfs:label "contacts"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "For numerical, number of decimal places to be reported"@en; @@ -4125,11 +4129,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:Class; - rdfs:comment "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)"@en; - rdfs:label "AcquisitionSourceCode"@en . - rdf:type owl:ObjectProperty; rdfs:comment "samples"@en; @@ -4137,6 +4136,11 @@ PREFIX xsd: rdfs:label "samples"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)"@en; + rdfs:label "AcquisitionSourceCode"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'."@en; @@ -4151,13 +4155,6 @@ PREFIX xsd: rdfs:label "abbreviation"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The percentage of the given germplasm in the seed lot mixture."@en; - rdfs:domain ; - rdfs:label "mixturePercentage"@en; - rdfs:range xsd:integer . - rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers\" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\"."@en; @@ -4172,9 +4169,12 @@ PREFIX xsd: rdfs:label "coordinateDescription"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The percentage of the given germplasm in the seed lot mixture."@en; + rdfs:domain ; + rdfs:label "mixturePercentage"@en; + rdfs:range xsd:integer . rdf:type owl:DatatypeProperty; @@ -4295,10 +4295,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing."@en; @@ -4309,6 +4305,13 @@ PREFIX xsd: rdfs:comment "The metadata for an image file that is connected to some phenotypic observation data."@en; rdfs:label "Image"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The number of CallSets included in this VariantSet"@en; @@ -4323,13 +4326,6 @@ PREFIX xsd: rdfs:label "unit"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "A persons contact information"@en; @@ -4368,6 +4364,10 @@ PREFIX xsd: rdfs:comment "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program."@en; rdfs:label "SeedLot"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'."@en; @@ -4396,10 +4396,6 @@ PREFIX xsd: rdfs:label "attributeValueDbId"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The type of documentation, which can be OBO Foundry, an RDF term or a webpage."@en; @@ -4495,6 +4491,9 @@ PREFIX xsd: rdfs:label "publishedDate"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "The number of linkage groups present in a `GenomeMap`"@en; @@ -4502,9 +4501,6 @@ PREFIX xsd: rdfs:label "linkageGroupCount"@en; rdfs:range xsd:integer . - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "The child locations that belong to this Location. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; @@ -4553,13 +4549,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; - rdfs:domain ; - rdfs:label "donorAccessionNumber"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a `Variant` within the given database server\n
A `Variant` can also represent a Marker "@en; @@ -4567,6 +4556,13 @@ PREFIX xsd: rdfs:label "variant"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; + rdfs:domain ; + rdfs:label "donorAccessionNumber"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Full scientific binomial format name. This includes Genus, Species, and Sub-species"@en; @@ -4574,6 +4570,10 @@ PREFIX xsd: rdfs:label "scientificName"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor."@en; @@ -4711,6 +4711,10 @@ PREFIX xsd: rdfs:label "sepUnphased"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard."@en; @@ -4913,6 +4917,10 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)"@en; @@ -4951,10 +4959,6 @@ PREFIX xsd: rdfs:label "parent2"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The number of markers present in a `GenomeMap`"@en; @@ -4962,6 +4966,10 @@ PREFIX xsd: rdfs:label "markerCount"@en; rdfs:range xsd:integer . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "A short human readable code for a study"@en; @@ -4969,6 +4977,11 @@ PREFIX xsd: rdfs:label "studyCode"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "Alternative names or IDs used to reference this germplasm"@en; + rdfs:label "Synonym"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "the unique identifier for a planned cross"@en; @@ -4976,11 +4989,6 @@ PREFIX xsd: rdfs:label "plannedCrossDbId"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "Alternative names or IDs used to reference this germplasm"@en; - rdfs:label "Synonym"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "Describes the level of protection/exposure for things like sun light and wind at a particular Location"@en; @@ -4993,10 +5001,6 @@ PREFIX xsd: rdfs:comment "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology"@en; rdfs:label "ExperimentalDesign"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "Information about an accession donor"@en; @@ -5082,13 +5086,6 @@ PREFIX xsd: rdfs:label "markerCount"@en; rdfs:range xsd:integer . - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a Location\n
The Parent Location defines the encompassing Location that a smaller Location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; - rdfs:domain ; - rdfs:label "parentLocation"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The time at which this variant was last updated."@en; @@ -5096,9 +5093,12 @@ PREFIX xsd: rdfs:label "updated"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a Location\n
The Parent Location defines the encompassing Location that a smaller Location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; + rdfs:domain ; + rdfs:label "parentLocation"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -5184,18 +5184,11 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A permanent unique identifier for the `Sample` (DOI, URL, UUID, etc)\n
MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible. "@en; - rdfs:domain ; - rdfs:label "samplePUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; - rdfs:domain ; - rdfs:label "type"@en; + + rdf:type owl:DatatypeProperty; + rdfs:comment "A permanent unique identifier for the `Sample` (DOI, URL, UUID, etc)\n
MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible. "@en; + rdfs:domain ; + rdfs:label "samplePUI"@en; rdfs:range xsd:string . @@ -5233,9 +5226,12 @@ PREFIX xsd: rdfs:label "toSeedLot"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -5300,6 +5296,10 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology"@en; @@ -5324,6 +5324,10 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "The type of positional coordinate. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; @@ -5378,13 +5382,6 @@ PREFIX xsd: rdfs:label "observationUnits"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies this attribute within the given database server"@en; - rdfs:domain ; - rdfs:label "attributeDbId"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "License and citation information for the data in this trial"@en; @@ -5427,6 +5424,13 @@ PREFIX xsd: rdfs:label "studyDbId"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies this attribute within the given database server"@en; + rdfs:domain ; + rdfs:label "attributeDbId"@en; + rdfs:range xsd:string . + rdf:type owl:NamedIndividual , . @@ -5473,6 +5477,10 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon."@en; @@ -5494,13 +5502,6 @@ PREFIX xsd: rdfs:label "term"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; - rdfs:domain ; - rdfs:label "growthStage"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The DOI or other permanent unique identifier for this published dataset"@en; @@ -5508,6 +5509,13 @@ PREFIX xsd: rdfs:label "datasetPUI"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; + rdfs:domain ; + rdfs:label "growthStage"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies an `ObservationUnit`"@en; @@ -5525,13 +5533,6 @@ PREFIX xsd: rdfs:comment "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present."@en; rdfs:label "Cross"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name used for display purposes"@en; - rdfs:domain ; - rdfs:label "defaultDisplayName"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the entity was last updated"@en; @@ -5539,6 +5540,13 @@ PREFIX xsd: rdfs:label "dateModified"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name used for display purposes"@en; + rdfs:domain ; + rdfs:label "defaultDisplayName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level."@en; @@ -5546,6 +5554,10 @@ PREFIX xsd: rdfs:label "subtaxaAuthority"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The version number for this data \n\nMIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data)."@en; @@ -5669,13 +5681,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation."@en; - rdfs:domain ; - rdfs:label "termURI"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "pedigreeNodes"@en; @@ -5683,6 +5688,13 @@ PREFIX xsd: rdfs:label "pedigreeNodes"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation."@en; + rdfs:domain ; + rdfs:label "termURI"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\")."@en; @@ -5760,6 +5772,15 @@ PREFIX xsd: rdfs:label "geoCoordinates"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:Class; + rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; + rdfs:label "ObservationUnitHierarchyLevel"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this Seed Lot"@en; @@ -5767,11 +5788,6 @@ PREFIX xsd: rdfs:label "seedLotName"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; - rdfs:label "ObservationUnitHierarchyLevel"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation"@en; @@ -5845,6 +5861,10 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -5925,11 +5945,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:Class; - rdfs:comment "A link to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; - rdfs:label "DataLink"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A Trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the Entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" "@en; @@ -5937,6 +5952,11 @@ PREFIX xsd: rdfs:label "entityPUI"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "A link to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; + rdfs:label "DataLink"@en . + rdf:type owl:ObjectProperty; rdfs:comment "The unique identifier for a VariantSet"@en; @@ -6004,13 +6024,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The URL or URI to the documentation"@en; - rdfs:domain ; - rdfs:label "URL"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The description of the source where this material was originally collected (wild, nursery, etc)"@en; @@ -6018,6 +6031,13 @@ PREFIX xsd: rdfs:label "sourceCollection"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The URL or URI to the documentation"@en; + rdfs:domain ; + rdfs:label "URL"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space."@en; @@ -6025,12 +6045,9 @@ PREFIX xsd: rdfs:label "germplasmName"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of field represented in this data matrix. This is intended to help parse the data out of JSON."@en; - rdfs:domain ; - rdfs:label "dataType"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -6046,6 +6063,13 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of field represented in this data matrix. This is intended to help parse the data out of JSON."@en; + rdfs:domain ; + rdfs:label "dataType"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this attribute"@en; @@ -6107,13 +6131,6 @@ PREFIX xsd: rdfs:label "software"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -6133,9 +6150,12 @@ PREFIX xsd: rdfs:label "discreteDates"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -6151,13 +6171,6 @@ PREFIX xsd: rdfs:label "attributePUI"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Bibliographical reference describing the method.\n
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method."@en; - rdfs:domain ; - rdfs:label "bibliographicalReference"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -6165,6 +6178,13 @@ PREFIX xsd: rdfs:label "programs"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Bibliographical reference describing the method.\n
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method."@en; + rdfs:domain ; + rdfs:label "bibliographicalReference"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)"@en; @@ -6179,14 +6199,6 @@ PREFIX xsd: rdfs:label "samples"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Description of a List"@en; @@ -6201,13 +6213,6 @@ PREFIX xsd: rdfs:label "synonyms"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name for a Location\n
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place."@en; - rdfs:domain ; - rdfs:label "locationName"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; @@ -6215,23 +6220,16 @@ PREFIX xsd: rdfs:label "trait"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "A URL which indicates the location of the file version of this VariantSet. Could be a static file URL or an API endpoint which generates the file."@en; - rdfs:domain ; - rdfs:label "fileURL"@en; + rdfs:comment "A human readable name for a Location\n
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place."@en; + rdfs:domain ; + rdfs:label "locationName"@en; rdfs:range xsd:string . rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a representation for missing data."@en; - rdfs:domain ; - rdfs:label "unknownString"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Common name for the crop associated with this trial"@en; @@ -6246,6 +6244,20 @@ PREFIX xsd: rdfs:label "scientist"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL which indicates the location of the file version of this VariantSet. Could be a static file URL or an API endpoint which generates the file."@en; + rdfs:domain ; + rdfs:label "fileURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a representation for missing data."@en; + rdfs:domain ; + rdfs:label "unknownString"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "samples"@en; @@ -6263,10 +6275,6 @@ PREFIX xsd: rdfs:comment "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap."@en; rdfs:label "MarkerPosition"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "URI pointing to an ontology class for the parameter"@en; @@ -6274,6 +6282,13 @@ PREFIX xsd: rdfs:label "parameterPUI"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "mapDbId"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group."@en; @@ -6300,13 +6315,6 @@ PREFIX xsd: rdfs:label "defaultDisplayName"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "mapDbId"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; @@ -6495,6 +6503,9 @@ PREFIX xsd: rdfs:label "dataType"@en; rdfs:range . + + rdf:type , , owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; @@ -6502,9 +6513,6 @@ PREFIX xsd: rdfs:label "instituteAddress"@en; rdfs:range xsd:string . - - rdf:type , , owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value."@en; @@ -6512,10 +6520,6 @@ PREFIX xsd: rdfs:label "filtersApplied"@en; rdfs:range xsd:boolean . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples."@en; @@ -6629,13 +6633,6 @@ PREFIX xsd: rdfs:label "row"@en; rdfs:range xsd:string . - - rdf:type , owl:NamedIndividual , . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "List of treatments applied to an observation unit.\n\nMIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit."@en; @@ -6643,6 +6640,9 @@ PREFIX xsd: rdfs:label "treatments"@en; rdfs:range . + + rdf:type , owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment ""@en; diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index 401d9015..06c0cedf 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -8866,6 +8866,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the details of a specific Observation Unit", @@ -8948,6 +8959,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Update an existing Observation Units", diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index df7cc557..a8a85b34 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -70,61 +70,14 @@ Changed response : **200** Changed items (array): - New properties: `mapPUI` - Deleted properties: `variantName` - * Changed property `mapDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `mapName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbId` (string): - - Nullable changed: `true` -> `null` - -##### `GET` /methods +##### `GET` /referencesets ###### Parameters: -Deleted: `externalReferenceID` in `query` - -##### `GET` /observationunits/{observationUnitDbId} - - -###### Return Type: - -New response : **404** - -##### `POST` /ontologies - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - * Changed property `ontologyName` (string): - - Nullable changed: `true` -> `null` - -##### `PUT` /ontologies/{ontologyDbId} - - -###### Request: - -* Changed content type : `application/json` - - * Changed property `ontologyName` (string): - - Nullable changed: `true` -> `null` - -##### `GET` /scales - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` +Added: `externalReferenceID` in `query` ##### `POST` /search/allelematrix @@ -442,19 +395,8 @@ Changed response : **200** Changed items (array): - New properties: `mapPUI` - Deleted properties: `variantName` - * Changed property `mapDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `mapName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbId` (string): - - Nullable changed: `true` -> `null` - ##### `GET` /search/markerpositions/{searchResultsDbId} @@ -472,19 +414,8 @@ Changed response : **200** Changed items (array): - New properties: `mapPUI` - Deleted properties: `variantName` - * Changed property `mapDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `mapName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbId` (string): - - Nullable changed: `true` -> `null` - ##### `GET` /search/observations/{searchResultsDbId} @@ -777,20 +708,6 @@ Deleted response : **404** Changed: `year` in `query`: - Type changed: `integer` -> `string` -##### `GET` /traits - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - -##### `GET` /attributevalues - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /attributevalues @@ -904,6 +821,10 @@ Changed response : **200** ##### `GET` /callsets +###### Parameters: + +Added: `externalReferenceID` in `query` + ###### Return Type: Changed response : **200** @@ -1015,13 +936,6 @@ Changed response : **200** * Changed property `fieldValue` (string): - Nullable changed: `null` -> `true` -##### `GET` /crosses - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /crosses @@ -1072,18 +986,6 @@ Deleted: `externalReferenceID` in `query` New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitName` (string): - - Nullable changed: `true` -> `null` - * Changed property `parentType` (string): - Added enum values: [CLONAL] @@ -1093,13 +995,6 @@ Deleted: `externalReferenceID` in `query` New properties: `crossDbId`, `crossName` -##### `GET` /crossingprojects - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /crossingprojects @@ -1133,18 +1028,6 @@ Deleted: `externalReferenceID` in `query` New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitName` (string): - - Nullable changed: `true` -> `null` - * Changed property `parentType` (string): - Added enum values: [CLONAL] @@ -1179,18 +1062,6 @@ Deleted: `externalReferenceID` in `query` New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitName` (string): - - Nullable changed: `true` -> `null` - * Changed property `parentType` (string): - Added enum values: [CLONAL] @@ -1233,13 +1104,6 @@ Changed response : **200** Deleted properties: `key`, `rdfValue` -##### `GET` /germplasm - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /germplasm @@ -1390,13 +1254,6 @@ Changed response : **200** New properties: `instituteAddress` -##### `GET` /lists - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /lists @@ -1445,13 +1302,6 @@ Deleted: `externalReferenceID` in `query` * Changed property `referenceSource` (string): - Nullable changed: `null` -> `true` -##### `GET` /observationunits - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /observationunits @@ -1526,13 +1376,6 @@ Deleted: `externalReferenceID` in `query` New properties: `observationUnitDbId`, `observationUnitName`, `observationUnitPUI` -##### `GET` /people - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /people @@ -1576,10 +1419,6 @@ Deleted: `externalReferenceID` in `query` ##### `GET` /plannedcrosses -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ###### Return Type: Changed response : **200** @@ -1618,18 +1457,6 @@ Changed response : **200** New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitName` (string): - - Nullable changed: `true` -> `null` - * Changed property `parentType` (string): - Added enum values: [CLONAL] @@ -1674,18 +1501,6 @@ Changed response : **200** New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitName` (string): - - Nullable changed: `true` -> `null` - * Changed property `parentType` (string): - Added enum values: [CLONAL] @@ -1729,18 +1544,6 @@ Changed response : **200** New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitName` (string): - - Nullable changed: `true` -> `null` - * Changed property `parentType` (string): - Added enum values: [CLONAL] @@ -1782,28 +1585,9 @@ Changed response : **200** New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitName` (string): - - Nullable changed: `true` -> `null` - * Changed property `parentType` (string): - Added enum values: [CLONAL] -##### `GET` /plates - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /plates @@ -1841,8 +1625,6 @@ Deleted: `externalReferenceID` in `query` ###### Parameters: -Deleted: `externalReferenceID` in `query` - Changed: `programType` in `query`: - Added enum values: [STANDARD] - Removed enum values: [STANARD] @@ -1904,6 +1686,10 @@ Changed: `programType` in `query`: ##### `GET` /references +###### Parameters: + +Added: `externalReferenceID` in `query` + ###### Return Type: Changed response : **200** @@ -1973,13 +1759,6 @@ Changed response : **200** * Changed property `referenceSource` (string): - Nullable changed: `null` -> `true` -##### `GET` /samples - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `PUT` /samples @@ -2684,13 +2463,6 @@ Changed response : **200** * Changed property `fieldName` (string): - Nullable changed: `null` -> `true` -##### `GET` /seedlots - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /seedlots @@ -2795,13 +2567,6 @@ Deleted: `externalReferenceID` in `query` * Changed property `referenceSource` (string): - Nullable changed: `null` -> `true` -##### `GET` /studies - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /studies @@ -2930,13 +2695,6 @@ Deleted: `externalReferenceID` in `query` New required properties: - `lastUpdateDbId` -##### `GET` /trials - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /trials @@ -3020,6 +2778,10 @@ Deleted: `externalReferenceID` in `query` ##### `GET` /variants +###### Parameters: + +Added: `externalReferenceID` in `query` + ###### Return Type: Changed response : **200** @@ -3158,6 +2920,10 @@ Changed response : **200** ##### `GET` /variantsets +###### Parameters: + +Added: `externalReferenceID` in `query` + ###### Return Type: Changed response : **200** @@ -3409,13 +3175,6 @@ Changed response : **200** * Changed property `referenceSource` (string): - Nullable changed: `null` -> `true` -##### `GET` /attributes - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /attributes @@ -3518,13 +3277,6 @@ Deleted: `externalReferenceID` in `query` * Changed property `type` (string): - Nullable changed: `null` -> `true` -##### `GET` /images - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /images @@ -3605,13 +3357,6 @@ Deleted: `externalReferenceID` in `query` * Changed property `geometry` (object -> null): - Type changed: `object` -> `null` -##### `GET` /locations - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /locations @@ -3678,13 +3423,6 @@ Deleted: `externalReferenceID` in `query` * Changed property `geometry` (object -> null): - Type changed: `object` -> `null` -##### `GET` /observations - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `PUT` /observations @@ -3754,6 +3492,10 @@ Deleted response : **404** ##### `GET` /pedigree +###### Parameters: + +Added: `externalReferenceID` in `query` + ###### Return Type: Deleted response : **404** @@ -4169,13 +3911,6 @@ Changed response : **200** * Changed property `germplasmName` (string): - Nullable changed: `true` -> `null` -##### `GET` /variables - - -###### Parameters: - -Deleted: `externalReferenceID` in `query` - ##### `POST` /variables From f053775132c3f1f02b4d69d8b6a2012cc8df219d Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Sat, 2 May 2026 20:01:05 +1200 Subject: [PATCH 28/62] Update title in GenomeMap.json from 'observationUnits' to 'linkageGroups' --- Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json index 89c0607b..9f2efc4a 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/GenomeMap.json @@ -41,7 +41,7 @@ ] }, "linkageGroups": { - "title": "observationUnits", + "title": "linkageGroups", "description": "The linkage groups present in a `GenomeMap`", "referencedAttribute": "genomeMap", "relationshipType": "one-to-many", From 9dee0df4e0c7c71c28642d8e5c706d8afd3f2d85 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Thu, 7 May 2026 18:26:06 +1200 Subject: [PATCH 29/62] Update AlleleMatrixRequest.json to allow null values for array types --- .../Requests/AlleleMatrixRequest.json | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json index f941b9b3..022e52e9 100644 --- a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json +++ b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json @@ -5,7 +5,7 @@ "properties": { "pagination": { "description": "Pagination for the matrix", - "type": "array", + "type": ["null", "array"], "items": { "type": "object", "title": "AlleleMatrixPagination", @@ -52,7 +52,7 @@ }, "dataMatrixNames": { "description": "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -63,7 +63,7 @@ }, "dataMatrixAbbreviations": { "description": "`dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -74,7 +74,7 @@ }, "positionRanges": { "description": "The postion range to search\n
\nUses the format \":-\" where is the chromosome name, is \nthe starting position of the range, and is the ending position of the range", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -85,7 +85,7 @@ }, "germplasmNames": { "description": "A list of human readable `Germplasm` names", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -96,7 +96,7 @@ }, "germplasmPUIs": { "description": "A list of permanent unique identifiers associated with `Germplasm`", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -107,7 +107,7 @@ }, "germplasmDbIds": { "description": "A list of IDs which uniquely identify `Germplasm` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -118,7 +118,7 @@ }, "sampleDbIds": { "description": "A list of IDs which uniquely identify `Samples` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -140,7 +140,7 @@ }, "variantDbIds": { "description": "A list of IDs which uniquely identify `Variants` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -151,7 +151,7 @@ }, "variantSetDbIds": { "description": "A list of IDs which uniquely identify `VariantSets` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -162,22 +162,22 @@ }, "expandHomozygotes": { "description": "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", - "type": "boolean", + "type": ["null", "boolean"], "example": true }, "sepPhased": { "description": "The string used as a separator for phased allele calls.", - "type": "string", + "type": ["null", "string"], "example": "|" }, "sepUnphased": { "description": "The string used as a separator for unphased allele calls.", - "type": "string", + "type": ["null", "string"], "example": "/" }, "unknownString": { "description": "The string used as a representation for missing data.", - "type": "string", + "type": ["null", "string"], "example": "." } }, From f4b6d8922606d75d32e8da8e3cfe647a7e2a7b25 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Thu, 7 May 2026 18:34:23 +1200 Subject: [PATCH 30/62] Update JSON schemas to allow null values for array types --- .../Requests/GermplasmRequest.json | 22 +++++++++---------- .../Requests/MarkerPositionRequest.json | 10 ++++----- .../BrAPI-Schema/Requests/PersonRequest.json | 16 +++++++------- .../BrAPI-Schema/Requests/PlateRequest.json | 14 ++++++------ .../BrAPI-Schema/Requests/ProgramRequest.json | 10 ++++----- .../Requests/ReferenceSetRequest.json | 8 +++---- .../BrAPI-Schema/Requests/SampleRequest.json | 12 +++++----- .../BrAPI-Schema/Requests/StudyRequest.json | 14 ++++++------ 8 files changed, 53 insertions(+), 53 deletions(-) diff --git a/Specification/BrAPI-Schema/Requests/GermplasmRequest.json b/Specification/BrAPI-Schema/Requests/GermplasmRequest.json index f2d2d6ec..69d78b7e 100644 --- a/Specification/BrAPI-Schema/Requests/GermplasmRequest.json +++ b/Specification/BrAPI-Schema/Requests/GermplasmRequest.json @@ -25,7 +25,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "http://pui.per/accession/A0000003", "http://pui.per/accession/A0000477" @@ -36,7 +36,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "A0000003", "A0000477" @@ -47,7 +47,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "RDP1", "MDP1" @@ -58,7 +58,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "fa000203", "fa009965" @@ -69,7 +69,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "PER001", "NOR001" @@ -80,7 +80,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "Aspergillus fructus", "Zea mays" @@ -91,7 +91,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "Aspergillus", "Zea" @@ -102,7 +102,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "fructus", "mays" @@ -113,7 +113,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "variety_1", "2c38f9b6" @@ -124,7 +124,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "72c1001f", "7346c553" @@ -135,7 +135,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "16e16a7e", "ce06cf9e" diff --git a/Specification/BrAPI-Schema/Requests/MarkerPositionRequest.json b/Specification/BrAPI-Schema/Requests/MarkerPositionRequest.json index f05b9bd4..8ba58649 100644 --- a/Specification/BrAPI-Schema/Requests/MarkerPositionRequest.json +++ b/Specification/BrAPI-Schema/Requests/MarkerPositionRequest.json @@ -7,7 +7,7 @@ "properties": { "mapDbIds": { "description": "A list of IDs which uniquely identify `GenomeMaps` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -18,7 +18,7 @@ }, "linkageGroupNames": { "description": "A list of Uniquely Identifiable linkage group names", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -29,7 +29,7 @@ }, "variantDbIds": { "description": "A list of IDs which uniquely identify `Variants` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -40,12 +40,12 @@ }, "minPosition": { "description": "The minimum position of markers in a given map", - "type": "integer", + "type": ["null", "integer"], "example": 250 }, "maxPosition": { "description": "The maximum position of markers in a given map", - "type": "integer", + "type": ["null", "integer"], "example": 4000 } } diff --git a/Specification/BrAPI-Schema/Requests/PersonRequest.json b/Specification/BrAPI-Schema/Requests/PersonRequest.json index 8c413826..f6a3832f 100644 --- a/Specification/BrAPI-Schema/Requests/PersonRequest.json +++ b/Specification/BrAPI-Schema/Requests/PersonRequest.json @@ -13,7 +13,7 @@ "properties": { "emailAddresses": { "description": "email address for this person", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -24,7 +24,7 @@ }, "firstNames": { "description": "Persons first name", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -35,7 +35,7 @@ }, "lastNames": { "description": "Persons last name", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -46,7 +46,7 @@ }, "mailingAddresses": { "description": "physical address of this person", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -57,7 +57,7 @@ }, "middleNames": { "description": "Persons middle name", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -68,7 +68,7 @@ }, "personDbIds": { "description": "Unique ID for this person", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -79,7 +79,7 @@ }, "phoneNumbers": { "description": "phone number of this person", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -90,7 +90,7 @@ }, "userIDs": { "description": "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, diff --git a/Specification/BrAPI-Schema/Requests/PlateRequest.json b/Specification/BrAPI-Schema/Requests/PlateRequest.json index ff02bea8..952d0232 100644 --- a/Specification/BrAPI-Schema/Requests/PlateRequest.json +++ b/Specification/BrAPI-Schema/Requests/PlateRequest.json @@ -25,7 +25,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "3cd0ca36", "983f3b14" @@ -36,7 +36,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "0cac98b8", "b96125fb" @@ -47,7 +47,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "0cac98b8", "b96125fb" @@ -58,7 +58,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "11223344", "55667788" @@ -69,7 +69,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "3bece2ca", "dd286cc6" @@ -80,7 +80,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "SA_111", "SA_222" @@ -91,7 +91,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "45e1e2d7", "6cc6dd28" diff --git a/Specification/BrAPI-Schema/Requests/ProgramRequest.json b/Specification/BrAPI-Schema/Requests/ProgramRequest.json index 3f6e16a9..06790352 100644 --- a/Specification/BrAPI-Schema/Requests/ProgramRequest.json +++ b/Specification/BrAPI-Schema/Requests/ProgramRequest.json @@ -16,7 +16,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "P1", "P2" @@ -27,7 +27,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "d8bd96c7", "a2b9c8e7" @@ -38,7 +38,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "Bob Robertson", "Rob Robertson" @@ -49,7 +49,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "Objective Code One", "This is a longer objective search query" @@ -65,7 +65,7 @@ "PROJECT" ] }, - "type": "array", + "type": ["null", "array"], "example": [ "STANDARD", "PROJECT" diff --git a/Specification/BrAPI-Schema/Requests/ReferenceSetRequest.json b/Specification/BrAPI-Schema/Requests/ReferenceSetRequest.json index a501d4b4..53c01d42 100644 --- a/Specification/BrAPI-Schema/Requests/ReferenceSetRequest.json +++ b/Specification/BrAPI-Schema/Requests/ReferenceSetRequest.json @@ -21,7 +21,7 @@ "type": "object", "properties": { "accessions": { - "type": "array", + "type": ["null", "array"], "description": "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match).", "items": { "type": "string" @@ -32,7 +32,7 @@ ] }, "assemblyPUIs": { - "type": "array", + "type": ["null", "array"], "description": "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match).", "items": { "type": "string" @@ -43,7 +43,7 @@ ] }, "md5checksums": { - "type": "array", + "type": ["null", "array"], "description": "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match).", "items": { "type": "string" @@ -53,7 +53,7 @@ ] }, "referenceSetDbIds": { - "type": "array", + "type": ["null", "array"], "description": "The `ReferenceSets` to search.", "items": { "type": "string" diff --git a/Specification/BrAPI-Schema/Requests/SampleRequest.json b/Specification/BrAPI-Schema/Requests/SampleRequest.json index a71f3847..0464be16 100644 --- a/Specification/BrAPI-Schema/Requests/SampleRequest.json +++ b/Specification/BrAPI-Schema/Requests/SampleRequest.json @@ -25,7 +25,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "3cd0ca36", "983f3b14" @@ -36,7 +36,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "0cac98b8", "b96125fb" @@ -47,7 +47,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "0cac98b8", "b96125fb" @@ -58,7 +58,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "3bece2ca", "dd286cc6" @@ -69,7 +69,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "SA_111", "SA_222" @@ -80,7 +80,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "45e1e2d7", "6cc6dd28" diff --git a/Specification/BrAPI-Schema/Requests/StudyRequest.json b/Specification/BrAPI-Schema/Requests/StudyRequest.json index 0cdbec78..e87f9134 100644 --- a/Specification/BrAPI-Schema/Requests/StudyRequest.json +++ b/Specification/BrAPI-Schema/Requests/StudyRequest.json @@ -28,7 +28,7 @@ "properties": { "active": { "description": "A flag to indicate if a Study is currently active and ongoing", - "type": "boolean", + "type": ["null", "boolean"], "example": true }, "seasonDbIds": { @@ -36,7 +36,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "Harvest Two 2017", "Summer 2018" @@ -47,7 +47,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "Yield Trial", "Disease Resistance Trial" @@ -58,7 +58,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "Grape_Yield_Spring_2018", "Walnut_Kenya" @@ -66,7 +66,7 @@ }, "studyPUIs": { "description": "Permanent unique identifier associated with study data. For example, a URI or DOI", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -88,7 +88,7 @@ "studyLocation", "programName" ], - "type": "string" + "type": ["null", "string"] }, "sortOrder": { "description": "Sort order direction. Ascending/Descending.", @@ -98,7 +98,7 @@ "desc", "DESC" ], - "type": "string" + "type": ["null", "string"] } } } From d8ea281f3d82db437c85a7ce6167dadcae84521d Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 8 May 2026 12:35:28 +1200 Subject: [PATCH 31/62] Update JSON schemas to allow null values for various types --- .../BrAPI-Schema/Requests/CallRequest.json | 14 +++++++------- .../BrAPI-Schema/Requests/CallSetRequest.json | 10 +++++----- .../Requests/GermplasmAttributeRequest.json | 8 ++++---- .../GermplasmAttributeValueRequest.json | 18 +++++++++--------- .../BrAPI-Schema/Requests/ListRequest.json | 18 +++++++++--------- .../Parameters/GermplasmParameters.json | 4 ++-- 6 files changed, 36 insertions(+), 36 deletions(-) diff --git a/Specification/BrAPI-Schema/Requests/CallRequest.json b/Specification/BrAPI-Schema/Requests/CallRequest.json index 7cd32a73..ae1efcb3 100644 --- a/Specification/BrAPI-Schema/Requests/CallRequest.json +++ b/Specification/BrAPI-Schema/Requests/CallRequest.json @@ -5,7 +5,7 @@ "properties": { "callSetDbIds": { "description": "A list of IDs which uniquely identify `CallSets` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -16,7 +16,7 @@ }, "variantDbIds": { "description": "A list of IDs which uniquely identify `Variant` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -27,7 +27,7 @@ }, "variantSetDbIds": { "description": "A list of IDs which uniquely identify `VariantSets` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -38,22 +38,22 @@ }, "expandHomozygotes": { "description": "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", - "type": "boolean", + "type": ["null", "boolean"], "example": true }, "sepPhased": { "description": "The string used as a separator for phased allele calls.", - "type": "string", + "type": ["null", "string"], "example": "|" }, "sepUnphased": { "description": "The string used as a separator for unphased allele calls.", - "type": "string", + "type": ["null", "string"], "example": "/" }, "unknownString": { "description": "The string used as a representation for missing data.", - "type": "string", + "type": ["null", "string"], "example": "." } }, diff --git a/Specification/BrAPI-Schema/Requests/CallSetRequest.json b/Specification/BrAPI-Schema/Requests/CallSetRequest.json index 82709225..edb72030 100644 --- a/Specification/BrAPI-Schema/Requests/CallSetRequest.json +++ b/Specification/BrAPI-Schema/Requests/CallSetRequest.json @@ -22,7 +22,7 @@ "properties": { "sampleDbIds": { "description": "A list of IDs which uniquely identify `Samples` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -33,7 +33,7 @@ }, "sampleNames": { "description": "A list of human readable names associated with `Samples`", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -44,7 +44,7 @@ }, "callSetDbIds": { "description": "A list of IDs which uniquely identify `CallSets` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -55,7 +55,7 @@ }, "callSetNames": { "description": "A list of human readable names associated with `CallSets`", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -66,7 +66,7 @@ }, "variantSetDbIds": { "description": "A list of IDs which uniquely identify `VariantSets` within the given database server", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, diff --git a/Specification/BrAPI-Schema/Requests/GermplasmAttributeRequest.json b/Specification/BrAPI-Schema/Requests/GermplasmAttributeRequest.json index a12755fc..b0ca1604 100644 --- a/Specification/BrAPI-Schema/Requests/GermplasmAttributeRequest.json +++ b/Specification/BrAPI-Schema/Requests/GermplasmAttributeRequest.json @@ -16,7 +16,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "2ef15c9f", "318e7f7d" @@ -27,7 +27,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "Plant Height 1", "Root Color" @@ -38,7 +38,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "http://my-traits.com/trait/CO_123:0008012", "http://my-traits.com/trait/CO_123:0007261" @@ -49,7 +49,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "Morphological", "Physical" diff --git a/Specification/BrAPI-Schema/Requests/GermplasmAttributeValueRequest.json b/Specification/BrAPI-Schema/Requests/GermplasmAttributeValueRequest.json index 41f39116..d1ba1f4f 100644 --- a/Specification/BrAPI-Schema/Requests/GermplasmAttributeValueRequest.json +++ b/Specification/BrAPI-Schema/Requests/GermplasmAttributeValueRequest.json @@ -19,7 +19,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "ca4636d0", "c8a92409" @@ -30,7 +30,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "2ef15c9f", "318e7f7d" @@ -41,7 +41,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "Plant Height 1", "Root Color" @@ -52,7 +52,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "f44f7b23", "a26b576e" @@ -63,7 +63,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "07e34f83", "d3d5517a" @@ -74,7 +74,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "a13ecffa", "7e1afe4f" @@ -85,7 +85,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "ef81147b", "78d82fad" @@ -96,7 +96,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "morphological", "phenological", @@ -108,7 +108,7 @@ "items": { "$ref": "../BrAPI-Common/TraitDataType.json#/$defs/TraitDataType" }, - "type": "array", + "type": ["null", "array"], "example": [ "Numerical", "Ordinal", diff --git a/Specification/BrAPI-Schema/Requests/ListRequest.json b/Specification/BrAPI-Schema/Requests/ListRequest.json index e99fa9e5..ff26a1c1 100644 --- a/Specification/BrAPI-Schema/Requests/ListRequest.json +++ b/Specification/BrAPI-Schema/Requests/ListRequest.json @@ -15,26 +15,26 @@ "dateCreatedRangeStart": { "description": "Define the beginning for an interval of time and only include Lists that are created within this interval.", "format": "date-time", - "type": "string" + "type": ["null", "string"] }, "dateCreatedRangeEnd": { "description": "Define the end for an interval of time and only include Lists that are created within this interval.", "format": "date-time", - "type": "string" + "type": ["null", "string"] }, "dateModifiedRangeStart": { "description": "Define the beginning for an interval of time and only include Lists that are modified within this interval.", "format": "date-time", - "type": "string" + "type": ["null", "string"] }, "dateModifiedRangeEnd": { "description": "Define the end for an interval of time and only include Lists that are modified within this interval.", "format": "date-time", - "type": "string" + "type": ["null", "string"] }, "listDbIds": { "description": "An array of primary database identifiers to identify a set of Lists", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -45,7 +45,7 @@ }, "listNames": { "description": "An array of human readable names to identify a set of Lists", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -56,7 +56,7 @@ }, "listOwnerNames": { "description": "An array of names for the people or entities who are responsible for a set of Lists", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -67,7 +67,7 @@ }, "listOwnerPersonDbIds": { "description": "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, @@ -78,7 +78,7 @@ }, "listSources": { "description": "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", - "type": "array", + "type": ["null", "array"], "items": { "type": "string" }, diff --git a/Specification/BrAPI-Schema/Requests/Parameters/GermplasmParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/GermplasmParameters.json index d5ca59c6..85d380af 100644 --- a/Specification/BrAPI-Schema/Requests/Parameters/GermplasmParameters.json +++ b/Specification/BrAPI-Schema/Requests/Parameters/GermplasmParameters.json @@ -8,7 +8,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "e9c6edd7", "1b1df4a6" @@ -19,7 +19,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["null", "array"], "example": [ "A0000003", "A0000477" From 241dc6716185a4f6cf2111ed3c1f78803df78813 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 8 May 2026 12:47:15 +1200 Subject: [PATCH 32/62] Update SearchRequestParametersGermplasm.yaml to allow null values for germplasmNames and germplasmIds --- .../SearchRequestSchemas/SearchRequestParametersGermplasm.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Specification/Components/Schemas/SearchRequestSchemas/SearchRequestParametersGermplasm.yaml b/Specification/Components/Schemas/SearchRequestSchemas/SearchRequestParametersGermplasm.yaml index 13d5fe36..82883490 100644 --- a/Specification/Components/Schemas/SearchRequestSchemas/SearchRequestParametersGermplasm.yaml +++ b/Specification/Components/Schemas/SearchRequestSchemas/SearchRequestParametersGermplasm.yaml @@ -13,10 +13,12 @@ components: items: type: string type: array + nullable: true example: ['e9c6edd7', '1b1df4a6'] germplasmNames: description: List of human readable names to identify germplasm to search for items: type: string type: array + nullable: true example: ['A0000003', 'A0000477'] From bd31d1da5373a792a9f8f7372be7b78d0e27beb0 Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Fri, 8 May 2026 00:54:02 +0000 Subject: [PATCH 33/62] Generate specifications (manually triggered) --- Specification/Generated/BrAPI-Core.yaml | 160 ++++ Specification/Generated/BrAPI-Genotyping.yaml | 187 ++++ Specification/Generated/BrAPI-Germplasm.yaml | 161 ++++ .../Generated/BrAPI-Phenotyping.yaml | 133 +++ Specification/Generated/brapi_generated.json | 270 +++++- Specification/Generated/brapi_generated.ttl | 824 +++++++++--------- Specification/Generated/brapi_openapi.json | 26 + .../Generated/brapi_openapi_comparison.md | 299 ------- 8 files changed, 1341 insertions(+), 719 deletions(-) diff --git a/Specification/Generated/BrAPI-Core.yaml b/Specification/Generated/BrAPI-Core.yaml index c3a5dce1..b560e8d6 100644 --- a/Specification/Generated/BrAPI-Core.yaml +++ b/Specification/Generated/BrAPI-Core.yaml @@ -1842,6 +1842,7 @@ components: description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ \ in the response." + nullable: true items: type: string dataMatrixNames: @@ -1849,32 +1850,38 @@ components: description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ \ Depth' etc). This list controls which data matrices are returned in\ \ the response." + nullable: true items: type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) + nullable: true example: true germplasmDbIds: type: array description: A list of IDs which uniquely identify `Germplasm` within the given database server + nullable: true items: type: string germplasmNames: type: array description: A list of human readable `Germplasm` names + nullable: true items: type: string germplasmPUIs: type: array description: A list of permanent unique identifiers associated with `Germplasm` + nullable: true items: type: string pagination: type: array description: Pagination for the matrix + nullable: true items: type: object properties: @@ -1901,6 +1908,7 @@ components: description: "The postion range to search\n
\nUses the format \":-\"\ \ where is the chromosome name, is \nthe starting position\ \ of the range, and is the ending position of the range" + nullable: true items: type: string preview: @@ -1917,30 +1925,36 @@ components: type: array description: A list of IDs which uniquely identify `Samples` within the given database server + nullable: true items: type: string sepPhased: type: string description: The string used as a separator for phased allele calls. + nullable: true example: '|' sepUnphased: type: string description: The string used as a separator for unphased allele calls. + nullable: true example: / unknownString: type: string description: The string used as a representation for missing data. + nullable: true example: "." variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the given database server + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string Attribute: @@ -2065,35 +2079,42 @@ components: type: array description: A list of IDs which uniquely identify `CallSets` within the given database server + nullable: true items: type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) + nullable: true example: true sepPhased: type: string description: The string used as a separator for phased allele calls. + nullable: true example: '|' sepUnphased: type: string description: The string used as a separator for unphased allele calls. + nullable: true example: / unknownString: type: string description: The string used as a representation for missing data. + nullable: true example: "." variantDbIds: type: array description: A list of IDs which uniquely identify `Variant` within the given database server + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string CallSetRequest: @@ -2103,11 +2124,13 @@ components: type: array description: A list of IDs which uniquely identify `CallSets` within the given database server + nullable: true items: type: string callSetNames: type: array description: A list of human readable names associated with `CallSets` + nullable: true items: type: string commonCropNames: @@ -2124,12 +2147,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programDbIds: @@ -2154,11 +2179,13 @@ components: type: array description: A list of IDs which uniquely identify `Samples` within the given database server + nullable: true items: type: string sampleNames: type: array description: A list of human readable names associated with `Samples` + nullable: true items: type: string studyDbIds: @@ -2185,6 +2212,7 @@ components: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string CommonCropNamesParameters: @@ -2784,23 +2812,27 @@ components: attributeCategories: type: array description: General category for the attribute. very similar to Trait class. + nullable: true items: type: string attributeDbIds: type: array description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string attributeNames: type: array description: List of human readable Germplasm Attribute names to search for + nullable: true items: type: string attributePUIs: type: array description: "The Permanent Unique Identifier of an Attribute, usually in\ \ the form of a URI" + nullable: true items: type: string commonCropNames: @@ -2822,12 +2854,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string methodDbIds: @@ -2973,17 +3007,20 @@ components: attributeDbIds: type: array description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string attributeNames: type: array description: List of human readable Germplasm Attribute names to search for + nullable: true items: type: string attributeValueDbIds: type: array description: List of Germplasm Attribute Value IDs to search for + nullable: true items: type: string commonCropNames: @@ -3000,27 +3037,32 @@ components: dataTypes: type: array description: List of scale data types to filter search results + nullable: true items: $ref: "#/components/schemas/TraitDataType" germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string methodDbIds: type: array description: List of methods to filter search results + nullable: true items: type: string ontologyDbIds: type: array description: List of ontology IDs to search for + nullable: true items: type: string programDbIds: @@ -3044,16 +3086,19 @@ components: scaleDbIds: type: array description: List of scales to filter search results + nullable: true items: type: string traitClasses: type: array description: List of trait classes to filter search results + nullable: true items: type: string traitDbIds: type: array description: List of trait unique ID to filter search results + nullable: true items: type: string GermplasmParameters: @@ -3062,12 +3107,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string GermplasmRequest: @@ -3079,18 +3126,21 @@ components: A collection of unique identifiers for materials or germplasm within a genebank MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true items: type: string binomialNames: type: array description: List of the full binomial name (scientific name) to identify a germplasm + nullable: true items: type: string collections: type: array description: A specific panel/collection/population name this germplasm belongs to. + nullable: true items: type: string commonCropNames: @@ -3108,27 +3158,32 @@ components: type: array description: A familyCode representing the family this germplasm belongs to. + nullable: true items: type: string genus: type: array description: List of Genus names to identify germplasm + nullable: true items: type: string germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string germplasmPUIs: type: array description: List of Permanent Unique Identifiers to identify germplasm + nullable: true items: type: string instituteCodes: @@ -3141,16 +3196,19 @@ components: \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ \ rules (v)\"." + nullable: true items: type: string parentDbIds: type: array description: Search for Germplasm with these parents + nullable: true items: type: string progenyDbIds: type: array description: Search for Germplasm with these children + nullable: true items: type: string programDbIds: @@ -3174,6 +3232,7 @@ components: species: type: array description: List of Species names to identify germplasm + nullable: true items: type: string studyDbIds: @@ -3189,6 +3248,7 @@ components: synonyms: type: array description: List of alternative names or IDs used to reference this germplasm + nullable: true items: type: string trialDbIds: @@ -3445,48 +3505,57 @@ components: description: Define the end for an interval of time and only include Lists that are created within this interval. format: date-time + nullable: true dateCreatedRangeStart: type: string description: Define the beginning for an interval of time and only include Lists that are created within this interval. format: date-time + nullable: true dateModifiedRangeEnd: type: string description: Define the end for an interval of time and only include Lists that are modified within this interval. format: date-time + nullable: true dateModifiedRangeStart: type: string description: Define the beginning for an interval of time and only include Lists that are modified within this interval. format: date-time + nullable: true listDbIds: type: array description: An array of primary database identifiers to identify a set of Lists + nullable: true items: type: string listNames: type: array description: An array of human readable names to identify a set of Lists + nullable: true items: type: string listOwnerNames: type: array description: An array of names for the people or entities who are responsible for a set of Lists + nullable: true items: type: string listOwnerPersonDbIds: type: array description: An array of primary database identifiers to identify people or entities who are responsible for a set of Lists + nullable: true items: type: string listSources: type: array description: "An array of terms identifying lists from different sources\ \ (ie 'USER', 'SYSTEM', etc)" + nullable: true items: type: string listType: @@ -3517,6 +3586,7 @@ components: description: Define the beginning for an interval of time and only include Lists that are created within this interval. format: date-time + nullable: true programNames: type: array description: |- @@ -3551,10 +3621,12 @@ components: description: Define the end for an interval of time and only include Lists that are modified within this interval. format: date-time + nullable: true listSources: type: array description: "An array of terms identifying lists from different sources\ \ (ie 'USER', 'SYSTEM', etc)" + nullable: true items: type: string listType: @@ -3564,21 +3636,25 @@ components: description: Define the end for an interval of time and only include Lists that are created within this interval. format: date-time + nullable: true listDbIds: type: array description: An array of primary database identifiers to identify a set of Lists + nullable: true items: type: string listNames: type: array description: An array of human readable names to identify a set of Lists + nullable: true items: type: string listOwnerPersonDbIds: type: array description: An array of primary database identifiers to identify people or entities who are responsible for a set of Lists + nullable: true items: type: string dateModifiedRangeStart: @@ -3586,10 +3662,12 @@ components: description: Define the beginning for an interval of time and only include Lists that are modified within this interval. format: date-time + nullable: true listOwnerNames: type: array description: An array of names for the people or entities who are responsible for a set of Lists + nullable: true items: type: string description: "A List represents a collection of other BrAPI data objects. Typically\ @@ -3950,28 +4028,33 @@ components: linkageGroupNames: type: array description: A list of Uniquely Identifiable linkage group names + nullable: true items: type: string mapDbIds: type: array description: A list of IDs which uniquely identify `GenomeMaps` within the given database server + nullable: true items: type: string maxPosition: type: integer description: The maximum position of markers in a given map format: int32 + nullable: true example: 4000 minPosition: type: integer description: The minimum position of markers in a given map format: int32 + nullable: true example: 250 variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the given database server + nullable: true items: type: string MethodRequest: @@ -4040,12 +4123,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -4268,12 +4353,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string includeObservations: @@ -4725,12 +4812,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string germplasmPUIs: @@ -4909,36 +4998,43 @@ components: emailAddresses: type: array description: email address for this person + nullable: true items: type: string firstNames: type: array description: Persons first name + nullable: true items: type: string lastNames: type: array description: Persons last name + nullable: true items: type: string mailingAddresses: type: array description: physical address of this person + nullable: true items: type: string middleNames: type: array description: Persons middle name + nullable: true items: type: string personDbIds: type: array description: Unique ID for this person + nullable: true items: type: string phoneNumbers: type: array description: phone number of this person + nullable: true items: type: string programDbIds: @@ -4963,6 +5059,7 @@ components: type: array description: A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system. + nullable: true items: type: string PersonSearchRequest: @@ -4971,22 +5068,26 @@ components: middleNames: type: array description: Persons middle name + nullable: true items: type: string emailAddresses: type: array description: email address for this person + nullable: true items: type: string userIDs: type: array description: A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system. + nullable: true items: type: string personDbIds: type: array description: Unique ID for this person + nullable: true items: type: string programNames: @@ -5021,21 +5122,25 @@ components: firstNames: type: array description: Persons first name + nullable: true items: type: string lastNames: type: array description: Persons last name + nullable: true items: type: string mailingAddresses: type: array description: physical address of this person + nullable: true items: type: string phoneNumbers: type: array description: phone number of this person + nullable: true items: type: string description: "A generic object used to maintain the metadata needed to describe\ @@ -5121,32 +5226,38 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: type: array description: The ID which uniquely identifies an observation unit + nullable: true items: type: string plateBarcodes: type: array description: A unique identifier physically attached to the plate + nullable: true items: type: string plateDbIds: type: array description: The ID which uniquely identifies a plate of samples + nullable: true items: type: string plateNames: type: array description: The human readable name of a plate of samples + nullable: true items: type: string programDbIds: @@ -5170,16 +5281,19 @@ components: sampleDbIds: type: array description: The ID which uniquely identifies a sample + nullable: true items: type: string sampleGroupDbIds: type: array description: The unique identifier for a group of related Samples + nullable: true items: type: string sampleNames: type: array description: The human readable name of the sample + nullable: true items: type: string studyDbIds: @@ -5299,6 +5413,7 @@ components: abbreviations: type: array description: A list of shortened human readable names for a set of Programs + nullable: true items: type: string commonCropNames: @@ -5315,16 +5430,19 @@ components: leadPersonDbIds: type: array description: The person DbIds of the program leader to search for + nullable: true items: type: string leadPersonNames: type: array description: The names of the program leader to search for + nullable: true items: type: string objectives: type: array description: A program objective to search for + nullable: true items: type: string programDbIds: @@ -5350,6 +5468,7 @@ components: description: "The type of program entity this object represents\n
'STANDARD'\ \ represents a standard, permanent breeding program\n
'PROJECT' represents\ \ a short term project, usually with a set time limit based on funding " + nullable: true items: type: string description: |- @@ -5365,6 +5484,7 @@ components: leadPersonNames: type: array description: The names of the program leader to search for + nullable: true items: type: string programNames: @@ -5399,11 +5519,13 @@ components: objectives: type: array description: A program objective to search for + nullable: true items: type: string leadPersonDbIds: type: array description: The person DbIds of the program leader to search for + nullable: true items: type: string programTypes: @@ -5411,6 +5533,7 @@ components: description: "The type of program entity this object represents\n
'STANDARD'\ \ represents a standard, permanent breeding program\n
'PROJECT' represents\ \ a short term project, usually with a set time limit based on funding " + nullable: true items: type: string description: |- @@ -5423,6 +5546,7 @@ components: abbreviations: type: array description: A list of shortened human readable names for a set of Programs + nullable: true items: type: string description: A BrAPI Program represents the high level organization or group @@ -5502,12 +5626,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string isDerived: @@ -5591,12 +5717,14 @@ components: type: array description: "If set, return the reference sets for which the `accession`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string assemblyPUIs: type: array description: "If set, return the reference sets for which the `assemblyId`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string commonCropNames: @@ -5613,18 +5741,21 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string md5checksums: type: array description: "If set, return the reference sets for which the `md5checksum`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string programDbIds: @@ -5648,6 +5779,7 @@ components: referenceSetDbIds: type: array description: The `ReferenceSets` to search. + nullable: true items: type: string studyDbIds: @@ -5687,27 +5819,32 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: type: array description: The ID which uniquely identifies an `ObservationUnit` + nullable: true items: type: string plateDbIds: type: array description: The ID which uniquely identifies a `Plate` of `Samples` + nullable: true items: type: string plateNames: type: array description: The human readable name of a `Plate` of `Samples` + nullable: true items: type: string programDbIds: @@ -5731,16 +5868,19 @@ components: sampleDbIds: type: array description: The ID which uniquely identifies a `Sample` + nullable: true items: type: string sampleGroupDbIds: type: array description: The unique identifier for a group of related `Samples` + nullable: true items: type: string sampleNames: type: array description: The human readable name of the `Sample` + nullable: true items: type: string studyDbIds: @@ -5889,12 +6029,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programDbIds: @@ -6117,6 +6259,7 @@ components: active: type: boolean description: A flag to indicate if a Study is currently active and ongoing + nullable: true example: true commonCropNames: type: array @@ -6132,12 +6275,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -6187,11 +6332,13 @@ components: seasonDbIds: type: array description: The ID which uniquely identifies a season + nullable: true items: type: string sortBy: type: string description: Name of the field to sort by. + nullable: true enum: - studyDbId - trialDbId @@ -6205,6 +6352,7 @@ components: sortOrder: type: string description: Sort order direction. Ascending/Descending. + nullable: true enum: - asc - ASC @@ -6213,6 +6361,7 @@ components: studyCodes: type: array description: A short human readable code for a study + nullable: true items: type: string studyDbIds: @@ -6229,11 +6378,13 @@ components: type: array description: "Permanent unique identifier associated with study data. For\ \ example, a URI or DOI" + nullable: true items: type: string studyTypes: type: array description: "The type of study being performed. ex. \"Yield Trial\", etc" + nullable: true items: type: string trialDbIds: @@ -6252,6 +6403,7 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -6268,6 +6420,7 @@ components: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programNames: @@ -6281,11 +6434,13 @@ components: seasonDbIds: type: array description: The ID which uniquely identifies a season + nullable: true items: type: string active: type: boolean description: A flag to indicate if a Study is currently active and ongoing + nullable: true example: true commonCropNames: type: array @@ -6311,12 +6466,14 @@ components: studyCodes: type: array description: A short human readable code for a study + nullable: true items: type: string studyPUIs: type: array description: "Permanent unique identifier associated with study data. For\ \ example, a URI or DOI" + nullable: true items: type: string observationVariablePUIs: @@ -6358,6 +6515,7 @@ components: sortOrder: type: string description: Sort order direction. Ascending/Descending. + nullable: true enum: - asc - ASC @@ -6366,6 +6524,7 @@ components: sortBy: type: string description: Name of the field to sort by. + nullable: true enum: - studyDbId - trialDbId @@ -6379,6 +6538,7 @@ components: studyTypes: type: array description: "The type of study being performed. ex. \"Yield Trial\", etc" + nullable: true items: type: string description: A Study represents an experiment that has taken place at a single diff --git a/Specification/Generated/BrAPI-Genotyping.yaml b/Specification/Generated/BrAPI-Genotyping.yaml index 52293db9..1a314080 100644 --- a/Specification/Generated/BrAPI-Genotyping.yaml +++ b/Specification/Generated/BrAPI-Genotyping.yaml @@ -2139,6 +2139,7 @@ components: description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ \ in the response." + nullable: true items: type: string dataMatrixNames: @@ -2146,32 +2147,38 @@ components: description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ \ Depth' etc). This list controls which data matrices are returned in\ \ the response." + nullable: true items: type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) + nullable: true example: true germplasmDbIds: type: array description: A list of IDs which uniquely identify `Germplasm` within the given database server + nullable: true items: type: string germplasmNames: type: array description: A list of human readable `Germplasm` names + nullable: true items: type: string germplasmPUIs: type: array description: A list of permanent unique identifiers associated with `Germplasm` + nullable: true items: type: string pagination: type: array description: Pagination for the matrix + nullable: true items: type: object properties: @@ -2198,6 +2205,7 @@ components: description: "The postion range to search\n
\nUses the format \":-\"\ \ where is the chromosome name, is \nthe starting position\ \ of the range, and is the ending position of the range" + nullable: true items: type: string preview: @@ -2214,30 +2222,36 @@ components: type: array description: A list of IDs which uniquely identify `Samples` within the given database server + nullable: true items: type: string sepPhased: type: string description: The string used as a separator for phased allele calls. + nullable: true example: '|' sepUnphased: type: string description: The string used as a separator for unphased allele calls. + nullable: true example: / unknownString: type: string description: The string used as a representation for missing data. + nullable: true example: "." variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the given database server + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string AlleleMatrixSearchRequest: @@ -2247,6 +2261,7 @@ components: type: array description: A list of IDs which uniquely identify `Germplasm` within the given database server + nullable: true items: type: string preview: @@ -2262,11 +2277,13 @@ components: germplasmNames: type: array description: A list of human readable `Germplasm` names + nullable: true items: type: string pagination: type: array description: Pagination for the matrix + nullable: true items: type: object properties: @@ -2291,10 +2308,12 @@ components: unknownString: type: string description: The string used as a representation for missing data. + nullable: true example: "." germplasmPUIs: type: array description: A list of permanent unique identifiers associated with `Germplasm` + nullable: true items: type: string positionRanges: @@ -2302,18 +2321,21 @@ components: description: "The postion range to search\n
\nUses the format \":-\"\ \ where is the chromosome name, is \nthe starting position\ \ of the range, and is the ending position of the range" + nullable: true items: type: string sampleDbIds: type: array description: A list of IDs which uniquely identify `Samples` within the given database server + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string dataMatrixAbbreviations: @@ -2321,17 +2343,20 @@ components: description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ \ in the response." + nullable: true items: type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) + nullable: true example: true variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the given database server + nullable: true items: type: string callSetDbIds: @@ -2345,15 +2370,18 @@ components: description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ \ Depth' etc). This list controls which data matrices are returned in\ \ the response." + nullable: true items: type: string sepPhased: type: string description: The string used as a separator for phased allele calls. + nullable: true example: '|' sepUnphased: type: string description: The string used as a separator for unphased allele calls. + nullable: true example: / description: "The AlleleMatrix object is used to describe a matrix of genotyping\ \ results. This 2d array of data reduces the overall size of the response\ @@ -2625,35 +2653,42 @@ components: type: array description: A list of IDs which uniquely identify `CallSets` within the given database server + nullable: true items: type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) + nullable: true example: true sepPhased: type: string description: The string used as a separator for phased allele calls. + nullable: true example: '|' sepUnphased: type: string description: The string used as a separator for unphased allele calls. + nullable: true example: / unknownString: type: string description: The string used as a representation for missing data. + nullable: true example: "." variantDbIds: type: array description: A list of IDs which uniquely identify `Variant` within the given database server + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string CallSearchRequest: @@ -2663,36 +2698,43 @@ components: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string unknownString: type: string description: The string used as a representation for missing data. + nullable: true example: "." expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) + nullable: true example: true variantDbIds: type: array description: A list of IDs which uniquely identify `Variant` within the given database server + nullable: true items: type: string callSetDbIds: type: array description: A list of IDs which uniquely identify `CallSets` within the given database server + nullable: true items: type: string sepPhased: type: string description: The string used as a separator for phased allele calls. + nullable: true example: '|' sepUnphased: type: string description: The string used as a separator for unphased allele calls. + nullable: true example: / description: "A `Call` represents the determination of genotype with respect\ \ to a particular `Variant`. \n\nIt may include associated information such\ @@ -2754,11 +2796,13 @@ components: type: array description: A list of IDs which uniquely identify `CallSets` within the given database server + nullable: true items: type: string callSetNames: type: array description: A list of human readable names associated with `CallSets` + nullable: true items: type: string commonCropNames: @@ -2775,12 +2819,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programDbIds: @@ -2805,11 +2851,13 @@ components: type: array description: A list of IDs which uniquely identify `Samples` within the given database server + nullable: true items: type: string sampleNames: type: array description: A list of human readable names associated with `Samples` + nullable: true items: type: string studyDbIds: @@ -2836,6 +2884,7 @@ components: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string CallSetSearchRequest: @@ -2844,12 +2893,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programNames: @@ -2890,6 +2941,7 @@ components: type: array description: A list of IDs which uniquely identify `Samples` within the given database server + nullable: true items: type: string studyDbIds: @@ -2906,11 +2958,13 @@ components: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string callSetNames: type: array description: A list of human readable names associated with `CallSets` + nullable: true items: type: string studyNames: @@ -2921,12 +2975,14 @@ components: sampleNames: type: array description: A list of human readable names associated with `Samples` + nullable: true items: type: string callSetDbIds: type: array description: A list of IDs which uniquely identify `CallSets` within the given database server + nullable: true items: type: string description: A CallSet is a collection of Calls that were generated by the same @@ -3484,23 +3540,27 @@ components: attributeCategories: type: array description: General category for the attribute. very similar to Trait class. + nullable: true items: type: string attributeDbIds: type: array description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string attributeNames: type: array description: List of human readable Germplasm Attribute names to search for + nullable: true items: type: string attributePUIs: type: array description: "The Permanent Unique Identifier of an Attribute, usually in\ \ the form of a URI" + nullable: true items: type: string commonCropNames: @@ -3522,12 +3582,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string methodDbIds: @@ -3673,17 +3735,20 @@ components: attributeDbIds: type: array description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string attributeNames: type: array description: List of human readable Germplasm Attribute names to search for + nullable: true items: type: string attributeValueDbIds: type: array description: List of Germplasm Attribute Value IDs to search for + nullable: true items: type: string commonCropNames: @@ -3700,27 +3765,32 @@ components: dataTypes: type: array description: List of scale data types to filter search results + nullable: true items: $ref: "#/components/schemas/TraitDataType" germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string methodDbIds: type: array description: List of methods to filter search results + nullable: true items: type: string ontologyDbIds: type: array description: List of ontology IDs to search for + nullable: true items: type: string programDbIds: @@ -3744,16 +3814,19 @@ components: scaleDbIds: type: array description: List of scales to filter search results + nullable: true items: type: string traitClasses: type: array description: List of trait classes to filter search results + nullable: true items: type: string traitDbIds: type: array description: List of trait unique ID to filter search results + nullable: true items: type: string GermplasmParameters: @@ -3762,12 +3835,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string GermplasmRequest: @@ -3779,18 +3854,21 @@ components: A collection of unique identifiers for materials or germplasm within a genebank MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true items: type: string binomialNames: type: array description: List of the full binomial name (scientific name) to identify a germplasm + nullable: true items: type: string collections: type: array description: A specific panel/collection/population name this germplasm belongs to. + nullable: true items: type: string commonCropNames: @@ -3808,27 +3886,32 @@ components: type: array description: A familyCode representing the family this germplasm belongs to. + nullable: true items: type: string genus: type: array description: List of Genus names to identify germplasm + nullable: true items: type: string germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string germplasmPUIs: type: array description: List of Permanent Unique Identifiers to identify germplasm + nullable: true items: type: string instituteCodes: @@ -3841,16 +3924,19 @@ components: \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ \ rules (v)\"." + nullable: true items: type: string parentDbIds: type: array description: Search for Germplasm with these parents + nullable: true items: type: string progenyDbIds: type: array description: Search for Germplasm with these children + nullable: true items: type: string programDbIds: @@ -3874,6 +3960,7 @@ components: species: type: array description: List of Species names to identify germplasm + nullable: true items: type: string studyDbIds: @@ -3889,6 +3976,7 @@ components: synonyms: type: array description: List of alternative names or IDs used to reference this germplasm + nullable: true items: type: string trialDbIds: @@ -4057,48 +4145,57 @@ components: description: Define the end for an interval of time and only include Lists that are created within this interval. format: date-time + nullable: true dateCreatedRangeStart: type: string description: Define the beginning for an interval of time and only include Lists that are created within this interval. format: date-time + nullable: true dateModifiedRangeEnd: type: string description: Define the end for an interval of time and only include Lists that are modified within this interval. format: date-time + nullable: true dateModifiedRangeStart: type: string description: Define the beginning for an interval of time and only include Lists that are modified within this interval. format: date-time + nullable: true listDbIds: type: array description: An array of primary database identifiers to identify a set of Lists + nullable: true items: type: string listNames: type: array description: An array of human readable names to identify a set of Lists + nullable: true items: type: string listOwnerNames: type: array description: An array of names for the people or entities who are responsible for a set of Lists + nullable: true items: type: string listOwnerPersonDbIds: type: array description: An array of primary database identifiers to identify people or entities who are responsible for a set of Lists + nullable: true items: type: string listSources: type: array description: "An array of terms identifying lists from different sources\ \ (ie 'USER', 'SYSTEM', etc)" + nullable: true items: type: string listType: @@ -4268,28 +4365,33 @@ components: linkageGroupNames: type: array description: A list of Uniquely Identifiable linkage group names + nullable: true items: type: string mapDbIds: type: array description: A list of IDs which uniquely identify `GenomeMaps` within the given database server + nullable: true items: type: string maxPosition: type: integer description: The maximum position of markers in a given map format: int32 + nullable: true example: 4000 minPosition: type: integer description: The minimum position of markers in a given map format: int32 + nullable: true example: 250 variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the given database server + nullable: true items: type: string MarkerPositionSearchRequest: @@ -4298,29 +4400,34 @@ components: linkageGroupNames: type: array description: A list of Uniquely Identifiable linkage group names + nullable: true items: type: string variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the given database server + nullable: true items: type: string mapDbIds: type: array description: A list of IDs which uniquely identify `GenomeMaps` within the given database server + nullable: true items: type: string maxPosition: type: integer description: The maximum position of markers in a given map format: int32 + nullable: true example: 4000 minPosition: type: integer description: The minimum position of markers in a given map format: int32 + nullable: true example: 250 description: A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data @@ -4423,12 +4530,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -4651,12 +4760,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string includeObservations: @@ -5143,12 +5254,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string germplasmPUIs: @@ -5265,36 +5378,43 @@ components: emailAddresses: type: array description: email address for this person + nullable: true items: type: string firstNames: type: array description: Persons first name + nullable: true items: type: string lastNames: type: array description: Persons last name + nullable: true items: type: string mailingAddresses: type: array description: physical address of this person + nullable: true items: type: string middleNames: type: array description: Persons middle name + nullable: true items: type: string personDbIds: type: array description: Unique ID for this person + nullable: true items: type: string phoneNumbers: type: array description: phone number of this person + nullable: true items: type: string programDbIds: @@ -5319,6 +5439,7 @@ components: type: array description: A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system. + nullable: true items: type: string PlannedCrossRequest: @@ -5483,32 +5604,38 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: type: array description: The ID which uniquely identifies an observation unit + nullable: true items: type: string plateBarcodes: type: array description: A unique identifier physically attached to the plate + nullable: true items: type: string plateDbIds: type: array description: The ID which uniquely identifies a plate of samples + nullable: true items: type: string plateNames: type: array description: The human readable name of a plate of samples + nullable: true items: type: string programDbIds: @@ -5532,16 +5659,19 @@ components: sampleDbIds: type: array description: The ID which uniquely identifies a sample + nullable: true items: type: string sampleGroupDbIds: type: array description: The unique identifier for a group of related Samples + nullable: true items: type: string sampleNames: type: array description: The human readable name of the sample + nullable: true items: type: string studyDbIds: @@ -5570,27 +5700,32 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: type: array description: The ID which uniquely identifies an observation unit + nullable: true items: type: string plateBarcodes: type: array description: A unique identifier physically attached to the plate + nullable: true items: type: string plateNames: type: array description: The human readable name of a plate of samples + nullable: true items: type: string programNames: @@ -5630,11 +5765,13 @@ components: sampleDbIds: type: array description: The ID which uniquely identifies a sample + nullable: true items: type: string plateDbIds: type: array description: The ID which uniquely identifies a plate of samples + nullable: true items: type: string studyDbIds: @@ -5650,6 +5787,7 @@ components: sampleGroupDbIds: type: array description: The unique identifier for a group of related Samples + nullable: true items: type: string studyNames: @@ -5660,6 +5798,7 @@ components: sampleNames: type: array description: The human readable name of the sample + nullable: true items: type: string description: "A Plate represents the metadata for a collection of Samples. The\ @@ -5695,6 +5834,7 @@ components: abbreviations: type: array description: A list of shortened human readable names for a set of Programs + nullable: true items: type: string commonCropNames: @@ -5711,16 +5851,19 @@ components: leadPersonDbIds: type: array description: The person DbIds of the program leader to search for + nullable: true items: type: string leadPersonNames: type: array description: The names of the program leader to search for + nullable: true items: type: string objectives: type: array description: A program objective to search for + nullable: true items: type: string programDbIds: @@ -5746,6 +5889,7 @@ components: description: "The type of program entity this object represents\n
'STANDARD'\ \ represents a standard, permanent breeding program\n
'PROJECT' represents\ \ a short term project, usually with a set time limit based on funding " + nullable: true items: type: string description: |- @@ -5913,12 +6057,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string isDerived: @@ -6001,6 +6147,7 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string isDerived: @@ -6015,6 +6162,7 @@ components: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string minLength: @@ -6209,12 +6357,14 @@ components: type: array description: "If set, return the reference sets for which the `accession`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string assemblyPUIs: type: array description: "If set, return the reference sets for which the `assemblyId`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string commonCropNames: @@ -6231,18 +6381,21 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string md5checksums: type: array description: "If set, return the reference sets for which the `md5checksum`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string programDbIds: @@ -6266,6 +6419,7 @@ components: referenceSetDbIds: type: array description: The `ReferenceSets` to search. + nullable: true items: type: string studyDbIds: @@ -6294,12 +6448,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programNames: @@ -6339,6 +6495,7 @@ components: referenceSetDbIds: type: array description: The `ReferenceSets` to search. + nullable: true items: type: string studyDbIds: @@ -6355,12 +6512,14 @@ components: type: array description: "If set, return the reference sets for which the `md5checksum`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string assemblyPUIs: type: array description: "If set, return the reference sets for which the `assemblyId`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string studyNames: @@ -6372,6 +6531,7 @@ components: type: array description: "If set, return the reference sets for which the `accession`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ @@ -6529,27 +6689,32 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: type: array description: The ID which uniquely identifies an `ObservationUnit` + nullable: true items: type: string plateDbIds: type: array description: The ID which uniquely identifies a `Plate` of `Samples` + nullable: true items: type: string plateNames: type: array description: The human readable name of a `Plate` of `Samples` + nullable: true items: type: string programDbIds: @@ -6573,16 +6738,19 @@ components: sampleDbIds: type: array description: The ID which uniquely identifies a `Sample` + nullable: true items: type: string sampleGroupDbIds: type: array description: The unique identifier for a group of related `Samples` + nullable: true items: type: string sampleNames: type: array description: The human readable name of the `Sample` + nullable: true items: type: string studyDbIds: @@ -6611,22 +6779,26 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: type: array description: The ID which uniquely identifies an `ObservationUnit` + nullable: true items: type: string plateNames: type: array description: The human readable name of a `Plate` of `Samples` + nullable: true items: type: string programNames: @@ -6666,11 +6838,13 @@ components: sampleDbIds: type: array description: The ID which uniquely identifies a `Sample` + nullable: true items: type: string plateDbIds: type: array description: The ID which uniquely identifies a `Plate` of `Samples` + nullable: true items: type: string studyDbIds: @@ -6686,6 +6860,7 @@ components: sampleGroupDbIds: type: array description: The unique identifier for a group of related `Samples` + nullable: true items: type: string studyNames: @@ -6696,6 +6871,7 @@ components: sampleNames: type: array description: The human readable name of the `Sample` + nullable: true items: type: string description: "The identifiers and metadata associated with a physical piece\ @@ -6812,12 +6988,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programDbIds: @@ -6883,6 +7061,7 @@ components: active: type: boolean description: A flag to indicate if a Study is currently active and ongoing + nullable: true example: true commonCropNames: type: array @@ -6898,12 +7077,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -6953,11 +7134,13 @@ components: seasonDbIds: type: array description: The ID which uniquely identifies a season + nullable: true items: type: string sortBy: type: string description: Name of the field to sort by. + nullable: true enum: - studyDbId - trialDbId @@ -6971,6 +7154,7 @@ components: sortOrder: type: string description: Sort order direction. Ascending/Descending. + nullable: true enum: - asc - ASC @@ -6979,6 +7163,7 @@ components: studyCodes: type: array description: A short human readable code for a study + nullable: true items: type: string studyDbIds: @@ -6995,11 +7180,13 @@ components: type: array description: "Permanent unique identifier associated with study data. For\ \ example, a URI or DOI" + nullable: true items: type: string studyTypes: type: array description: "The type of study being performed. ex. \"Yield Trial\", etc" + nullable: true items: type: string trialDbIds: diff --git a/Specification/Generated/BrAPI-Germplasm.yaml b/Specification/Generated/BrAPI-Germplasm.yaml index a1ada153..293761af 100644 --- a/Specification/Generated/BrAPI-Germplasm.yaml +++ b/Specification/Generated/BrAPI-Germplasm.yaml @@ -1771,6 +1771,7 @@ components: description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ \ in the response." + nullable: true items: type: string dataMatrixNames: @@ -1778,32 +1779,38 @@ components: description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ \ Depth' etc). This list controls which data matrices are returned in\ \ the response." + nullable: true items: type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) + nullable: true example: true germplasmDbIds: type: array description: A list of IDs which uniquely identify `Germplasm` within the given database server + nullable: true items: type: string germplasmNames: type: array description: A list of human readable `Germplasm` names + nullable: true items: type: string germplasmPUIs: type: array description: A list of permanent unique identifiers associated with `Germplasm` + nullable: true items: type: string pagination: type: array description: Pagination for the matrix + nullable: true items: type: object properties: @@ -1830,6 +1837,7 @@ components: description: "The postion range to search\n
\nUses the format \":-\"\ \ where is the chromosome name, is \nthe starting position\ \ of the range, and is the ending position of the range" + nullable: true items: type: string preview: @@ -1846,30 +1854,36 @@ components: type: array description: A list of IDs which uniquely identify `Samples` within the given database server + nullable: true items: type: string sepPhased: type: string description: The string used as a separator for phased allele calls. + nullable: true example: '|' sepUnphased: type: string description: The string used as a separator for unphased allele calls. + nullable: true example: / unknownString: type: string description: The string used as a representation for missing data. + nullable: true example: "." variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the given database server + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string Attribute: @@ -2053,35 +2067,42 @@ components: type: array description: A list of IDs which uniquely identify `CallSets` within the given database server + nullable: true items: type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) + nullable: true example: true sepPhased: type: string description: The string used as a separator for phased allele calls. + nullable: true example: '|' sepUnphased: type: string description: The string used as a separator for unphased allele calls. + nullable: true example: / unknownString: type: string description: The string used as a representation for missing data. + nullable: true example: "." variantDbIds: type: array description: A list of IDs which uniquely identify `Variant` within the given database server + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string CallSetRequest: @@ -2091,11 +2112,13 @@ components: type: array description: A list of IDs which uniquely identify `CallSets` within the given database server + nullable: true items: type: string callSetNames: type: array description: A list of human readable names associated with `CallSets` + nullable: true items: type: string commonCropNames: @@ -2112,12 +2135,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programDbIds: @@ -2142,11 +2167,13 @@ components: type: array description: A list of IDs which uniquely identify `Samples` within the given database server + nullable: true items: type: string sampleNames: type: array description: A list of human readable names associated with `Samples` + nullable: true items: type: string studyDbIds: @@ -2173,6 +2200,7 @@ components: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string CollectingInfo: @@ -3126,23 +3154,27 @@ components: attributeCategories: type: array description: General category for the attribute. very similar to Trait class. + nullable: true items: type: string attributeDbIds: type: array description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string attributeNames: type: array description: List of human readable Germplasm Attribute names to search for + nullable: true items: type: string attributePUIs: type: array description: "The Permanent Unique Identifier of an Attribute, usually in\ \ the form of a URI" + nullable: true items: type: string commonCropNames: @@ -3164,12 +3196,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string methodDbIds: @@ -3316,6 +3350,7 @@ components: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string methodDbIds: @@ -3334,6 +3369,7 @@ components: attributeDbIds: type: array description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string trialNames: @@ -3356,6 +3392,7 @@ components: type: array description: List of human readable Germplasm Attribute names to search for + nullable: true items: type: string methodPUIs: @@ -3393,6 +3430,7 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string methodNames: @@ -3423,6 +3461,7 @@ components: attributeCategories: type: array description: General category for the attribute. very similar to Trait class. + nullable: true items: type: string commonCropNames: @@ -3475,6 +3514,7 @@ components: type: array description: "The Permanent Unique Identifier of an Attribute, usually in\ \ the form of a URI" + nullable: true items: type: string traitNames: @@ -3559,17 +3599,20 @@ components: attributeDbIds: type: array description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string attributeNames: type: array description: List of human readable Germplasm Attribute names to search for + nullable: true items: type: string attributeValueDbIds: type: array description: List of Germplasm Attribute Value IDs to search for + nullable: true items: type: string commonCropNames: @@ -3586,27 +3629,32 @@ components: dataTypes: type: array description: List of scale data types to filter search results + nullable: true items: $ref: "#/components/schemas/TraitDataType" germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string methodDbIds: type: array description: List of methods to filter search results + nullable: true items: type: string ontologyDbIds: type: array description: List of ontology IDs to search for + nullable: true items: type: string programDbIds: @@ -3630,16 +3678,19 @@ components: scaleDbIds: type: array description: List of scales to filter search results + nullable: true items: type: string traitClasses: type: array description: List of trait classes to filter search results + nullable: true items: type: string traitDbIds: type: array description: List of trait unique ID to filter search results + nullable: true items: type: string GermplasmAttributeValueSearchRequest: @@ -3648,22 +3699,26 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string methodDbIds: type: array description: List of methods to filter search results + nullable: true items: type: string traitClasses: type: array description: List of trait classes to filter search results + nullable: true items: type: string programNames: @@ -3698,37 +3753,44 @@ components: attributeValueDbIds: type: array description: List of Germplasm Attribute Value IDs to search for + nullable: true items: type: string attributeDbIds: type: array description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string ontologyDbIds: type: array description: List of ontology IDs to search for + nullable: true items: type: string dataTypes: type: array description: List of scale data types to filter search results + nullable: true items: $ref: "#/components/schemas/TraitDataType" attributeNames: type: array description: List of human readable Germplasm Attribute names to search for + nullable: true items: type: string traitDbIds: type: array description: List of trait unique ID to filter search results + nullable: true items: type: string scaleDbIds: type: array description: List of scales to filter search results + nullable: true items: type: string description: "The value recorded for a particular Trait/Attribute and a particular\ @@ -4442,12 +4504,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string GermplasmParent: @@ -4479,18 +4543,21 @@ components: A collection of unique identifiers for materials or germplasm within a genebank MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true items: type: string binomialNames: type: array description: List of the full binomial name (scientific name) to identify a germplasm + nullable: true items: type: string collections: type: array description: A specific panel/collection/population name this germplasm belongs to. + nullable: true items: type: string commonCropNames: @@ -4508,27 +4575,32 @@ components: type: array description: A familyCode representing the family this germplasm belongs to. + nullable: true items: type: string genus: type: array description: List of Genus names to identify germplasm + nullable: true items: type: string germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string germplasmPUIs: type: array description: List of Permanent Unique Identifiers to identify germplasm + nullable: true items: type: string instituteCodes: @@ -4541,16 +4613,19 @@ components: \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ \ rules (v)\"." + nullable: true items: type: string parentDbIds: type: array description: Search for Germplasm with these parents + nullable: true items: type: string progenyDbIds: type: array description: Search for Germplasm with these children + nullable: true items: type: string programDbIds: @@ -4574,6 +4649,7 @@ components: species: type: array description: List of Species names to identify germplasm + nullable: true items: type: string studyDbIds: @@ -4589,6 +4665,7 @@ components: synonyms: type: array description: List of alternative names or IDs used to reference this germplasm + nullable: true items: type: string trialDbIds: @@ -4607,6 +4684,7 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string accessionNumbers: @@ -4615,17 +4693,20 @@ components: A collection of unique identifiers for materials or germplasm within a genebank MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string synonyms: type: array description: List of alternative names or IDs used to reference this germplasm + nullable: true items: type: string programNames: @@ -4665,11 +4746,13 @@ components: germplasmPUIs: type: array description: List of Permanent Unique Identifiers to identify germplasm + nullable: true items: type: string parentDbIds: type: array description: Search for Germplasm with these parents + nullable: true items: type: string studyDbIds: @@ -4686,6 +4769,7 @@ components: type: array description: A familyCode representing the family this germplasm belongs to. + nullable: true items: type: string studyNames: @@ -4697,22 +4781,26 @@ components: type: array description: A specific panel/collection/population name this germplasm belongs to. + nullable: true items: type: string genus: type: array description: List of Genus names to identify germplasm + nullable: true items: type: string species: type: array description: List of Species names to identify germplasm + nullable: true items: type: string binomialNames: type: array description: List of the full binomial name (scientific name) to identify a germplasm + nullable: true items: type: string instituteCodes: @@ -4725,11 +4813,13 @@ components: \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ \ rules (v)\"." + nullable: true items: type: string progenyDbIds: type: array description: Search for Germplasm with these children + nullable: true items: type: string description: "The conceptual identifiers and metadata describing a genetically\ @@ -4898,48 +4988,57 @@ components: description: Define the end for an interval of time and only include Lists that are created within this interval. format: date-time + nullable: true dateCreatedRangeStart: type: string description: Define the beginning for an interval of time and only include Lists that are created within this interval. format: date-time + nullable: true dateModifiedRangeEnd: type: string description: Define the end for an interval of time and only include Lists that are modified within this interval. format: date-time + nullable: true dateModifiedRangeStart: type: string description: Define the beginning for an interval of time and only include Lists that are modified within this interval. format: date-time + nullable: true listDbIds: type: array description: An array of primary database identifiers to identify a set of Lists + nullable: true items: type: string listNames: type: array description: An array of human readable names to identify a set of Lists + nullable: true items: type: string listOwnerNames: type: array description: An array of names for the people or entities who are responsible for a set of Lists + nullable: true items: type: string listOwnerPersonDbIds: type: array description: An array of primary database identifiers to identify people or entities who are responsible for a set of Lists + nullable: true items: type: string listSources: type: array description: "An array of terms identifying lists from different sources\ \ (ie 'USER', 'SYSTEM', etc)" + nullable: true items: type: string listType: @@ -5081,28 +5180,33 @@ components: linkageGroupNames: type: array description: A list of Uniquely Identifiable linkage group names + nullable: true items: type: string mapDbIds: type: array description: A list of IDs which uniquely identify `GenomeMaps` within the given database server + nullable: true items: type: string maxPosition: type: integer description: The maximum position of markers in a given map format: int32 + nullable: true example: 4000 minPosition: type: integer description: The minimum position of markers in a given map format: int32 + nullable: true example: 250 variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the given database server + nullable: true items: type: string MethodRequest: @@ -5183,12 +5287,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -5411,12 +5517,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string includeObservations: @@ -5978,12 +6086,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string germplasmPUIs: @@ -6089,6 +6199,7 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string accessionNumbers: @@ -6103,6 +6214,7 @@ components: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string includeParents: @@ -6257,36 +6369,43 @@ components: emailAddresses: type: array description: email address for this person + nullable: true items: type: string firstNames: type: array description: Persons first name + nullable: true items: type: string lastNames: type: array description: Persons last name + nullable: true items: type: string mailingAddresses: type: array description: physical address of this person + nullable: true items: type: string middleNames: type: array description: Persons middle name + nullable: true items: type: string personDbIds: type: array description: Unique ID for this person + nullable: true items: type: string phoneNumbers: type: array description: phone number of this person + nullable: true items: type: string programDbIds: @@ -6311,6 +6430,7 @@ components: type: array description: A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system. + nullable: true items: type: string PlannedCross: @@ -6447,32 +6567,38 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: type: array description: The ID which uniquely identifies an observation unit + nullable: true items: type: string plateBarcodes: type: array description: A unique identifier physically attached to the plate + nullable: true items: type: string plateDbIds: type: array description: The ID which uniquely identifies a plate of samples + nullable: true items: type: string plateNames: type: array description: The human readable name of a plate of samples + nullable: true items: type: string programDbIds: @@ -6496,16 +6622,19 @@ components: sampleDbIds: type: array description: The ID which uniquely identifies a sample + nullable: true items: type: string sampleGroupDbIds: type: array description: The unique identifier for a group of related Samples + nullable: true items: type: string sampleNames: type: array description: The human readable name of the sample + nullable: true items: type: string studyDbIds: @@ -6576,6 +6705,7 @@ components: abbreviations: type: array description: A list of shortened human readable names for a set of Programs + nullable: true items: type: string commonCropNames: @@ -6592,16 +6722,19 @@ components: leadPersonDbIds: type: array description: The person DbIds of the program leader to search for + nullable: true items: type: string leadPersonNames: type: array description: The names of the program leader to search for + nullable: true items: type: string objectives: type: array description: A program objective to search for + nullable: true items: type: string programDbIds: @@ -6627,6 +6760,7 @@ components: description: "The type of program entity this object represents\n
'STANDARD'\ \ represents a standard, permanent breeding program\n
'PROJECT' represents\ \ a short term project, usually with a set time limit based on funding " + nullable: true items: type: string description: |- @@ -6681,12 +6815,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string isDerived: @@ -6770,12 +6906,14 @@ components: type: array description: "If set, return the reference sets for which the `accession`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string assemblyPUIs: type: array description: "If set, return the reference sets for which the `assemblyId`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string commonCropNames: @@ -6792,18 +6930,21 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string md5checksums: type: array description: "If set, return the reference sets for which the `md5checksum`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string programDbIds: @@ -6827,6 +6968,7 @@ components: referenceSetDbIds: type: array description: The `ReferenceSets` to search. + nullable: true items: type: string studyDbIds: @@ -6866,27 +7008,32 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: type: array description: The ID which uniquely identifies an `ObservationUnit` + nullable: true items: type: string plateDbIds: type: array description: The ID which uniquely identifies a `Plate` of `Samples` + nullable: true items: type: string plateNames: type: array description: The human readable name of a `Plate` of `Samples` + nullable: true items: type: string programDbIds: @@ -6910,16 +7057,19 @@ components: sampleDbIds: type: array description: The ID which uniquely identifies a `Sample` + nullable: true items: type: string sampleGroupDbIds: type: array description: The unique identifier for a group of related `Samples` + nullable: true items: type: string sampleNames: type: array description: The human readable name of the `Sample` + nullable: true items: type: string studyDbIds: @@ -7144,12 +7294,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programDbIds: @@ -7313,6 +7465,7 @@ components: active: type: boolean description: A flag to indicate if a Study is currently active and ongoing + nullable: true example: true commonCropNames: type: array @@ -7328,12 +7481,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -7383,11 +7538,13 @@ components: seasonDbIds: type: array description: The ID which uniquely identifies a season + nullable: true items: type: string sortBy: type: string description: Name of the field to sort by. + nullable: true enum: - studyDbId - trialDbId @@ -7401,6 +7558,7 @@ components: sortOrder: type: string description: Sort order direction. Ascending/Descending. + nullable: true enum: - asc - ASC @@ -7409,6 +7567,7 @@ components: studyCodes: type: array description: A short human readable code for a study + nullable: true items: type: string studyDbIds: @@ -7425,11 +7584,13 @@ components: type: array description: "Permanent unique identifier associated with study data. For\ \ example, a URI or DOI" + nullable: true items: type: string studyTypes: type: array description: "The type of study being performed. ex. \"Yield Trial\", etc" + nullable: true items: type: string trialDbIds: diff --git a/Specification/Generated/BrAPI-Phenotyping.yaml b/Specification/Generated/BrAPI-Phenotyping.yaml index 73af2c46..857506ff 100644 --- a/Specification/Generated/BrAPI-Phenotyping.yaml +++ b/Specification/Generated/BrAPI-Phenotyping.yaml @@ -1861,6 +1861,7 @@ components: description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ \ in the response." + nullable: true items: type: string dataMatrixNames: @@ -1868,32 +1869,38 @@ components: description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ \ Depth' etc). This list controls which data matrices are returned in\ \ the response." + nullable: true items: type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) + nullable: true example: true germplasmDbIds: type: array description: A list of IDs which uniquely identify `Germplasm` within the given database server + nullable: true items: type: string germplasmNames: type: array description: A list of human readable `Germplasm` names + nullable: true items: type: string germplasmPUIs: type: array description: A list of permanent unique identifiers associated with `Germplasm` + nullable: true items: type: string pagination: type: array description: Pagination for the matrix + nullable: true items: type: object properties: @@ -1920,6 +1927,7 @@ components: description: "The postion range to search\n
\nUses the format \":-\"\ \ where is the chromosome name, is \nthe starting position\ \ of the range, and is the ending position of the range" + nullable: true items: type: string preview: @@ -1936,30 +1944,36 @@ components: type: array description: A list of IDs which uniquely identify `Samples` within the given database server + nullable: true items: type: string sepPhased: type: string description: The string used as a separator for phased allele calls. + nullable: true example: '|' sepUnphased: type: string description: The string used as a separator for unphased allele calls. + nullable: true example: / unknownString: type: string description: The string used as a representation for missing data. + nullable: true example: "." variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the given database server + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string Attribute: @@ -2084,35 +2098,42 @@ components: type: array description: A list of IDs which uniquely identify `CallSets` within the given database server + nullable: true items: type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) + nullable: true example: true sepPhased: type: string description: The string used as a separator for phased allele calls. + nullable: true example: '|' sepUnphased: type: string description: The string used as a separator for unphased allele calls. + nullable: true example: / unknownString: type: string description: The string used as a representation for missing data. + nullable: true example: "." variantDbIds: type: array description: A list of IDs which uniquely identify `Variant` within the given database server + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string CallSetRequest: @@ -2122,11 +2143,13 @@ components: type: array description: A list of IDs which uniquely identify `CallSets` within the given database server + nullable: true items: type: string callSetNames: type: array description: A list of human readable names associated with `CallSets` + nullable: true items: type: string commonCropNames: @@ -2143,12 +2166,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programDbIds: @@ -2173,11 +2198,13 @@ components: type: array description: A list of IDs which uniquely identify `Samples` within the given database server + nullable: true items: type: string sampleNames: type: array description: A list of human readable names associated with `Samples` + nullable: true items: type: string studyDbIds: @@ -2204,6 +2231,7 @@ components: type: array description: A list of IDs which uniquely identify `VariantSets` within the given database server + nullable: true items: type: string CommonCropNamesParameters: @@ -2770,23 +2798,27 @@ components: attributeCategories: type: array description: General category for the attribute. very similar to Trait class. + nullable: true items: type: string attributeDbIds: type: array description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string attributeNames: type: array description: List of human readable Germplasm Attribute names to search for + nullable: true items: type: string attributePUIs: type: array description: "The Permanent Unique Identifier of an Attribute, usually in\ \ the form of a URI" + nullable: true items: type: string commonCropNames: @@ -2808,12 +2840,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string methodDbIds: @@ -2959,17 +2993,20 @@ components: attributeDbIds: type: array description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string attributeNames: type: array description: List of human readable Germplasm Attribute names to search for + nullable: true items: type: string attributeValueDbIds: type: array description: List of Germplasm Attribute Value IDs to search for + nullable: true items: type: string commonCropNames: @@ -2986,27 +3023,32 @@ components: dataTypes: type: array description: List of scale data types to filter search results + nullable: true items: $ref: "#/components/schemas/TraitDataType" germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string methodDbIds: type: array description: List of methods to filter search results + nullable: true items: type: string ontologyDbIds: type: array description: List of ontology IDs to search for + nullable: true items: type: string programDbIds: @@ -3030,16 +3072,19 @@ components: scaleDbIds: type: array description: List of scales to filter search results + nullable: true items: type: string traitClasses: type: array description: List of trait classes to filter search results + nullable: true items: type: string traitDbIds: type: array description: List of trait unique ID to filter search results + nullable: true items: type: string GermplasmParameters: @@ -3048,12 +3093,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string GermplasmRequest: @@ -3065,18 +3112,21 @@ components: A collection of unique identifiers for materials or germplasm within a genebank MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true items: type: string binomialNames: type: array description: List of the full binomial name (scientific name) to identify a germplasm + nullable: true items: type: string collections: type: array description: A specific panel/collection/population name this germplasm belongs to. + nullable: true items: type: string commonCropNames: @@ -3094,27 +3144,32 @@ components: type: array description: A familyCode representing the family this germplasm belongs to. + nullable: true items: type: string genus: type: array description: List of Genus names to identify germplasm + nullable: true items: type: string germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string germplasmPUIs: type: array description: List of Permanent Unique Identifiers to identify germplasm + nullable: true items: type: string instituteCodes: @@ -3127,16 +3182,19 @@ components: \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ \ rules (v)\"." + nullable: true items: type: string parentDbIds: type: array description: Search for Germplasm with these parents + nullable: true items: type: string progenyDbIds: type: array description: Search for Germplasm with these children + nullable: true items: type: string programDbIds: @@ -3160,6 +3218,7 @@ components: species: type: array description: List of Species names to identify germplasm + nullable: true items: type: string studyDbIds: @@ -3175,6 +3234,7 @@ components: synonyms: type: array description: List of alternative names or IDs used to reference this germplasm + nullable: true items: type: string trialDbIds: @@ -3524,48 +3584,57 @@ components: description: Define the end for an interval of time and only include Lists that are created within this interval. format: date-time + nullable: true dateCreatedRangeStart: type: string description: Define the beginning for an interval of time and only include Lists that are created within this interval. format: date-time + nullable: true dateModifiedRangeEnd: type: string description: Define the end for an interval of time and only include Lists that are modified within this interval. format: date-time + nullable: true dateModifiedRangeStart: type: string description: Define the beginning for an interval of time and only include Lists that are modified within this interval. format: date-time + nullable: true listDbIds: type: array description: An array of primary database identifiers to identify a set of Lists + nullable: true items: type: string listNames: type: array description: An array of human readable names to identify a set of Lists + nullable: true items: type: string listOwnerNames: type: array description: An array of names for the people or entities who are responsible for a set of Lists + nullable: true items: type: string listOwnerPersonDbIds: type: array description: An array of primary database identifiers to identify people or entities who are responsible for a set of Lists + nullable: true items: type: string listSources: type: array description: "An array of terms identifying lists from different sources\ \ (ie 'USER', 'SYSTEM', etc)" + nullable: true items: type: string listType: @@ -3707,28 +3776,33 @@ components: linkageGroupNames: type: array description: A list of Uniquely Identifiable linkage group names + nullable: true items: type: string mapDbIds: type: array description: A list of IDs which uniquely identify `GenomeMaps` within the given database server + nullable: true items: type: string maxPosition: type: integer description: The maximum position of markers in a given map format: int32 + nullable: true example: 4000 minPosition: type: integer description: The minimum position of markers in a given map format: int32 + nullable: true example: 250 variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the given database server + nullable: true items: type: string Method: @@ -3943,12 +4017,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -4127,6 +4203,7 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -4143,6 +4220,7 @@ components: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: @@ -4575,12 +4653,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string includeObservations: @@ -4758,6 +4838,7 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -4774,6 +4855,7 @@ components: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitNames: @@ -5529,12 +5611,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string germplasmPUIs: @@ -5651,36 +5735,43 @@ components: emailAddresses: type: array description: email address for this person + nullable: true items: type: string firstNames: type: array description: Persons first name + nullable: true items: type: string lastNames: type: array description: Persons last name + nullable: true items: type: string mailingAddresses: type: array description: physical address of this person + nullable: true items: type: string middleNames: type: array description: Persons middle name + nullable: true items: type: string personDbIds: type: array description: Unique ID for this person + nullable: true items: type: string phoneNumbers: type: array description: phone number of this person + nullable: true items: type: string programDbIds: @@ -5705,6 +5796,7 @@ components: type: array description: A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system. + nullable: true items: type: string PlannedCrossRequest: @@ -5787,32 +5879,38 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: type: array description: The ID which uniquely identifies an observation unit + nullable: true items: type: string plateBarcodes: type: array description: A unique identifier physically attached to the plate + nullable: true items: type: string plateDbIds: type: array description: The ID which uniquely identifies a plate of samples + nullable: true items: type: string plateNames: type: array description: The human readable name of a plate of samples + nullable: true items: type: string programDbIds: @@ -5836,16 +5934,19 @@ components: sampleDbIds: type: array description: The ID which uniquely identifies a sample + nullable: true items: type: string sampleGroupDbIds: type: array description: The unique identifier for a group of related Samples + nullable: true items: type: string sampleNames: type: array description: The human readable name of the sample + nullable: true items: type: string studyDbIds: @@ -5916,6 +6017,7 @@ components: abbreviations: type: array description: A list of shortened human readable names for a set of Programs + nullable: true items: type: string commonCropNames: @@ -5932,16 +6034,19 @@ components: leadPersonDbIds: type: array description: The person DbIds of the program leader to search for + nullable: true items: type: string leadPersonNames: type: array description: The names of the program leader to search for + nullable: true items: type: string objectives: type: array description: A program objective to search for + nullable: true items: type: string programDbIds: @@ -5967,6 +6072,7 @@ components: description: "The type of program entity this object represents\n
'STANDARD'\ \ represents a standard, permanent breeding program\n
'PROJECT' represents\ \ a short term project, usually with a set time limit based on funding " + nullable: true items: type: string description: |- @@ -6021,12 +6127,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string isDerived: @@ -6110,12 +6218,14 @@ components: type: array description: "If set, return the reference sets for which the `accession`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string assemblyPUIs: type: array description: "If set, return the reference sets for which the `assemblyId`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string commonCropNames: @@ -6132,18 +6242,21 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string md5checksums: type: array description: "If set, return the reference sets for which the `md5checksum`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string programDbIds: @@ -6167,6 +6280,7 @@ components: referenceSetDbIds: type: array description: The `ReferenceSets` to search. + nullable: true items: type: string studyDbIds: @@ -6206,27 +6320,32 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string observationUnitDbIds: type: array description: The ID which uniquely identifies an `ObservationUnit` + nullable: true items: type: string plateDbIds: type: array description: The ID which uniquely identifies a `Plate` of `Samples` + nullable: true items: type: string plateNames: type: array description: The human readable name of a `Plate` of `Samples` + nullable: true items: type: string programDbIds: @@ -6250,16 +6369,19 @@ components: sampleDbIds: type: array description: The ID which uniquely identifies a `Sample` + nullable: true items: type: string sampleGroupDbIds: type: array description: The unique identifier for a group of related `Samples` + nullable: true items: type: string sampleNames: type: array description: The human readable name of the `Sample` + nullable: true items: type: string studyDbIds: @@ -6467,12 +6589,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string programDbIds: @@ -6538,6 +6662,7 @@ components: active: type: boolean description: A flag to indicate if a Study is currently active and ongoing + nullable: true example: true commonCropNames: type: array @@ -6553,12 +6678,14 @@ components: germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string germplasmNames: type: array description: List of human readable names to identify germplasm to search for + nullable: true items: type: string locationDbIds: @@ -6608,11 +6735,13 @@ components: seasonDbIds: type: array description: The ID which uniquely identifies a season + nullable: true items: type: string sortBy: type: string description: Name of the field to sort by. + nullable: true enum: - studyDbId - trialDbId @@ -6626,6 +6755,7 @@ components: sortOrder: type: string description: Sort order direction. Ascending/Descending. + nullable: true enum: - asc - ASC @@ -6634,6 +6764,7 @@ components: studyCodes: type: array description: A short human readable code for a study + nullable: true items: type: string studyDbIds: @@ -6650,11 +6781,13 @@ components: type: array description: "Permanent unique identifier associated with study data. For\ \ example, a URI or DOI" + nullable: true items: type: string studyTypes: type: array description: "The type of study being performed. ex. \"Yield Trial\", etc" + nullable: true items: type: string trialDbIds: diff --git a/Specification/Generated/brapi_generated.json b/Specification/Generated/brapi_generated.json index acde9b4b..1b763f4e 100644 --- a/Specification/Generated/brapi_generated.json +++ b/Specification/Generated/brapi_generated.json @@ -10167,6 +10167,7 @@ "dataMatrixAbbreviations" : { "type" : "array", "description" : "`dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "nullable" : true, "items" : { "type" : "string" } @@ -10174,6 +10175,7 @@ "dataMatrixNames" : { "type" : "array", "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "nullable" : true, "items" : { "type" : "string" } @@ -10181,11 +10183,13 @@ "expandHomozygotes" : { "type" : "boolean", "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "nullable" : true, "example" : true }, "germplasmDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Germplasm` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10193,6 +10197,7 @@ "germplasmNames" : { "type" : "array", "description" : "A list of human readable `Germplasm` names", + "nullable" : true, "items" : { "type" : "string" } @@ -10200,6 +10205,7 @@ "germplasmPUIs" : { "type" : "array", "description" : "A list of permanent unique identifiers associated with `Germplasm`", + "nullable" : true, "items" : { "type" : "string" } @@ -10207,6 +10213,7 @@ "pagination" : { "type" : "array", "description" : "Pagination for the matrix", + "nullable" : true, "items" : { "type" : "object", "properties" : { @@ -10237,6 +10244,7 @@ "positionRanges" : { "type" : "array", "description" : "The postion range to search\n
\nUses the format \":-\" where is the chromosome name, is \nthe starting position of the range, and is the ending position of the range", + "nullable" : true, "items" : { "type" : "string" } @@ -10249,6 +10257,7 @@ "sampleDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10256,21 +10265,25 @@ "sepPhased" : { "type" : "string", "description" : "The string used as a separator for phased allele calls.", + "nullable" : true, "example" : "|" }, "sepUnphased" : { "type" : "string", "description" : "The string used as a separator for unphased allele calls.", + "nullable" : true, "example" : "/" }, "unknownString" : { "type" : "string", "description" : "The string used as a representation for missing data.", + "nullable" : true, "example" : "." }, "variantDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10278,6 +10291,7 @@ "variantSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10290,6 +10304,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Germplasm` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10302,6 +10317,7 @@ "germplasmNames" : { "type" : "array", "description" : "A list of human readable `Germplasm` names", + "nullable" : true, "items" : { "type" : "string" } @@ -10309,6 +10325,7 @@ "pagination" : { "type" : "array", "description" : "Pagination for the matrix", + "nullable" : true, "items" : { "type" : "object", "properties" : { @@ -10339,11 +10356,13 @@ "unknownString" : { "type" : "string", "description" : "The string used as a representation for missing data.", + "nullable" : true, "example" : "." }, "germplasmPUIs" : { "type" : "array", "description" : "A list of permanent unique identifiers associated with `Germplasm`", + "nullable" : true, "items" : { "type" : "string" } @@ -10351,6 +10370,7 @@ "positionRanges" : { "type" : "array", "description" : "The postion range to search\n
\nUses the format \":-\" where is the chromosome name, is \nthe starting position of the range, and is the ending position of the range", + "nullable" : true, "items" : { "type" : "string" } @@ -10358,6 +10378,7 @@ "sampleDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10365,6 +10386,7 @@ "variantSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10372,6 +10394,7 @@ "dataMatrixAbbreviations" : { "type" : "array", "description" : "`dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "nullable" : true, "items" : { "type" : "string" } @@ -10379,11 +10402,13 @@ "expandHomozygotes" : { "type" : "boolean", "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "nullable" : true, "example" : true }, "variantDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10398,6 +10423,7 @@ "dataMatrixNames" : { "type" : "array", "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "nullable" : true, "items" : { "type" : "string" } @@ -10405,11 +10431,13 @@ "sepPhased" : { "type" : "string", "description" : "The string used as a separator for phased allele calls.", + "nullable" : true, "example" : "|" }, "sepUnphased" : { "type" : "string", "description" : "The string used as a separator for unphased allele calls.", + "nullable" : true, "example" : "/" } }, @@ -10781,6 +10809,7 @@ "callSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10788,26 +10817,31 @@ "expandHomozygotes" : { "type" : "boolean", "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "nullable" : true, "example" : true }, "sepPhased" : { "type" : "string", "description" : "The string used as a separator for phased allele calls.", + "nullable" : true, "example" : "|" }, "sepUnphased" : { "type" : "string", "description" : "The string used as a separator for unphased allele calls.", + "nullable" : true, "example" : "/" }, "unknownString" : { "type" : "string", "description" : "The string used as a representation for missing data.", + "nullable" : true, "example" : "." }, "variantDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Variant` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10815,6 +10849,7 @@ "variantSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10827,6 +10862,7 @@ "variantSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10834,16 +10870,19 @@ "unknownString" : { "type" : "string", "description" : "The string used as a representation for missing data.", + "nullable" : true, "example" : "." }, "expandHomozygotes" : { "type" : "boolean", "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "nullable" : true, "example" : true }, "variantDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Variant` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10851,6 +10890,7 @@ "callSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10858,11 +10898,13 @@ "sepPhased" : { "type" : "string", "description" : "The string used as a separator for phased allele calls.", + "nullable" : true, "example" : "|" }, "sepUnphased" : { "type" : "string", "description" : "The string used as a separator for unphased allele calls.", + "nullable" : true, "example" : "/" } }, @@ -10933,6 +10975,7 @@ "callSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10940,6 +10983,7 @@ "callSetNames" : { "type" : "array", "description" : "A list of human readable names associated with `CallSets`", + "nullable" : true, "items" : { "type" : "string" } @@ -10954,6 +10998,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -10961,6 +11006,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -10982,6 +11028,7 @@ "sampleDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -10989,6 +11036,7 @@ "sampleNames" : { "type" : "array", "description" : "A list of human readable names associated with `Samples`", + "nullable" : true, "items" : { "type" : "string" } @@ -11024,6 +11072,7 @@ "variantSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -11036,6 +11085,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -11043,6 +11093,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -11078,6 +11129,7 @@ "sampleDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -11099,6 +11151,7 @@ "variantSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -11106,6 +11159,7 @@ "callSetNames" : { "type" : "array", "description" : "A list of human readable names associated with `CallSets`", + "nullable" : true, "items" : { "type" : "string" } @@ -11120,6 +11174,7 @@ "sampleNames" : { "type" : "array", "description" : "A list of human readable names associated with `Samples`", + "nullable" : true, "items" : { "type" : "string" } @@ -11127,6 +11182,7 @@ "callSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -12759,6 +12815,7 @@ "attributeCategories" : { "type" : "array", "description" : "General category for the attribute. very similar to Trait class.", + "nullable" : true, "items" : { "type" : "string" } @@ -12766,6 +12823,7 @@ "attributeDbIds" : { "type" : "array", "description" : "List of Germplasm Attribute IDs to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -12773,6 +12831,7 @@ "attributeNames" : { "type" : "array", "description" : "List of human readable Germplasm Attribute names to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -12780,6 +12839,7 @@ "attributePUIs" : { "type" : "array", "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", + "nullable" : true, "items" : { "type" : "string" } @@ -12801,6 +12861,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -12808,6 +12869,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -12974,6 +13036,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -12995,6 +13058,7 @@ "attributeDbIds" : { "type" : "array", "description" : "List of Germplasm Attribute IDs to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13023,6 +13087,7 @@ "attributeNames" : { "type" : "array", "description" : "List of human readable Germplasm Attribute names to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13065,6 +13130,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13100,6 +13166,7 @@ "attributeCategories" : { "type" : "array", "description" : "General category for the attribute. very similar to Trait class.", + "nullable" : true, "items" : { "type" : "string" } @@ -13156,6 +13223,7 @@ "attributePUIs" : { "type" : "array", "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", + "nullable" : true, "items" : { "type" : "string" } @@ -13256,6 +13324,7 @@ "attributeDbIds" : { "type" : "array", "description" : "List of Germplasm Attribute IDs to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13263,6 +13332,7 @@ "attributeNames" : { "type" : "array", "description" : "List of human readable Germplasm Attribute names to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13270,6 +13340,7 @@ "attributeValueDbIds" : { "type" : "array", "description" : "List of Germplasm Attribute Value IDs to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13284,6 +13355,7 @@ "dataTypes" : { "type" : "array", "description" : "List of scale data types to filter search results", + "nullable" : true, "items" : { "$ref" : "#/components/schemas/TraitDataType" } @@ -13291,6 +13363,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13298,6 +13371,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13305,6 +13379,7 @@ "methodDbIds" : { "type" : "array", "description" : "List of methods to filter search results", + "nullable" : true, "items" : { "type" : "string" } @@ -13312,6 +13387,7 @@ "ontologyDbIds" : { "type" : "array", "description" : "List of ontology IDs to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13333,6 +13409,7 @@ "scaleDbIds" : { "type" : "array", "description" : "List of scales to filter search results", + "nullable" : true, "items" : { "type" : "string" } @@ -13340,6 +13417,7 @@ "traitClasses" : { "type" : "array", "description" : "List of trait classes to filter search results", + "nullable" : true, "items" : { "type" : "string" } @@ -13347,6 +13425,7 @@ "traitDbIds" : { "type" : "array", "description" : "List of trait unique ID to filter search results", + "nullable" : true, "items" : { "type" : "string" } @@ -13359,6 +13438,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13366,6 +13446,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13373,6 +13454,7 @@ "methodDbIds" : { "type" : "array", "description" : "List of methods to filter search results", + "nullable" : true, "items" : { "type" : "string" } @@ -13380,6 +13462,7 @@ "traitClasses" : { "type" : "array", "description" : "List of trait classes to filter search results", + "nullable" : true, "items" : { "type" : "string" } @@ -13408,6 +13491,7 @@ "attributeValueDbIds" : { "type" : "array", "description" : "List of Germplasm Attribute Value IDs to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13415,6 +13499,7 @@ "attributeDbIds" : { "type" : "array", "description" : "List of Germplasm Attribute IDs to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13422,6 +13507,7 @@ "ontologyDbIds" : { "type" : "array", "description" : "List of ontology IDs to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13429,6 +13515,7 @@ "dataTypes" : { "type" : "array", "description" : "List of scale data types to filter search results", + "nullable" : true, "items" : { "$ref" : "#/components/schemas/TraitDataType" } @@ -13436,6 +13523,7 @@ "attributeNames" : { "type" : "array", "description" : "List of human readable Germplasm Attribute names to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -13443,6 +13531,7 @@ "traitDbIds" : { "type" : "array", "description" : "List of trait unique ID to filter search results", + "nullable" : true, "items" : { "type" : "string" } @@ -13450,6 +13539,7 @@ "scaleDbIds" : { "type" : "array", "description" : "List of scales to filter search results", + "nullable" : true, "items" : { "type" : "string" } @@ -14054,6 +14144,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -14061,6 +14152,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -14100,6 +14192,7 @@ "accessionNumbers" : { "type" : "array", "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "nullable" : true, "items" : { "type" : "string" } @@ -14107,6 +14200,7 @@ "binomialNames" : { "type" : "array", "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -14114,6 +14208,7 @@ "collections" : { "type" : "array", "description" : "A specific panel/collection/population name this germplasm belongs to.", + "nullable" : true, "items" : { "type" : "string" } @@ -14128,6 +14223,7 @@ "familyCodes" : { "type" : "array", "description" : "A familyCode representing the family this germplasm belongs to.", + "nullable" : true, "items" : { "type" : "string" } @@ -14135,6 +14231,7 @@ "genus" : { "type" : "array", "description" : "List of Genus names to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -14142,6 +14239,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -14149,6 +14247,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -14156,6 +14255,7 @@ "germplasmPUIs" : { "type" : "array", "description" : "List of Permanent Unique Identifiers to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -14163,6 +14263,7 @@ "instituteCodes" : { "type" : "array", "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "nullable" : true, "items" : { "type" : "string" } @@ -14170,6 +14271,7 @@ "parentDbIds" : { "type" : "array", "description" : "Search for Germplasm with these parents", + "nullable" : true, "items" : { "type" : "string" } @@ -14177,6 +14279,7 @@ "progenyDbIds" : { "type" : "array", "description" : "Search for Germplasm with these children", + "nullable" : true, "items" : { "type" : "string" } @@ -14198,6 +14301,7 @@ "species" : { "type" : "array", "description" : "List of Species names to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -14219,6 +14323,7 @@ "synonyms" : { "type" : "array", "description" : "List of alternative names or IDs used to reference this germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -14245,6 +14350,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -14252,6 +14358,7 @@ "accessionNumbers" : { "type" : "array", "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "nullable" : true, "items" : { "type" : "string" } @@ -14259,6 +14366,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -14266,6 +14374,7 @@ "synonyms" : { "type" : "array", "description" : "List of alternative names or IDs used to reference this germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -14301,6 +14410,7 @@ "germplasmPUIs" : { "type" : "array", "description" : "List of Permanent Unique Identifiers to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -14308,6 +14418,7 @@ "parentDbIds" : { "type" : "array", "description" : "Search for Germplasm with these parents", + "nullable" : true, "items" : { "type" : "string" } @@ -14329,6 +14440,7 @@ "familyCodes" : { "type" : "array", "description" : "A familyCode representing the family this germplasm belongs to.", + "nullable" : true, "items" : { "type" : "string" } @@ -14343,6 +14455,7 @@ "collections" : { "type" : "array", "description" : "A specific panel/collection/population name this germplasm belongs to.", + "nullable" : true, "items" : { "type" : "string" } @@ -14350,6 +14463,7 @@ "genus" : { "type" : "array", "description" : "List of Genus names to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -14357,6 +14471,7 @@ "species" : { "type" : "array", "description" : "List of Species names to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -14364,6 +14479,7 @@ "binomialNames" : { "type" : "array", "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -14371,6 +14487,7 @@ "instituteCodes" : { "type" : "array", "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "nullable" : true, "items" : { "type" : "string" } @@ -14378,6 +14495,7 @@ "progenyDbIds" : { "type" : "array", "description" : "Search for Germplasm with these children", + "nullable" : true, "items" : { "type" : "string" } @@ -14957,26 +15075,31 @@ "dateCreatedRangeEnd" : { "type" : "string", "description" : "Define the end for an interval of time and only include Lists that are created within this interval.", - "format" : "date-time" + "format" : "date-time", + "nullable" : true }, "dateCreatedRangeStart" : { "type" : "string", "description" : "Define the beginning for an interval of time and only include Lists that are created within this interval.", - "format" : "date-time" + "format" : "date-time", + "nullable" : true }, "dateModifiedRangeEnd" : { "type" : "string", "description" : "Define the end for an interval of time and only include Lists that are modified within this interval.", - "format" : "date-time" + "format" : "date-time", + "nullable" : true }, "dateModifiedRangeStart" : { "type" : "string", "description" : "Define the beginning for an interval of time and only include Lists that are modified within this interval.", - "format" : "date-time" + "format" : "date-time", + "nullable" : true }, "listDbIds" : { "type" : "array", "description" : "An array of primary database identifiers to identify a set of Lists", + "nullable" : true, "items" : { "type" : "string" } @@ -14984,6 +15107,7 @@ "listNames" : { "type" : "array", "description" : "An array of human readable names to identify a set of Lists", + "nullable" : true, "items" : { "type" : "string" } @@ -14991,6 +15115,7 @@ "listOwnerNames" : { "type" : "array", "description" : "An array of names for the people or entities who are responsible for a set of Lists", + "nullable" : true, "items" : { "type" : "string" } @@ -14998,6 +15123,7 @@ "listOwnerPersonDbIds" : { "type" : "array", "description" : "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", + "nullable" : true, "items" : { "type" : "string" } @@ -15005,6 +15131,7 @@ "listSources" : { "type" : "array", "description" : "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", + "nullable" : true, "items" : { "type" : "string" } @@ -15034,7 +15161,8 @@ "dateCreatedRangeStart" : { "type" : "string", "description" : "Define the beginning for an interval of time and only include Lists that are created within this interval.", - "format" : "date-time" + "format" : "date-time", + "nullable" : true }, "programNames" : { "type" : "array", @@ -15060,11 +15188,13 @@ "dateModifiedRangeEnd" : { "type" : "string", "description" : "Define the end for an interval of time and only include Lists that are modified within this interval.", - "format" : "date-time" + "format" : "date-time", + "nullable" : true }, "listSources" : { "type" : "array", "description" : "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", + "nullable" : true, "items" : { "type" : "string" } @@ -15075,11 +15205,13 @@ "dateCreatedRangeEnd" : { "type" : "string", "description" : "Define the end for an interval of time and only include Lists that are created within this interval.", - "format" : "date-time" + "format" : "date-time", + "nullable" : true }, "listDbIds" : { "type" : "array", "description" : "An array of primary database identifiers to identify a set of Lists", + "nullable" : true, "items" : { "type" : "string" } @@ -15087,6 +15219,7 @@ "listNames" : { "type" : "array", "description" : "An array of human readable names to identify a set of Lists", + "nullable" : true, "items" : { "type" : "string" } @@ -15094,6 +15227,7 @@ "listOwnerPersonDbIds" : { "type" : "array", "description" : "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", + "nullable" : true, "items" : { "type" : "string" } @@ -15101,11 +15235,13 @@ "dateModifiedRangeStart" : { "type" : "string", "description" : "Define the beginning for an interval of time and only include Lists that are modified within this interval.", - "format" : "date-time" + "format" : "date-time", + "nullable" : true }, "listOwnerNames" : { "type" : "array", "description" : "An array of names for the people or entities who are responsible for a set of Lists", + "nullable" : true, "items" : { "type" : "string" } @@ -15533,6 +15669,7 @@ "linkageGroupNames" : { "type" : "array", "description" : "A list of Uniquely Identifiable linkage group names", + "nullable" : true, "items" : { "type" : "string" } @@ -15540,6 +15677,7 @@ "mapDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `GenomeMaps` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -15548,17 +15686,20 @@ "type" : "integer", "description" : "The maximum position of markers in a given map", "format" : "int32", + "nullable" : true, "example" : 4000 }, "minPosition" : { "type" : "integer", "description" : "The minimum position of markers in a given map", "format" : "int32", + "nullable" : true, "example" : 250 }, "variantDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -15571,6 +15712,7 @@ "linkageGroupNames" : { "type" : "array", "description" : "A list of Uniquely Identifiable linkage group names", + "nullable" : true, "items" : { "type" : "string" } @@ -15578,6 +15720,7 @@ "variantDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -15585,6 +15728,7 @@ "mapDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `GenomeMaps` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -15593,12 +15737,14 @@ "type" : "integer", "description" : "The maximum position of markers in a given map", "format" : "int32", + "nullable" : true, "example" : 4000 }, "minPosition" : { "type" : "integer", "description" : "The minimum position of markers in a given map", "format" : "int32", + "nullable" : true, "example" : 250 } }, @@ -15883,6 +16029,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -15890,6 +16037,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -16073,6 +16221,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -16094,6 +16243,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -16500,6 +16650,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -16507,6 +16658,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -16685,6 +16837,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -16706,6 +16859,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -17723,6 +17877,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -17730,6 +17885,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -17844,6 +18000,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -17858,6 +18015,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18092,6 +18250,7 @@ "emailAddresses" : { "type" : "array", "description" : "email address for this person", + "nullable" : true, "items" : { "type" : "string" } @@ -18099,6 +18258,7 @@ "firstNames" : { "type" : "array", "description" : "Persons first name", + "nullable" : true, "items" : { "type" : "string" } @@ -18106,6 +18266,7 @@ "lastNames" : { "type" : "array", "description" : "Persons last name", + "nullable" : true, "items" : { "type" : "string" } @@ -18113,6 +18274,7 @@ "mailingAddresses" : { "type" : "array", "description" : "physical address of this person", + "nullable" : true, "items" : { "type" : "string" } @@ -18120,6 +18282,7 @@ "middleNames" : { "type" : "array", "description" : "Persons middle name", + "nullable" : true, "items" : { "type" : "string" } @@ -18127,6 +18290,7 @@ "personDbIds" : { "type" : "array", "description" : "Unique ID for this person", + "nullable" : true, "items" : { "type" : "string" } @@ -18134,6 +18298,7 @@ "phoneNumbers" : { "type" : "array", "description" : "phone number of this person", + "nullable" : true, "items" : { "type" : "string" } @@ -18155,6 +18320,7 @@ "userIDs" : { "type" : "array", "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", + "nullable" : true, "items" : { "type" : "string" } @@ -18167,6 +18333,7 @@ "middleNames" : { "type" : "array", "description" : "Persons middle name", + "nullable" : true, "items" : { "type" : "string" } @@ -18174,6 +18341,7 @@ "emailAddresses" : { "type" : "array", "description" : "email address for this person", + "nullable" : true, "items" : { "type" : "string" } @@ -18181,6 +18349,7 @@ "userIDs" : { "type" : "array", "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", + "nullable" : true, "items" : { "type" : "string" } @@ -18188,6 +18357,7 @@ "personDbIds" : { "type" : "array", "description" : "Unique ID for this person", + "nullable" : true, "items" : { "type" : "string" } @@ -18216,6 +18386,7 @@ "firstNames" : { "type" : "array", "description" : "Persons first name", + "nullable" : true, "items" : { "type" : "string" } @@ -18223,6 +18394,7 @@ "lastNames" : { "type" : "array", "description" : "Persons last name", + "nullable" : true, "items" : { "type" : "string" } @@ -18230,6 +18402,7 @@ "mailingAddresses" : { "type" : "array", "description" : "physical address of this person", + "nullable" : true, "items" : { "type" : "string" } @@ -18237,6 +18410,7 @@ "phoneNumbers" : { "type" : "array", "description" : "phone number of this person", + "nullable" : true, "items" : { "type" : "string" } @@ -18484,6 +18658,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18491,6 +18666,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18498,6 +18674,7 @@ "observationUnitDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies an observation unit", + "nullable" : true, "items" : { "type" : "string" } @@ -18505,6 +18682,7 @@ "plateBarcodes" : { "type" : "array", "description" : "A unique identifier physically attached to the plate", + "nullable" : true, "items" : { "type" : "string" } @@ -18512,6 +18690,7 @@ "plateDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a plate of samples", + "nullable" : true, "items" : { "type" : "string" } @@ -18519,6 +18698,7 @@ "plateNames" : { "type" : "array", "description" : "The human readable name of a plate of samples", + "nullable" : true, "items" : { "type" : "string" } @@ -18540,6 +18720,7 @@ "sampleDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a sample", + "nullable" : true, "items" : { "type" : "string" } @@ -18547,6 +18728,7 @@ "sampleGroupDbIds" : { "type" : "array", "description" : "The unique identifier for a group of related Samples", + "nullable" : true, "items" : { "type" : "string" } @@ -18554,6 +18736,7 @@ "sampleNames" : { "type" : "array", "description" : "The human readable name of the sample", + "nullable" : true, "items" : { "type" : "string" } @@ -18594,6 +18777,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18601,6 +18785,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18608,6 +18793,7 @@ "observationUnitDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies an observation unit", + "nullable" : true, "items" : { "type" : "string" } @@ -18615,6 +18801,7 @@ "plateBarcodes" : { "type" : "array", "description" : "A unique identifier physically attached to the plate", + "nullable" : true, "items" : { "type" : "string" } @@ -18622,6 +18809,7 @@ "plateNames" : { "type" : "array", "description" : "The human readable name of a plate of samples", + "nullable" : true, "items" : { "type" : "string" } @@ -18657,6 +18845,7 @@ "sampleDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a sample", + "nullable" : true, "items" : { "type" : "string" } @@ -18664,6 +18853,7 @@ "plateDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a plate of samples", + "nullable" : true, "items" : { "type" : "string" } @@ -18685,6 +18875,7 @@ "sampleGroupDbIds" : { "type" : "array", "description" : "The unique identifier for a group of related Samples", + "nullable" : true, "items" : { "type" : "string" } @@ -18699,6 +18890,7 @@ "sampleNames" : { "type" : "array", "description" : "The human readable name of the sample", + "nullable" : true, "items" : { "type" : "string" } @@ -18855,6 +19047,7 @@ "abbreviations" : { "type" : "array", "description" : "A list of shortened human readable names for a set of Programs", + "nullable" : true, "items" : { "type" : "string" } @@ -18869,6 +19062,7 @@ "leadPersonDbIds" : { "type" : "array", "description" : "The person DbIds of the program leader to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18876,6 +19070,7 @@ "leadPersonNames" : { "type" : "array", "description" : "The names of the program leader to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18883,6 +19078,7 @@ "objectives" : { "type" : "array", "description" : "A program objective to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18904,6 +19100,7 @@ "programTypes" : { "type" : "array", "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "nullable" : true, "items" : { "type" : "string", "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding.", @@ -18921,6 +19118,7 @@ "leadPersonNames" : { "type" : "array", "description" : "The names of the program leader to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18949,6 +19147,7 @@ "objectives" : { "type" : "array", "description" : "A program objective to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18956,6 +19155,7 @@ "leadPersonDbIds" : { "type" : "array", "description" : "The person DbIds of the program leader to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -18963,6 +19163,7 @@ "programTypes" : { "type" : "array", "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "nullable" : true, "items" : { "type" : "string", "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding.", @@ -18975,6 +19176,7 @@ "abbreviations" : { "type" : "array", "description" : "A list of shortened human readable names for a set of Programs", + "nullable" : true, "items" : { "type" : "string" } @@ -19172,6 +19374,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19179,6 +19382,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19271,6 +19475,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19283,6 +19488,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19500,6 +19706,7 @@ "accessions" : { "type" : "array", "description" : "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match).", + "nullable" : true, "items" : { "type" : "string" } @@ -19507,6 +19714,7 @@ "assemblyPUIs" : { "type" : "array", "description" : "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match).", + "nullable" : true, "items" : { "type" : "string" } @@ -19521,6 +19729,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19528,6 +19737,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19535,6 +19745,7 @@ "md5checksums" : { "type" : "array", "description" : "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match).", + "nullable" : true, "items" : { "type" : "string" } @@ -19556,6 +19767,7 @@ "referenceSetDbIds" : { "type" : "array", "description" : "The `ReferenceSets` to search.", + "nullable" : true, "items" : { "type" : "string" } @@ -19596,6 +19808,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19603,6 +19816,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19638,6 +19852,7 @@ "referenceSetDbIds" : { "type" : "array", "description" : "The `ReferenceSets` to search.", + "nullable" : true, "items" : { "type" : "string" } @@ -19659,6 +19874,7 @@ "md5checksums" : { "type" : "array", "description" : "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match).", + "nullable" : true, "items" : { "type" : "string" } @@ -19666,6 +19882,7 @@ "assemblyPUIs" : { "type" : "array", "description" : "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match).", + "nullable" : true, "items" : { "type" : "string" } @@ -19680,6 +19897,7 @@ "accessions" : { "type" : "array", "description" : "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match).", + "nullable" : true, "items" : { "type" : "string" } @@ -19855,6 +20073,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19862,6 +20081,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19869,6 +20089,7 @@ "observationUnitDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies an `ObservationUnit`", + "nullable" : true, "items" : { "type" : "string" } @@ -19876,6 +20097,7 @@ "plateDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a `Plate` of `Samples`", + "nullable" : true, "items" : { "type" : "string" } @@ -19883,6 +20105,7 @@ "plateNames" : { "type" : "array", "description" : "The human readable name of a `Plate` of `Samples`", + "nullable" : true, "items" : { "type" : "string" } @@ -19904,6 +20127,7 @@ "sampleDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a `Sample`", + "nullable" : true, "items" : { "type" : "string" } @@ -19911,6 +20135,7 @@ "sampleGroupDbIds" : { "type" : "array", "description" : "The unique identifier for a group of related `Samples`", + "nullable" : true, "items" : { "type" : "string" } @@ -19918,6 +20143,7 @@ "sampleNames" : { "type" : "array", "description" : "The human readable name of the `Sample`", + "nullable" : true, "items" : { "type" : "string" } @@ -19958,6 +20184,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19965,6 +20192,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -19972,6 +20200,7 @@ "observationUnitDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies an `ObservationUnit`", + "nullable" : true, "items" : { "type" : "string" } @@ -19979,6 +20208,7 @@ "plateNames" : { "type" : "array", "description" : "The human readable name of a `Plate` of `Samples`", + "nullable" : true, "items" : { "type" : "string" } @@ -20014,6 +20244,7 @@ "sampleDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a `Sample`", + "nullable" : true, "items" : { "type" : "string" } @@ -20021,6 +20252,7 @@ "plateDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a `Plate` of `Samples`", + "nullable" : true, "items" : { "type" : "string" } @@ -20042,6 +20274,7 @@ "sampleGroupDbIds" : { "type" : "array", "description" : "The unique identifier for a group of related `Samples`", + "nullable" : true, "items" : { "type" : "string" } @@ -20056,6 +20289,7 @@ "sampleNames" : { "type" : "array", "description" : "The human readable name of the `Sample`", + "nullable" : true, "items" : { "type" : "string" } @@ -20393,6 +20627,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -20400,6 +20635,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -20742,6 +20978,7 @@ "active" : { "type" : "boolean", "description" : "A flag to indicate if a Study is currently active and ongoing", + "nullable" : true, "example" : true }, "commonCropNames" : { @@ -20754,6 +20991,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -20761,6 +20999,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -20817,6 +21056,7 @@ "seasonDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a season", + "nullable" : true, "items" : { "type" : "string" } @@ -20824,6 +21064,7 @@ "sortBy" : { "type" : "string", "description" : "Name of the field to sort by.", + "nullable" : true, "enum" : [ "studyDbId", "trialDbId", @@ -20839,6 +21080,7 @@ "sortOrder" : { "type" : "string", "description" : "Sort order direction. Ascending/Descending.", + "nullable" : true, "enum" : [ "asc", "ASC", @@ -20849,6 +21091,7 @@ "studyCodes" : { "type" : "array", "description" : "A short human readable code for a study", + "nullable" : true, "items" : { "type" : "string" } @@ -20870,6 +21113,7 @@ "studyPUIs" : { "type" : "array", "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", + "nullable" : true, "items" : { "type" : "string" } @@ -20877,6 +21121,7 @@ "studyTypes" : { "type" : "array", "description" : "The type of study being performed. ex. \"Yield Trial\", etc", + "nullable" : true, "items" : { "type" : "string" } @@ -20903,6 +21148,7 @@ "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -20924,6 +21170,7 @@ "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -20938,6 +21185,7 @@ "seasonDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a season", + "nullable" : true, "items" : { "type" : "string" } @@ -20945,6 +21193,7 @@ "active" : { "type" : "boolean", "description" : "A flag to indicate if a Study is currently active and ongoing", + "nullable" : true, "example" : true }, "commonCropNames" : { @@ -20964,6 +21213,7 @@ "studyCodes" : { "type" : "array", "description" : "A short human readable code for a study", + "nullable" : true, "items" : { "type" : "string" } @@ -20971,6 +21221,7 @@ "studyPUIs" : { "type" : "array", "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", + "nullable" : true, "items" : { "type" : "string" } @@ -21027,6 +21278,7 @@ "sortOrder" : { "type" : "string", "description" : "Sort order direction. Ascending/Descending.", + "nullable" : true, "enum" : [ "asc", "ASC", @@ -21037,6 +21289,7 @@ "sortBy" : { "type" : "string", "description" : "Name of the field to sort by.", + "nullable" : true, "enum" : [ "studyDbId", "trialDbId", @@ -21052,6 +21305,7 @@ "studyTypes" : { "type" : "array", "description" : "The type of study being performed. ex. \"Yield Trial\", etc", + "nullable" : true, "items" : { "type" : "string" } diff --git a/Specification/Generated/brapi_generated.ttl b/Specification/Generated/brapi_generated.ttl index fc2b3bde..a9fec8d0 100644 --- a/Specification/Generated/brapi_generated.ttl +++ b/Specification/Generated/brapi_generated.ttl @@ -114,13 +114,6 @@ PREFIX xsd: rdfs:label "map"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "observationUnits"@en; - rdfs:domain ; - rdfs:label "observationUnits"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; @@ -128,13 +121,6 @@ PREFIX xsd: rdfs:label "analysis"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "associated seedLot"@en; @@ -142,6 +128,20 @@ PREFIX xsd: rdfs:label "seedLot"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "observationUnits"@en; + rdfs:domain ; + rdfs:label "observationUnits"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "The unique DbId of the breeding program this Seed Lot belongs to"@en; @@ -156,13 +156,6 @@ PREFIX xsd: rdfs:label "code"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)"@en; - rdfs:domain ; - rdfs:label "locationType"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source"@en; @@ -184,6 +177,13 @@ PREFIX xsd: rdfs:label "trialDescription"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)"@en; + rdfs:domain ; + rdfs:label "locationType"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -245,13 +245,6 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . - rdf:type owl:NamedIndividual , . @@ -281,6 +274,13 @@ PREFIX xsd: rdfs:comment "Links to various ontology documentation"@en; rdfs:label "DocumentationLink"@en . + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The name or identifier of the entity which took the `Sample` from the field"@en; @@ -295,6 +295,11 @@ PREFIX xsd: rdfs:label "method"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended."@en; + rdfs:label "Publication"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "A Permanent Unique Identifier for an observation unit\n\nMIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible."@en; @@ -302,11 +307,6 @@ PREFIX xsd: rdfs:label "observationUnitPUI"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended."@en; - rdfs:label "Publication"@en . - rdf:type owl:Class; rdfs:comment "The type of documentation, which can be OBO Foundry, an RDF term or a webpage."@en; @@ -317,6 +317,10 @@ PREFIX xsd: rdfs:comment "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"."@en; rdfs:label "Season"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The version of the update."@en; @@ -338,10 +342,6 @@ PREFIX xsd: rdfs:label "instituteCode"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; @@ -366,6 +366,10 @@ PREFIX xsd: rdfs:label "sampleName"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "germplasm"@en; @@ -397,6 +401,10 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "A human readable description of the analysis"@en; @@ -446,6 +454,11 @@ PREFIX xsd: rdfs:label "progeny"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; + rdfs:label "GermplasmOrigin"@en . + rdf:type owl:ObjectProperty; rdfs:comment "associated ontology reference"@en; @@ -453,11 +466,6 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; - rdfs:label "GermplasmOrigin"@en . - rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -543,13 +551,6 @@ PREFIX xsd: rdfs:label "crossAttributeValue"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "the unique identifier for a program"@en; @@ -557,6 +558,13 @@ PREFIX xsd: rdfs:label "program"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Common name for the crop"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; @@ -621,6 +629,10 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -674,6 +686,10 @@ PREFIX xsd: rdfs:label "callSet"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "The Ontology for this reference"@en; @@ -684,10 +700,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type , owl:NamedIndividual , . @@ -744,9 +756,6 @@ PREFIX xsd: rdfs:label "programType"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "Environment parameters associated with a study"@en; @@ -754,6 +763,9 @@ PREFIX xsd: rdfs:label "study"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The start position at which this variant occurs (0-based). This corresponds to the first base of the string \nof reference bases. Genomic positions are non-negative integers less than reference length. Variants spanning \nthe join of circular genomes are represented as two variants one on each side of the join (position 0)."@en; @@ -882,13 +894,6 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The reference bases for this variant. They start at the given start position."@en; - rdfs:domain ; - rdfs:label "referenceBases"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The human readable name for a crossing project"@en; @@ -896,6 +901,13 @@ PREFIX xsd: rdfs:label "crossingProjectName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The reference bases for this variant. They start at the given start position."@en; + rdfs:domain ; + rdfs:label "referenceBases"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The literal string \"Point\""@en; @@ -1123,13 +1135,6 @@ PREFIX xsd: rdfs:label "abbreviation"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name of the institute that maintains the material"@en; - rdfs:domain ; - rdfs:label "instituteName"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The description of where a List originated from"@en; @@ -1137,6 +1142,13 @@ PREFIX xsd: rdfs:label "listSource"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name of the institute that maintains the material"@en; + rdfs:domain ; + rdfs:label "instituteName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076"@en; @@ -1230,13 +1242,6 @@ PREFIX xsd: rdfs:label "collector"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name or id of the user who uploaded the observation to the database system"@en; - rdfs:domain ; - rdfs:label "uploadedBy"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The unique identifier for a `Reference`"@en; @@ -1258,6 +1263,13 @@ PREFIX xsd: rdfs:label "documentationURL"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name or id of the user who uploaded the observation to the database system"@en; + rdfs:domain ; + rdfs:label "uploadedBy"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -1402,6 +1414,11 @@ PREFIX xsd: rdfs:label "traitPUI"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; + rdfs:label "FileFormat"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "Unique DbId for the Seed Lot"@en; @@ -1409,11 +1426,6 @@ PREFIX xsd: rdfs:label "seedLotDbId"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; - rdfs:label "FileFormat"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository."@en; @@ -1585,10 +1597,6 @@ PREFIX xsd: rdfs:comment "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc."@en; rdfs:label "Location"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The string representation of the pedigree for this germplasm in PURDY notation"@en; @@ -1800,6 +1808,13 @@ PREFIX xsd: rdfs:label "breedingMethod"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:domain ; + rdfs:label "coordinates"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . @@ -1810,13 +1825,6 @@ PREFIX xsd: rdfs:label "observationUnit"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:domain ; - rdfs:label "coordinates"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; @@ -1868,6 +1876,10 @@ PREFIX xsd: rdfs:label "trialName"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string."@en; @@ -1944,6 +1956,14 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -1989,6 +2009,10 @@ PREFIX xsd: rdfs:label "variantSet"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "The ID of the reference set that describes the sequences used by the variants in this set."@en; @@ -2014,13 +2038,6 @@ PREFIX xsd: rdf:type owl:Class; rdfs:label "ObservationVariable"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "donors associated with a germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted."@en; @@ -2028,6 +2045,13 @@ PREFIX xsd: rdfs:label "variantSet"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "donors associated with a germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "samples"@en; @@ -2077,10 +2101,6 @@ PREFIX xsd: rdfs:label "sampleBarcode"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "Identifier assigned to an accession by the material donor."@en; @@ -2134,7 +2154,7 @@ PREFIX xsd: rdfs:range xsd:string . [ rdf:type owl:Class; - owl:oneOf ( ) + owl:oneOf ( ) ] . @@ -2189,10 +2209,6 @@ PREFIX xsd: rdfs:label "variants"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -2233,6 +2249,13 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Description the storage location"@en; + rdfs:domain ; + rdfs:label "storageLocation"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Information describing the grant or funding source for this program"@en; @@ -2247,13 +2270,6 @@ PREFIX xsd: rdfs:label "observationTimeStamp"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Description the storage location"@en; - rdfs:domain ; - rdfs:label "storageLocation"@en; - rdfs:range xsd:string . - rdf:type owl:NamedIndividual , . @@ -2313,13 +2329,6 @@ PREFIX xsd: rdfs:label "observations"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of scientist submitting the variable."@en; - rdfs:domain ; - rdfs:label "scientist"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; @@ -2341,7 +2350,14 @@ PREFIX xsd: rdfs:label "publicReleaseDate"@en; rdfs:range xsd:string . - + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of scientist submitting the variable."@en; + rdfs:domain ; + rdfs:label "scientist"@en; + rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; rdfs:comment "Information about the location where the sample was collected"@en; rdfs:domain ; @@ -2424,13 +2440,6 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The identifier (name, ID, URI) of a particular taxonomy within the source provider"@en; - rdfs:domain ; - rdfs:label "taxonId"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The mixture of germplasm present in the seed lot.\n
\nIf this seed lot only contains a single germplasm, the response should contain the name \nand DbId of that germplasm with a mixturePercentage value of 100\n
\nIf the seed lot contains a mixture of different germplasm, the response should contain \nthe name and DbId every germplasm present. The mixturePercentage field should contain \nthe ratio of each germplasm in the total mixture. All of the mixturePercentage values \nin this array should sum to equal 100."@en; @@ -2438,6 +2447,13 @@ PREFIX xsd: rdfs:label "contentMixture"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The identifier (name, ID, URI) of a particular taxonomy within the source provider"@en; + rdfs:domain ; + rdfs:label "taxonId"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "the maximum number of elements per page in this dimension of the matrix"@en; @@ -2537,13 +2553,6 @@ PREFIX xsd: rdfs:comment "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'."@en; rdfs:label "CrossType"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name for this analysis"@en; - rdfs:domain ; - rdfs:label "analysisName"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "True if the pollination was successful"@en; @@ -2551,6 +2560,13 @@ PREFIX xsd: rdfs:label "pollinationSuccessful"@en; rdfs:range xsd:boolean . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable name for this analysis"@en; + rdfs:domain ; + rdfs:label "analysisName"@en; + rdfs:range xsd:string . + rdf:type , owl:NamedIndividual , . @@ -2585,10 +2601,6 @@ PREFIX xsd: rdfs:label "genus"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Persons last name"@en; @@ -2706,6 +2718,9 @@ PREFIX xsd: rdfs:label "georeferencingMethod"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "the requested page number (zero indexed)"@en; @@ -2713,19 +2728,16 @@ PREFIX xsd: rdfs:label "page"@en; rdfs:range xsd:integer . - - rdf:type owl:NamedIndividual , . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -2799,13 +2811,6 @@ PREFIX xsd: rdfs:label "modality"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter."@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - rdf:type , owl:NamedIndividual , . @@ -2844,9 +2849,12 @@ PREFIX xsd: rdfs:label "plate"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter."@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -2874,6 +2882,13 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated \nby `start + referenceBases.length`."@en; @@ -2902,13 +2917,6 @@ PREFIX xsd: rdfs:label "variants"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; @@ -2926,6 +2934,11 @@ PREFIX xsd: rdfs:label "seedSource"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program."@en; + rdfs:label "Person"@en . + rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -2933,11 +2946,6 @@ PREFIX xsd: rdfs:label "studies"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program."@en; - rdfs:label "Person"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "The human readable name for a VariantSet"@en; @@ -3156,6 +3164,9 @@ PREFIX xsd: rdfs:label "sampleDescription"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; @@ -3163,9 +3174,6 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3173,13 +3181,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "alleleMatrices"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The unique identifier for a crossing project"@en; @@ -3187,6 +3188,13 @@ PREFIX xsd: rdfs:label "crossingProjectDbId"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "alleleMatrices"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3263,7 +3271,7 @@ PREFIX xsd: rdfs:label "TaxonId"@en . [ rdf:type owl:Class; - owl:oneOf ( ) + owl:oneOf ( ) ] . @@ -3280,13 +3288,6 @@ PREFIX xsd: rdfs:label "variantSets"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed."@en; - rdfs:domain ; - rdfs:label "geometry"@en; - rdfs:range , . - rdf:type owl:Class; rdfs:comment "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')."@en; @@ -3306,6 +3307,13 @@ PREFIX xsd: rdfs:label "methodName"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed."@en; + rdfs:domain ; + rdfs:label "geometry"@en; + rdfs:range , . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of institution submitting the variable"@en; @@ -3437,6 +3445,10 @@ PREFIX xsd: rdfs:label "speciesAuthority"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; @@ -3502,7 +3514,12 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - rdf:type owl:Ontology . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The timestamp when the pollination took place"@en; + rdfs:domain ; + rdfs:label "pollinationTimeStamp"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -3511,19 +3528,7 @@ PREFIX xsd: rdfs:label "pollinationNumber"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The time at which this record was created, in ISO 8601 format."@en; - rdfs:domain ; - rdfs:label "created"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The timestamp when the pollination took place"@en; - rdfs:domain ; - rdfs:label "pollinationTimeStamp"@en; - rdfs:range xsd:string . + rdf:type owl:Ontology . rdf:type owl:DatatypeProperty; @@ -3532,10 +3537,12 @@ PREFIX xsd: rdfs:label "commonCropName"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "If the Scale is a categorical type, these objects define the valid options"@en; - rdfs:label "ValidValuesCategory"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The time at which this record was created, in ISO 8601 format."@en; + rdfs:domain ; + rdfs:label "created"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -3544,6 +3551,15 @@ PREFIX xsd: rdfs:label "genomeMap"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "If the Scale is a categorical type, these objects define the valid options"@en; + rdfs:label "ValidValuesCategory"@en . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'."@en; @@ -3750,6 +3766,13 @@ PREFIX xsd: rdfs:label "created"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Common name for the crop"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Other variable names"@en; @@ -3760,13 +3783,6 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3831,10 +3847,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The type of analysis."@en; @@ -3924,6 +3936,10 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100."@en; @@ -3965,10 +3981,6 @@ PREFIX xsd: rdfs:comment "The identifying information gor the parent material of a cross."@en; rdfs:label "CrossParent"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for a `Plate`"@en; @@ -4016,6 +4028,10 @@ PREFIX xsd: rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. "@en; rdfs:label "ParentType"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; @@ -4278,6 +4294,10 @@ PREFIX xsd: rdfs:label "variants"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -4331,13 +4351,6 @@ PREFIX xsd: rdfs:comment "A persons contact information"@en; rdfs:label "Contact"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; - rdfs:domain ; - rdfs:label "method"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The number of Variants included in this VariantSet"@en; @@ -4345,6 +4358,13 @@ PREFIX xsd: rdfs:label "variantCount"@en; rdfs:range xsd:integer . + + rdf:type owl:ObjectProperty; + rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; + rdfs:domain ; + rdfs:label "method"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "the first parent used in the cross"@en; @@ -4364,10 +4384,6 @@ PREFIX xsd: rdfs:comment "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program."@en; rdfs:label "SeedLot"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'."@en; @@ -4410,6 +4426,10 @@ PREFIX xsd: rdfs:label "publications"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The MIME type of the file (ie text/csv, application/excel, application/zip).\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; @@ -4422,6 +4442,9 @@ PREFIX xsd: rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; rdfs:label "ObservationUnitLevel"@en . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\""@en; @@ -4429,9 +4452,6 @@ PREFIX xsd: rdfs:label "attribute"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -4477,13 +4497,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a program"@en; - rdfs:domain ; - rdfs:label "program"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The date this `GenomeMap` was published"@en; @@ -4491,8 +4504,12 @@ PREFIX xsd: rdfs:label "publishedDate"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a program"@en; + rdfs:domain ; + rdfs:label "program"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -4501,6 +4518,9 @@ PREFIX xsd: rdfs:label "linkageGroupCount"@en; rdfs:range xsd:integer . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "The child locations that belong to this Location. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; @@ -4534,8 +4554,12 @@ PREFIX xsd: rdfs:label "listDbId"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; rdfs:domain ; rdfs:label "documentationURL"@en; @@ -4549,13 +4573,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Variant` within the given database server\n
A `Variant` can also represent a Marker "@en; - rdfs:domain ; - rdfs:label "variant"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; @@ -4563,6 +4580,13 @@ PREFIX xsd: rdfs:label "donorAccessionNumber"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Variant` within the given database server\n
A `Variant` can also represent a Marker "@en; + rdfs:domain ; + rdfs:label "variant"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "Full scientific binomial format name. This includes Genus, Species, and Sub-species"@en; @@ -4570,10 +4594,6 @@ PREFIX xsd: rdfs:label "scientificName"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor."@en; @@ -4711,10 +4731,6 @@ PREFIX xsd: rdfs:label "sepUnphased"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard."@en; @@ -4797,20 +4813,6 @@ PREFIX xsd: rdfs:label "potentialParents"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name which identifies a germplasm within the given database server"@en; - rdfs:domain ; - rdfs:label "callSetName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -4865,6 +4867,20 @@ PREFIX xsd: rdfs:label "levelOrder"@en; rdfs:range xsd:integer . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name which identifies a germplasm within the given database server"@en; + rdfs:domain ; + rdfs:label "callSetName"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "images"@en; @@ -4917,10 +4933,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)"@en; @@ -4952,12 +4964,9 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:ObjectProperty; - rdfs:comment "the second parent used in the cross"@en; - rdfs:domain ; - rdfs:label "parent2"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -4966,9 +4975,12 @@ PREFIX xsd: rdfs:label "markerCount"@en; rdfs:range xsd:integer . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "the second parent used in the cross"@en; + rdfs:domain ; + rdfs:label "parent2"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -4977,11 +4989,6 @@ PREFIX xsd: rdfs:label "studyCode"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "Alternative names or IDs used to reference this germplasm"@en; - rdfs:label "Synonym"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "the unique identifier for a planned cross"@en; @@ -4989,6 +4996,11 @@ PREFIX xsd: rdfs:label "plannedCrossDbId"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "Alternative names or IDs used to reference this germplasm"@en; + rdfs:label "Synonym"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "Describes the level of protection/exposure for things like sun light and wind at a particular Location"@en; @@ -5006,6 +5018,10 @@ PREFIX xsd: rdfs:comment "Information about an accession donor"@en; rdfs:label "DonorInfo"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; @@ -5086,13 +5102,6 @@ PREFIX xsd: rdfs:label "markerCount"@en; rdfs:range xsd:integer . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The time at which this variant was last updated."@en; - rdfs:domain ; - rdfs:label "updated"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The unique identifier for a Location\n
The Parent Location defines the encompassing Location that a smaller Location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; @@ -5100,6 +5109,13 @@ PREFIX xsd: rdfs:label "parentLocation"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The time at which this variant was last updated."@en; + rdfs:domain ; + rdfs:label "updated"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation"@en; @@ -5191,6 +5207,13 @@ PREFIX xsd: rdfs:label "samplePUI"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "The season for this Observation"@en; @@ -5226,13 +5249,6 @@ PREFIX xsd: rdfs:label "toSeedLot"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -5252,12 +5268,9 @@ PREFIX xsd: rdfs:label "institution"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI"@en; - rdfs:domain ; - rdfs:label "eventParameters"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -5266,12 +5279,12 @@ PREFIX xsd: rdfs:label "code"@en; rdfs:range . - + rdf:type owl:ObjectProperty; - rdfs:comment "the first parent used in the cross"@en; - rdfs:domain ; - rdfs:label "parent1"@en; - rdfs:range . + rdfs:comment "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI"@en; + rdfs:domain ; + rdfs:label "eventParameters"@en; + rdfs:range . rdf:type , owl:NamedIndividual , . @@ -5293,13 +5306,16 @@ PREFIX xsd: rdfs:label "variantSetDbId"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "the first parent used in the cross"@en; + rdfs:domain ; + rdfs:label "parent1"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology"@en; @@ -5324,10 +5340,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "The type of positional coordinate. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; @@ -5382,6 +5394,13 @@ PREFIX xsd: rdfs:label "observationUnits"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies this attribute within the given database server"@en; + rdfs:domain ; + rdfs:label "attributeDbId"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "License and citation information for the data in this trial"@en; @@ -5424,12 +5443,12 @@ PREFIX xsd: rdfs:label "studyDbId"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies this attribute within the given database server"@en; - rdfs:domain ; - rdfs:label "attributeDbId"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . rdf:type owl:NamedIndividual , . @@ -5441,13 +5460,6 @@ PREFIX xsd: rdfs:label "ontologyName"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "The unique identifier for a Location"@en; @@ -5477,10 +5489,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon."@en; @@ -5554,10 +5562,6 @@ PREFIX xsd: rdfs:label "subtaxaAuthority"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The version number for this data \n\nMIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data)."@en; @@ -5591,6 +5595,10 @@ PREFIX xsd: rdfs:label "imageHeight"@en; rdfs:range xsd:integer . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The units or data type of the 'value'. \n
If the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'. \n
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. \n
If the value IS a number, then 'unit' should specify the units used eg. 'ml', 'cm', etc\n
ICASA \"Unit_or_type\""@en; @@ -5772,15 +5780,6 @@ PREFIX xsd: rdfs:label "geoCoordinates"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:Class; - rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; - rdfs:label "ObservationUnitHierarchyLevel"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this Seed Lot"@en; @@ -5788,6 +5787,11 @@ PREFIX xsd: rdfs:label "seedLotName"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; + rdfs:label "ObservationUnitHierarchyLevel"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation"@en; @@ -5861,9 +5865,12 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Program` within the given database server"@en; + rdfs:domain ; + rdfs:label "program"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -5872,13 +5879,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Program` within the given database server"@en; - rdfs:domain ; - rdfs:label "program"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; @@ -5945,6 +5945,11 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:Class; + rdfs:comment "A link to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; + rdfs:label "DataLink"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A Trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the Entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" "@en; @@ -5952,10 +5957,9 @@ PREFIX xsd: rdfs:label "entityPUI"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "A link to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; - rdfs:label "DataLink"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -6045,9 +6049,12 @@ PREFIX xsd: rdfs:label "germplasmName"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of field represented in this data matrix. This is intended to help parse the data out of JSON."@en; + rdfs:domain ; + rdfs:label "dataType"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -6063,13 +6070,6 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of field represented in this data matrix. This is intended to help parse the data out of JSON."@en; - rdfs:domain ; - rdfs:label "dataType"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this attribute"@en; @@ -6131,6 +6131,13 @@ PREFIX xsd: rdfs:label "software"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -6150,13 +6157,6 @@ PREFIX xsd: rdfs:label "discreteDates"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "Last update associated with a study"@en; @@ -6213,6 +6213,13 @@ PREFIX xsd: rdfs:label "synonyms"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable name for a Location\n
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place."@en; + rdfs:domain ; + rdfs:label "locationName"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; @@ -6220,16 +6227,23 @@ PREFIX xsd: rdfs:label "trait"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name for a Location\n
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place."@en; - rdfs:domain ; - rdfs:label "locationName"@en; + rdfs:comment "A URL which indicates the location of the file version of this VariantSet. Could be a static file URL or an API endpoint which generates the file."@en; + rdfs:domain ; + rdfs:label "fileURL"@en; rdfs:range xsd:string . rdf:type owl:NamedIndividual , . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a representation for missing data."@en; + rdfs:domain ; + rdfs:label "unknownString"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Common name for the crop associated with this trial"@en; @@ -6244,20 +6258,6 @@ PREFIX xsd: rdfs:label "scientist"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL which indicates the location of the file version of this VariantSet. Could be a static file URL or an API endpoint which generates the file."@en; - rdfs:domain ; - rdfs:label "fileURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a representation for missing data."@en; - rdfs:domain ; - rdfs:label "unknownString"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "samples"@en; @@ -6375,9 +6375,6 @@ PREFIX xsd: rdfs:comment "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)."@en; rdfs:label "EnvironmentParameter"@en . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "Name of scientist submitting the variable."@en; @@ -6385,6 +6382,9 @@ PREFIX xsd: rdfs:label "scientist"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the entity was first created"@en; @@ -6503,9 +6503,6 @@ PREFIX xsd: rdfs:label "dataType"@en; rdfs:range . - - rdf:type , , owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; @@ -6513,6 +6510,9 @@ PREFIX xsd: rdfs:label "instituteAddress"@en; rdfs:range xsd:string . + + rdf:type , , owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value."@en; diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index 06c0cedf..c775b517 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -25149,6 +25149,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -25157,6 +25158,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "page" : { @@ -26663,6 +26665,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -26671,6 +26674,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "methodDbIds" : { @@ -27086,6 +27090,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -27094,6 +27099,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "methodDbIds" : { @@ -27649,6 +27655,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -27657,6 +27664,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmPUIs" : { @@ -29723,6 +29731,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -29731,6 +29740,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "locationDbIds" : { @@ -30441,6 +30451,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -30449,6 +30460,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "includeObservations" : { @@ -31669,6 +31681,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -31677,6 +31690,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmPUIs" : { @@ -32473,6 +32487,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "observationUnitDbIds" : { @@ -33200,6 +33215,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -33208,6 +33224,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "md5checksums" : { @@ -33339,6 +33356,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -33347,6 +33365,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "isDerived" : { @@ -33799,6 +33818,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "observationUnitDbIds" : { @@ -34116,6 +34136,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -34124,6 +34145,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" } }, @@ -35493,6 +35515,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -35501,6 +35524,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "locationDbIds" : { @@ -39693,6 +39717,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "germplasmNames" : { @@ -39701,6 +39726,7 @@ "items" : { "type" : "string" }, + "nullable" : true, "type" : "array" }, "locationDbIds" : { diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index a8a85b34..a1e2257c 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -86,51 +86,9 @@ Added: `externalReferenceID` in `query` * Changed content type : `application/json` - * Changed property `dataMatrixAbbreviations` (array): - - Nullable changed: `true` -> `null` - - * Changed property `dataMatrixNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `expandHomozygotes` (boolean): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmPUIs` (array): - - Nullable changed: `true` -> `null` - - * Changed property `pagination` (array): - - Nullable changed: `true` -> `null` - - * Changed property `positionRanges` (array): - - Nullable changed: `true` -> `null` - * Changed property `preview` (boolean): - Default changed: `false` -> `none` - * Changed property `sampleDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `sepPhased` (string): - - Nullable changed: `true` -> `null` - - * Changed property `sepUnphased` (string): - - Nullable changed: `true` -> `null` - - * Changed property `unknownString` (string): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `variantSetDbIds` (array): - - Nullable changed: `true` -> `null` - ###### Return Type: Changed response : **200** @@ -183,18 +141,6 @@ Changed response : **200** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `attributeCategories` (array): - - Nullable changed: `true` -> `null` - - * Changed property `attributeDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `attributeNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `attributePUIs` (array): - - Nullable changed: `true` -> `null` - * Changed property `studyDbId` (array): - Deprecated status changed @@ -216,33 +162,6 @@ Deleted response : **404** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `attributeDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `attributeNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `attributeValueDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `dataTypes` (array): - - Nullable changed: `true` -> `null` - - * Changed property `methodDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `ontologyDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `scaleDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `traitClasses` (array): - - Nullable changed: `true` -> `null` - - * Changed property `traitDbIds` (array): - - Nullable changed: `true` -> `null` - ##### `GET` /search/attributevalues/{searchResultsDbId} @@ -261,39 +180,6 @@ Deleted response : **404** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `accessionNumbers` (array): - - Nullable changed: `true` -> `null` - - * Changed property `binomialNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `collections` (array): - - Nullable changed: `true` -> `null` - - * Changed property `familyCodes` (array): - - Nullable changed: `true` -> `null` - - * Changed property `genus` (array): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmPUIs` (array): - - Nullable changed: `true` -> `null` - - * Changed property `instituteCodes` (array): - - Nullable changed: `true` -> `null` - - * Changed property `parentDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `progenyDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `species` (array): - - Nullable changed: `true` -> `null` - - * Changed property `synonyms` (array): - - Nullable changed: `true` -> `null` - ##### `GET` /search/germplasm/{searchResultsDbId} @@ -321,33 +207,6 @@ Deleted response : **404** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `dateCreatedRangeEnd` (string): - - Nullable changed: `true` -> `null` - - * Changed property `dateCreatedRangeStart` (string): - - Nullable changed: `true` -> `null` - - * Changed property `dateModifiedRangeEnd` (string): - - Nullable changed: `true` -> `null` - - * Changed property `dateModifiedRangeStart` (string): - - Nullable changed: `true` -> `null` - - * Changed property `listDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `listNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `listOwnerNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `listOwnerPersonDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `listSources` (array): - - Nullable changed: `true` -> `null` - * Changed property `listType` (string): - Nullable changed: `true` -> `null` @@ -374,15 +233,6 @@ Deleted response : **202** Deleted properties: `page`, `pageSize` - * Changed property `linkageGroupNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `mapDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbIds` (array): - - Nullable changed: `true` -> `null` - ###### Return Type: Changed response : **200** @@ -445,30 +295,6 @@ Deleted response : **404** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `emailAddresses` (array): - - Nullable changed: `true` -> `null` - - * Changed property `firstNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `lastNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `mailingAddresses` (array): - - Nullable changed: `true` -> `null` - - * Changed property `middleNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `personDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `phoneNumbers` (array): - - Nullable changed: `true` -> `null` - - * Changed property `userIDs` (array): - - Nullable changed: `true` -> `null` - ##### `GET` /search/people/{searchResultsDbId} @@ -485,30 +311,6 @@ Deleted response : **202** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `germplasmDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `plateBarcodes` (array): - - Nullable changed: `true` -> `null` - - * Changed property `plateDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `plateNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `sampleDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `sampleGroupDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `sampleNames` (array): - - Nullable changed: `true` -> `null` - ##### `GET` /search/plates/{searchResultsDbId} @@ -527,21 +329,6 @@ Deleted response : **404** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `abbreviations` (array): - - Nullable changed: `true` -> `null` - - * Changed property `leadPersonDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `leadPersonNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `objectives` (array): - - Nullable changed: `true` -> `null` - - * Changed property `programTypes` (array): - - Nullable changed: `true` -> `null` - ##### `GET` /search/programs/{searchResultsDbId} @@ -560,18 +347,6 @@ Deleted response : **404** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `accessions` (array): - - Nullable changed: `true` -> `null` - - * Changed property `assemblyPUIs` (array): - - Nullable changed: `true` -> `null` - - * Changed property `md5checksums` (array): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetDbIds` (array): - - Nullable changed: `true` -> `null` - ##### `GET` /search/referencesets/{searchResultsDbId} @@ -588,27 +363,6 @@ Deleted response : **202** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `germplasmDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `plateDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `plateNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `sampleDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `sampleGroupDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `sampleNames` (array): - - Nullable changed: `true` -> `null` - ##### `GET` /search/samples/{searchResultsDbId} @@ -627,29 +381,12 @@ Deleted response : **404** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `active` (boolean): - - Nullable changed: `true` -> `null` - - * Changed property `seasonDbIds` (array): - - Nullable changed: `true` -> `null` - * Changed property `sortBy` (string): - - Nullable changed: `true` -> `null` - Removed enum values: [germplasmDbId, observationVariableDbId] * Changed property `sortOrder` (string): - - Nullable changed: `true` -> `null` - Added enum values: [asc, desc] - * Changed property `studyCodes` (array): - - Nullable changed: `true` -> `null` - - * Changed property `studyPUIs` (array): - - Nullable changed: `true` -> `null` - - * Changed property `studyTypes` (array): - - Nullable changed: `true` -> `null` - ##### `GET` /search/studies/{searchResultsDbId} @@ -1822,27 +1559,6 @@ Deleted response : **404** Deleted properties: `page`, `pageSize`, `pageToken` - * Changed property `callSetDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `expandHomozygotes` (boolean): - - Nullable changed: `true` -> `null` - - * Changed property `sepPhased` (string): - - Nullable changed: `true` -> `null` - - * Changed property `sepUnphased` (string): - - Nullable changed: `true` -> `null` - - * Changed property `unknownString` (string): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `variantSetDbIds` (array): - - Nullable changed: `true` -> `null` - ###### Return Type: Changed response : **200** @@ -1939,21 +1655,6 @@ Changed response : **200** Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `callSetDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `callSetNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `sampleDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `sampleNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `variantSetDbIds` (array): - - Nullable changed: `true` -> `null` - ###### Return Type: Changed response : **200** From 273461e2e41fe0c15d89c22079020f6fd03f798f Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Mon, 11 May 2026 18:58:07 +1200 Subject: [PATCH 34/62] Add 404 response handling to various search result endpoints --- .../BrAPI-Core/Lists/Search_Lists_SearchResultsDbId_GET.yaml | 2 ++ .../Locations/Search_Locations_SearchResultsDbId_GET.yaml | 2 ++ .../BrAPI-Core/People/Search_People_SearchResultsDbId_GET.yaml | 2 ++ .../AlleleMatrix/Search_AlleleMatrix_SearchResultsDbId_GET.yaml | 2 ++ .../CallSets/Search_CallSets_SearchResultsDbId_GET.yaml | 2 ++ .../Calls/Search_Calls_SearchResultsDbId_GET.yaml | 2 ++ .../Search_MarkerPositions_SearchResultsDbId_GET.yaml | 2 ++ .../Search_ReferenceSets_SearchResultsDbId_GET.yaml | 2 ++ .../References/Search_References_SearchResultsDbId_GET.yaml | 2 ++ .../VariantSets/Search_VariantSets_SearchResultsDbId_GET.yaml | 2 ++ .../VariantSets/VariantSets_VariantSetId_CallSets_GET.yaml | 2 ++ .../VariantSets/VariantSets_VariantSetId_Variants_GET.yaml | 2 ++ .../Variants/Search_Variants_SearchResultsDbId_GET.yaml | 2 ++ 13 files changed, 26 insertions(+) diff --git a/Specification/BrAPI-Core/Lists/Search_Lists_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Core/Lists/Search_Lists_SearchResultsDbId_GET.yaml index a61016d0..13b55f3d 100644 --- a/Specification/BrAPI-Core/Lists/Search_Lists_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Core/Lists/Search_Lists_SearchResultsDbId_GET.yaml @@ -29,5 +29,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Lists diff --git a/Specification/BrAPI-Core/Locations/Search_Locations_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Core/Locations/Search_Locations_SearchResultsDbId_GET.yaml index 0d267291..bf2892eb 100644 --- a/Specification/BrAPI-Core/Locations/Search_Locations_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Core/Locations/Search_Locations_SearchResultsDbId_GET.yaml @@ -29,5 +29,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Locations diff --git a/Specification/BrAPI-Core/People/Search_People_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Core/People/Search_People_SearchResultsDbId_GET.yaml index 4c6b7bcc..fe0b8307 100644 --- a/Specification/BrAPI-Core/People/Search_People_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Core/People/Search_People_SearchResultsDbId_GET.yaml @@ -29,5 +29,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - People \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_SearchResultsDbId_GET.yaml index bc1e61f7..05d5f638 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/Search_AlleleMatrix_SearchResultsDbId_GET.yaml @@ -25,5 +25,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Allele Matrix \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_SearchResultsDbId_GET.yaml index e0c2853b..ce8c45a5 100644 --- a/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/Search_CallSets_SearchResultsDbId_GET.yaml @@ -29,5 +29,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Call Sets \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/Calls/Search_Calls_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Genotyping/Calls/Search_Calls_SearchResultsDbId_GET.yaml index c8880b58..a56a9734 100644 --- a/Specification/BrAPI-Genotyping/Calls/Search_Calls_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/Calls/Search_Calls_SearchResultsDbId_GET.yaml @@ -31,5 +31,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Calls \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/GenomeMaps/Search_MarkerPositions_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Genotyping/GenomeMaps/Search_MarkerPositions_SearchResultsDbId_GET.yaml index 810e68a5..cce9a2a4 100644 --- a/Specification/BrAPI-Genotyping/GenomeMaps/Search_MarkerPositions_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/GenomeMaps/Search_MarkerPositions_SearchResultsDbId_GET.yaml @@ -29,5 +29,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Genome Maps diff --git a/Specification/BrAPI-Genotyping/ReferenceSets/Search_ReferenceSets_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Genotyping/ReferenceSets/Search_ReferenceSets_SearchResultsDbId_GET.yaml index 8e4e3b45..45366ef8 100644 --- a/Specification/BrAPI-Genotyping/ReferenceSets/Search_ReferenceSets_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/ReferenceSets/Search_ReferenceSets_SearchResultsDbId_GET.yaml @@ -29,5 +29,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Reference Sets \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/References/Search_References_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Genotyping/References/Search_References_SearchResultsDbId_GET.yaml index 515b9485..e06b8d06 100644 --- a/Specification/BrAPI-Genotyping/References/Search_References_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/References/Search_References_SearchResultsDbId_GET.yaml @@ -29,5 +29,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - References \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/VariantSets/Search_VariantSets_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Genotyping/VariantSets/Search_VariantSets_SearchResultsDbId_GET.yaml index 1eb4c1a1..911facb4 100644 --- a/Specification/BrAPI-Genotyping/VariantSets/Search_VariantSets_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/VariantSets/Search_VariantSets_SearchResultsDbId_GET.yaml @@ -29,5 +29,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Variant Sets \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_CallSets_GET.yaml b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_CallSets_GET.yaml index b2d9633d..08e1cbed 100644 --- a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_CallSets_GET.yaml +++ b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_CallSets_GET.yaml @@ -38,5 +38,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Variant Sets \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_Variants_GET.yaml b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_Variants_GET.yaml index 40cdc20e..7ebb0688 100644 --- a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_Variants_GET.yaml +++ b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_VariantSetId_Variants_GET.yaml @@ -34,5 +34,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Variant Sets \ No newline at end of file diff --git a/Specification/BrAPI-Genotyping/Variants/Search_Variants_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Genotyping/Variants/Search_Variants_SearchResultsDbId_GET.yaml index da9659a9..26207af2 100644 --- a/Specification/BrAPI-Genotyping/Variants/Search_Variants_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Search_Variants_SearchResultsDbId_GET.yaml @@ -31,5 +31,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Variants \ No newline at end of file From 12b29a2300168ea3fe959e8fac812b748959e8b7 Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Mon, 11 May 2026 07:01:56 +0000 Subject: [PATCH 35/62] Generate specifications (manually triggered) --- Specification/Generated/brapi_generated.ttl | 820 +++++++++--------- Specification/Generated/brapi_openapi.json | 143 +++ .../Generated/brapi_openapi_comparison.md | 26 +- 3 files changed, 575 insertions(+), 414 deletions(-) diff --git a/Specification/Generated/brapi_generated.ttl b/Specification/Generated/brapi_generated.ttl index a9fec8d0..572ccd7d 100644 --- a/Specification/Generated/brapi_generated.ttl +++ b/Specification/Generated/brapi_generated.ttl @@ -39,6 +39,10 @@ PREFIX xsd: rdfs:label "slope"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; @@ -114,20 +118,6 @@ PREFIX xsd: rdfs:label "map"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; - rdfs:domain ; - rdfs:label "analysis"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated seedLot"@en; - rdfs:domain ; - rdfs:label "seedLot"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "observationUnits"@en; @@ -135,6 +125,13 @@ PREFIX xsd: rdfs:label "observationUnits"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; + rdfs:domain ; + rdfs:label "analysis"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -142,6 +139,13 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "associated seedLot"@en; + rdfs:domain ; + rdfs:label "seedLot"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "The unique DbId of the breeding program this Seed Lot belongs to"@en; @@ -156,6 +160,13 @@ PREFIX xsd: rdfs:label "code"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)"@en; + rdfs:domain ; + rdfs:label "locationType"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source"@en; @@ -163,13 +174,6 @@ PREFIX xsd: rdfs:label "seedSourceDescription"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "If the event parameter 'unit' field is 'code', then use 'valueDescription' to add a human readable description to the value."@en; - rdfs:domain ; - rdfs:label "valueDescription"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The human readable description of a trial\n\nMIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail."@en; @@ -177,11 +181,11 @@ PREFIX xsd: rdfs:label "trialDescription"@en; rdfs:range xsd:string . - + rdf:type owl:DatatypeProperty; - rdfs:comment "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)"@en; - rdfs:domain ; - rdfs:label "locationType"@en; + rdfs:comment "If the event parameter 'unit' field is 'code', then use 'valueDescription' to add a human readable description to the value."@en; + rdfs:domain ; + rdfs:label "valueDescription"@en; rdfs:range xsd:string . @@ -245,6 +249,13 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . @@ -274,13 +285,6 @@ PREFIX xsd: rdfs:comment "Links to various ontology documentation"@en; rdfs:label "DocumentationLink"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The name or identifier of the entity which took the `Sample` from the field"@en; @@ -295,11 +299,6 @@ PREFIX xsd: rdfs:label "method"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended."@en; - rdfs:label "Publication"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "A Permanent Unique Identifier for an observation unit\n\nMIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible."@en; @@ -307,6 +306,11 @@ PREFIX xsd: rdfs:label "observationUnitPUI"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended."@en; + rdfs:label "Publication"@en . + rdf:type owl:Class; rdfs:comment "The type of documentation, which can be OBO Foundry, an RDF term or a webpage."@en; @@ -317,10 +321,6 @@ PREFIX xsd: rdfs:comment "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"."@en; rdfs:label "Season"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The version of the update."@en; @@ -366,10 +366,6 @@ PREFIX xsd: rdfs:label "sampleName"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "germplasm"@en; @@ -401,10 +397,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "A human readable description of the analysis"@en; @@ -454,11 +446,6 @@ PREFIX xsd: rdfs:label "progeny"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; - rdfs:label "GermplasmOrigin"@en . - rdf:type owl:ObjectProperty; rdfs:comment "associated ontology reference"@en; @@ -466,6 +453,11 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; + rdfs:label "GermplasmOrigin"@en . + rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -513,13 +505,6 @@ PREFIX xsd: rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; rdfs:label "BiologicalStatusOfAccessionCode"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows."@en; - rdfs:domain ; - rdfs:label "dataMatrices"@en; - rdfs:range . - rdf:type owl:NamedIndividual , . @@ -565,6 +550,10 @@ PREFIX xsd: rdfs:label "commonCropName"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; @@ -572,6 +561,13 @@ PREFIX xsd: rdfs:label "growthStage"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows."@en; + rdfs:domain ; + rdfs:label "dataMatrices"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered names or other designations given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase."@en; @@ -629,10 +625,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -686,10 +678,6 @@ PREFIX xsd: rdfs:label "callSet"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The Ontology for this reference"@en; @@ -703,13 +691,6 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . - - rdf:type owl:ObjectProperty; - rdfs:comment "All known corresponding Germplasm"@en; - rdfs:domain ; - rdfs:label "sourceGermplasm"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "observationUnits"@en; @@ -727,6 +708,13 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "All known corresponding Germplasm"@en; + rdfs:domain ; + rdfs:label "sourceGermplasm"@en; + rdfs:range . + rdf:type owl:Class; rdfs:comment "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier."@en; @@ -818,6 +806,10 @@ PREFIX xsd: rdfs:label "crossType"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -866,6 +858,13 @@ PREFIX xsd: rdfs:comment "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit."@en; rdfs:label "Observation"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; + rdfs:domain ; + rdfs:label "contextOfUse"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -873,12 +872,12 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; rdfs:domain ; - rdfs:label "contextOfUse"@en; - rdfs:range xsd:string . + rdfs:label "ontologyReference"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -887,13 +886,6 @@ PREFIX xsd: rdfs:label "latitudeDecimal"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The human readable name for a crossing project"@en; @@ -983,6 +975,11 @@ PREFIX xsd: rdfs:label "sampleType"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "All positional and layout information related to this Observation Unit"@en; + rdfs:label "ObservationUnitPosition"@en . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -990,11 +987,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "All positional and layout information related to this Observation Unit"@en; - rdfs:label "ObservationUnitPosition"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)"@en; @@ -1166,6 +1158,10 @@ PREFIX xsd: rdfs:comment "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy."@en; rdfs:label "Germplasm"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy."@en; @@ -1306,6 +1302,10 @@ PREFIX xsd: rdfs:label "germplasmOrigin"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "Supplemental text description for 'biologicalStatusOfAccessionCode'"@en; @@ -1353,12 +1353,12 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:NamedIndividual , . + + rdf:type owl:NamedIndividual , . + rdf:type owl:NamedIndividual , . @@ -1414,11 +1414,6 @@ PREFIX xsd: rdfs:label "traitPUI"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; - rdfs:label "FileFormat"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "Unique DbId for the Seed Lot"@en; @@ -1426,6 +1421,11 @@ PREFIX xsd: rdfs:label "seedLotDbId"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; + rdfs:label "FileFormat"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository."@en; @@ -1723,6 +1723,10 @@ PREFIX xsd: rdfs:label "siblingPedigreeNodes"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit"@en; @@ -1876,10 +1880,6 @@ PREFIX xsd: rdfs:label "trialName"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string."@en; @@ -1892,6 +1892,10 @@ PREFIX xsd: rdfs:comment "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard "@en; rdfs:label "MetadataField"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; @@ -1911,13 +1915,6 @@ PREFIX xsd: rdfs:label "crosses"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a separator for unphased allele calls."@en; - rdfs:domain ; - rdfs:label "sepUnphased"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "the description for a crossing project"@en; @@ -1925,6 +1922,13 @@ PREFIX xsd: rdfs:label "crossingProjectDescription"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a separator for unphased allele calls."@en; + rdfs:domain ; + rdfs:label "sepUnphased"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The time stamp for when this seed lot was created"@en; @@ -1956,14 +1960,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -2009,10 +2005,6 @@ PREFIX xsd: rdfs:label "variantSet"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The ID of the reference set that describes the sequences used by the variants in this set."@en; @@ -2038,13 +2030,6 @@ PREFIX xsd: rdf:type owl:Class; rdfs:label "ObservationVariable"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted."@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "donors associated with a germplasm"@en; @@ -2052,6 +2037,13 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted."@en; + rdfs:domain ; + rdfs:label "variantSet"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "samples"@en; @@ -2154,7 +2146,7 @@ PREFIX xsd: rdfs:range xsd:string . [ rdf:type owl:Class; - owl:oneOf ( ) + owl:oneOf ( ) ] . @@ -2164,6 +2156,9 @@ PREFIX xsd: rdfs:label "parentPedigreeNodes"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space."@en; @@ -2171,9 +2166,6 @@ PREFIX xsd: rdfs:label "instituteAddress"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a trial"@en; @@ -2329,6 +2321,13 @@ PREFIX xsd: rdfs:label "observations"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of scientist submitting the variable."@en; + rdfs:domain ; + rdfs:label "scientist"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; @@ -2350,13 +2349,6 @@ PREFIX xsd: rdfs:label "publicReleaseDate"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of scientist submitting the variable."@en; - rdfs:domain ; - rdfs:label "scientist"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "Information about the location where the sample was collected"@en; @@ -2629,6 +2621,10 @@ PREFIX xsd: rdfs:label "study"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "the human readable name for a planned cross"@en; @@ -2718,9 +2714,6 @@ PREFIX xsd: rdfs:label "georeferencingMethod"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "the requested page number (zero indexed)"@en; @@ -2728,16 +2721,19 @@ PREFIX xsd: rdfs:label "page"@en; rdfs:range xsd:integer . + + rdf:type owl:NamedIndividual , . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -2811,6 +2807,13 @@ PREFIX xsd: rdfs:label "modality"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter."@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + rdf:type , owl:NamedIndividual , . @@ -2849,13 +2852,6 @@ PREFIX xsd: rdfs:label "plate"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter."@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The Cross associated with this Pollination Event"@en; @@ -2882,13 +2878,6 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated \nby `start + referenceBases.length`."@en; @@ -2896,6 +2885,13 @@ PREFIX xsd: rdfs:label "end"@en; rdfs:range xsd:integer . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "phone number of this person"@en; @@ -2934,11 +2930,6 @@ PREFIX xsd: rdfs:label "seedSource"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program."@en; - rdfs:label "Person"@en . - rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -2946,6 +2937,11 @@ PREFIX xsd: rdfs:label "studies"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program."@en; + rdfs:label "Person"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "The human readable name for a VariantSet"@en; @@ -3131,6 +3127,10 @@ PREFIX xsd: rdfs:label "dataMatrixAbbreviation"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; @@ -3164,9 +3164,6 @@ PREFIX xsd: rdfs:label "sampleDescription"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:ObjectProperty; rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; @@ -3174,6 +3171,9 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3181,13 +3181,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a crossing project"@en; - rdfs:domain ; - rdfs:label "crossingProjectDbId"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment ""@en; @@ -3195,6 +3188,13 @@ PREFIX xsd: rdfs:label "alleleMatrices"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a crossing project"@en; + rdfs:domain ; + rdfs:label "crossingProjectDbId"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3270,10 +3270,6 @@ PREFIX xsd: rdfs:comment "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended."@en; rdfs:label "TaxonId"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The literal string \"Feature\""@en; @@ -3288,6 +3284,13 @@ PREFIX xsd: rdfs:label "variantSets"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed."@en; + rdfs:domain ; + rdfs:label "geometry"@en; + rdfs:range , . + rdf:type owl:Class; rdfs:comment "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')."@en; @@ -3307,13 +3310,6 @@ PREFIX xsd: rdfs:label "methodName"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed."@en; - rdfs:domain ; - rdfs:label "geometry"@en; - rdfs:range , . - rdf:type owl:DatatypeProperty; rdfs:comment "Name of institution submitting the variable"@en; @@ -3445,10 +3441,6 @@ PREFIX xsd: rdfs:label "speciesAuthority"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; @@ -3556,10 +3548,6 @@ PREFIX xsd: rdfs:comment "If the Scale is a categorical type, these objects define the valid options"@en; rdfs:label "ValidValuesCategory"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'."@en; @@ -3727,12 +3715,10 @@ PREFIX xsd: rdfs:label "biologicalStatusOfAccessionCode"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The value of this attribute for a given germplasm"@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; + rdfs:label "StorageTypeCode"@en . rdf:type owl:ObjectProperty; @@ -3741,10 +3727,12 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; - rdfs:label "StorageTypeCode"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The value of this attribute for a given germplasm"@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -3802,13 +3790,6 @@ PREFIX xsd: rdfs:comment "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis."@en; rdfs:label "Plate"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The 4 digit year of the season."@en; - rdfs:domain ; - rdfs:label "year"@en; - rdfs:range xsd:integer . - rdf:type owl:ObjectProperty; rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; @@ -3816,6 +3797,13 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The 4 digit year of the season."@en; + rdfs:domain ; + rdfs:label "year"@en; + rdfs:range xsd:integer . + rdf:type owl:DatatypeProperty; rdfs:comment "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; @@ -3859,13 +3847,6 @@ PREFIX xsd: rdfs:comment "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies."@en; rdfs:label "Study"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Alternative name or ID used to reference this germplasm"@en; - rdfs:domain ; - rdfs:label "synonym"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "URL describing the location of this data file to view or download\n\nMIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission."@en; @@ -3880,6 +3861,13 @@ PREFIX xsd: rdfs:label "referenceSet"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Alternative name or ID used to reference this germplasm"@en; + rdfs:domain ; + rdfs:label "synonym"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of scientist submitting the variable."@en; @@ -3937,7 +3925,7 @@ PREFIX xsd: rdfs:range . [ rdf:type owl:Class; - owl:oneOf ( ) + owl:oneOf ( ) ] . @@ -3995,6 +3983,10 @@ PREFIX xsd: rdfs:label "crossingProject"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "the Observation Unit of the cross parent"@en; @@ -4028,10 +4020,6 @@ PREFIX xsd: rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. "@en; rdfs:label "ParentType"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; @@ -4065,6 +4053,10 @@ PREFIX xsd: rdfs:label "parent2"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; @@ -4294,10 +4286,6 @@ PREFIX xsd: rdfs:label "variants"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -4332,12 +4320,14 @@ PREFIX xsd: rdfs:label "commonCropName"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of CallSets included in this VariantSet"@en; - rdfs:domain ; - rdfs:label "callSetCount"@en; - rdfs:range xsd:integer . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:Class; + rdfs:comment "A persons contact information"@en; + rdfs:label "Contact"@en . rdf:type owl:DatatypeProperty; @@ -4346,10 +4336,12 @@ PREFIX xsd: rdfs:label "unit"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "A persons contact information"@en; - rdfs:label "Contact"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of CallSets included in this VariantSet"@en; + rdfs:domain ; + rdfs:label "callSetCount"@en; + rdfs:range xsd:integer . rdf:type owl:DatatypeProperty; @@ -4426,10 +4418,6 @@ PREFIX xsd: rdfs:label "publications"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The MIME type of the file (ie text/csv, application/excel, application/zip).\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; @@ -4442,6 +4430,10 @@ PREFIX xsd: rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; rdfs:label "ObservationUnitLevel"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -4497,13 +4489,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date this `GenomeMap` was published"@en; - rdfs:domain ; - rdfs:label "publishedDate"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a program"@en; @@ -4511,6 +4496,13 @@ PREFIX xsd: rdfs:label "program"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date this `GenomeMap` was published"@en; + rdfs:domain ; + rdfs:label "publishedDate"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The number of linkage groups present in a `GenomeMap`"@en; @@ -4555,7 +4547,7 @@ PREFIX xsd: rdfs:range xsd:string . [ rdf:type owl:Class; - owl:oneOf ( ) + owl:oneOf ( ) ] . @@ -4731,6 +4723,10 @@ PREFIX xsd: rdfs:label "sepUnphased"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard."@en; @@ -4813,18 +4809,32 @@ PREFIX xsd: rdfs:label "potentialParents"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - + rdf:type owl:DatatypeProperty; - rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; - rdfs:domain ; - rdfs:label "defaultValue"@en; + rdfs:comment "The human readable name which identifies a germplasm within the given database server"@en; + rdfs:domain ; + rdfs:label "callSetName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; + rdfs:domain ; + rdfs:label "defaultValue"@en; rdfs:range xsd:string . @@ -4867,20 +4877,6 @@ PREFIX xsd: rdfs:label "levelOrder"@en; rdfs:range xsd:integer . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name which identifies a germplasm within the given database server"@en; - rdfs:domain ; - rdfs:label "callSetName"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "images"@en; @@ -4964,10 +4960,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The number of markers present in a `GenomeMap`"@en; @@ -5018,10 +5010,6 @@ PREFIX xsd: rdfs:comment "Information about an accession donor"@en; rdfs:label "DonorInfo"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; @@ -5074,12 +5062,9 @@ PREFIX xsd: rdfs:label "fieldValue"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The content of the image"@en; - rdfs:domain ; - rdfs:label "imageContent"@en; - rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -5088,6 +5073,13 @@ PREFIX xsd: rdfs:label "coordinateUncertainty"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The content of the image"@en; + rdfs:domain ; + rdfs:label "imageContent"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; @@ -5228,13 +5220,6 @@ PREFIX xsd: rdfs:label "position"@en; rdfs:range xsd:integer . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; - rdfs:domain ; - rdfs:label "growthStage"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. "@en; @@ -5249,6 +5234,13 @@ PREFIX xsd: rdfs:label "toSeedLot"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; + rdfs:domain ; + rdfs:label "growthStage"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -5268,9 +5260,12 @@ PREFIX xsd: rdfs:label "institution"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI"@en; + rdfs:domain ; + rdfs:label "eventParameters"@en; + rdfs:range . rdf:type owl:ObjectProperty; @@ -5279,12 +5274,12 @@ PREFIX xsd: rdfs:label "code"@en; rdfs:range . - + rdf:type owl:ObjectProperty; - rdfs:comment "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI"@en; - rdfs:domain ; - rdfs:label "eventParameters"@en; - rdfs:range . + rdfs:comment "the first parent used in the cross"@en; + rdfs:domain ; + rdfs:label "parent1"@en; + rdfs:range . rdf:type , owl:NamedIndividual , . @@ -5306,13 +5301,6 @@ PREFIX xsd: rdfs:label "variantSetDbId"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "the first parent used in the cross"@en; - rdfs:domain ; - rdfs:label "parent1"@en; - rdfs:range . - rdf:type owl:NamedIndividual , . @@ -5408,18 +5396,18 @@ PREFIX xsd: rdfs:label "datasetAuthorships"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group)."@en; + rdfs:comment "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\")."@en; rdfs:domain ; - rdfs:label "subtaxa"@en; + rdfs:label "accessionNumber"@en; rdfs:range xsd:string . - + rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\")."@en; + rdfs:comment "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group)."@en; rdfs:domain ; - rdfs:label "accessionNumber"@en; + rdfs:label "subtaxa"@en; rdfs:range xsd:string . @@ -5429,13 +5417,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The ID which uniquely identifies a study within the given database server\n\nMIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution."@en; @@ -5443,12 +5424,12 @@ PREFIX xsd: rdfs:label "studyDbId"@en; rdfs:range xsd:string . - + rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . rdf:type owl:NamedIndividual , . @@ -5460,6 +5441,13 @@ PREFIX xsd: rdfs:label "ontologyName"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "The unique identifier for a Location"@en; @@ -5510,12 +5498,9 @@ PREFIX xsd: rdfs:label "term"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The DOI or other permanent unique identifier for this published dataset"@en; - rdfs:domain ; - rdfs:label "datasetPUI"@en; - rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -5524,12 +5509,16 @@ PREFIX xsd: rdfs:label "growthStage"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies an `ObservationUnit`"@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The DOI or other permanent unique identifier for this published dataset"@en; + rdfs:domain ; + rdfs:label "datasetPUI"@en; + rdfs:range xsd:string . rdf:type owl:Class; @@ -5541,6 +5530,13 @@ PREFIX xsd: rdfs:comment "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present."@en; rdfs:label "Cross"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name used for display purposes"@en; + rdfs:domain ; + rdfs:label "defaultDisplayName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the entity was last updated"@en; @@ -5548,12 +5544,12 @@ PREFIX xsd: rdfs:label "dateModified"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name used for display purposes"@en; - rdfs:domain ; - rdfs:label "defaultDisplayName"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies an `ObservationUnit`"@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -5595,10 +5591,6 @@ PREFIX xsd: rdfs:label "imageHeight"@en; rdfs:range xsd:integer . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The units or data type of the 'value'. \n
If the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'. \n
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. \n
If the value IS a number, then 'unit' should specify the units used eg. 'ml', 'cm', etc\n
ICASA \"Unit_or_type\""@en; @@ -5623,6 +5615,10 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The Permanent Unique Identifier of a Method, usually in the form of a URI"@en; @@ -5738,6 +5734,10 @@ PREFIX xsd: rdfs:label "trial"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -5780,6 +5780,11 @@ PREFIX xsd: rdfs:label "geoCoordinates"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; + rdfs:label "ObservationUnitHierarchyLevel"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this Seed Lot"@en; @@ -5787,11 +5792,6 @@ PREFIX xsd: rdfs:label "seedLotName"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; - rdfs:label "ObservationUnitHierarchyLevel"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation"@en; @@ -5865,13 +5865,6 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Program` within the given database server"@en; - rdfs:domain ; - rdfs:label "program"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -5879,6 +5872,13 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Program` within the given database server"@en; + rdfs:domain ; + rdfs:label "program"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; @@ -5957,10 +5957,6 @@ PREFIX xsd: rdfs:label "entityPUI"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "The unique identifier for a VariantSet"@en; @@ -6056,12 +6052,9 @@ PREFIX xsd: rdfs:label "dataType"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. \n
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response."@en; - rdfs:domain ; - rdfs:label "parents"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -6070,6 +6063,13 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. \n
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response."@en; + rdfs:domain ; + rdfs:label "parents"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this attribute"@en; @@ -6171,13 +6171,6 @@ PREFIX xsd: rdfs:label "attributePUI"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "programs"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "Bibliographical reference describing the method.\n
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method."@en; @@ -6185,6 +6178,13 @@ PREFIX xsd: rdfs:label "bibliographicalReference"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "programs"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)"@en; @@ -6282,13 +6282,6 @@ PREFIX xsd: rdfs:label "parameterPUI"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "mapDbId"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group."@en; @@ -6301,6 +6294,13 @@ PREFIX xsd: rdfs:label "startDate"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name used for display purposes"@en; + rdfs:domain ; + rdfs:label "defaultDisplayName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "A human readable description of this attribute"@en; @@ -6308,11 +6308,11 @@ PREFIX xsd: rdfs:label "attributeDescription"@en; rdfs:range xsd:string . - + rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name used for display purposes"@en; - rdfs:domain ; - rdfs:label "defaultDisplayName"@en; + rdfs:comment "The unique identifier for a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "mapDbId"@en; rdfs:range xsd:string . @@ -6322,13 +6322,6 @@ PREFIX xsd: rdfs:label "defaultValue"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The timestamp when this variant was created."@en; @@ -6336,6 +6329,13 @@ PREFIX xsd: rdfs:label "created"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The size of the image in Bytes."@en; @@ -6375,6 +6375,9 @@ PREFIX xsd: rdfs:comment "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)."@en; rdfs:label "EnvironmentParameter"@en . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of scientist submitting the variable."@en; @@ -6382,9 +6385,6 @@ PREFIX xsd: rdfs:label "scientist"@en; rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the entity was first created"@en; @@ -6503,13 +6503,6 @@ PREFIX xsd: rdfs:label "dataType"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; - rdfs:domain ; - rdfs:label "instituteAddress"@en; - rdfs:range xsd:string . - rdf:type , , owl:NamedIndividual , . @@ -6520,6 +6513,13 @@ PREFIX xsd: rdfs:label "filtersApplied"@en; rdfs:range xsd:boolean . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; + rdfs:domain ; + rdfs:label "instituteAddress"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples."@en; diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index c775b517..4cfb3ca5 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -13543,6 +13543,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a Allele Matrix search request", @@ -14151,6 +14162,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Calls` search request", @@ -14343,6 +14365,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `CallSets` search request", @@ -14938,6 +14971,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `List` search request", @@ -15129,6 +15173,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Locations` search request", @@ -15320,6 +15375,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `MarkerPositions` search request", @@ -16117,6 +16183,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `People` search request", @@ -16713,6 +16790,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `References` search request", @@ -16905,6 +16993,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `ReferenceSets` search request", @@ -17918,6 +18017,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Variants` search request", @@ -18110,6 +18220,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `VariantSets` search request", @@ -22559,6 +22680,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Gets a list of `CallSets` associated with a `VariantSet`.", @@ -22678,6 +22810,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Gets a `Variants` for a given `VariantSet`.", diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index a1e2257c..c2453225 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -115,6 +115,8 @@ Changed response : **200** Deleted response : **202** +Deleted response : **404** + Changed response : **200** * Changed content type : `application/json` @@ -217,6 +219,8 @@ Deleted response : **404** Deleted response : **202** +Deleted response : **404** + ##### `GET` /search/locations/{searchResultsDbId} @@ -224,6 +228,8 @@ Deleted response : **202** Deleted response : **202** +Deleted response : **404** + ##### `POST` /search/markerpositions @@ -254,6 +260,8 @@ Changed response : **200** Deleted response : **202** +Deleted response : **404** + Changed response : **200** * Changed content type : `application/json` @@ -302,6 +310,8 @@ Deleted response : **404** Deleted response : **202** +Deleted response : **404** + ##### `POST` /search/plates @@ -354,6 +364,8 @@ Deleted response : **404** Deleted response : **202** +Deleted response : **404** + ##### `POST` /search/samples @@ -1609,6 +1621,8 @@ Deleted: `pageToken` in `query` Deleted response : **202** +Deleted response : **404** + Changed response : **200** * Changed content type : `application/json` @@ -1697,6 +1711,8 @@ Changed response : **200** Deleted response : **202** +Deleted response : **404** + Changed response : **200** * Changed content type : `application/json` @@ -1867,6 +1883,8 @@ Changed response : **200** Deleted response : **202** +Deleted response : **404** + Changed response : **200** * Changed content type : `application/json` @@ -1987,6 +2005,8 @@ Deleted: `pageToken` in `query` Deleted response : **202** +Deleted response : **404** + Changed response : **200** * Changed content type : `application/json` @@ -2107,6 +2127,8 @@ Changed response : **200** Deleted response : **202** +Deleted response : **404** + Changed response : **200** * Changed content type : `application/json` @@ -2789,8 +2811,6 @@ Changed response : **200** ###### Return Type: -New response : **404** - Changed response : **200** * Changed content type : `application/json` @@ -2829,8 +2849,6 @@ Changed response : **200** ###### Return Type: -New response : **404** - Changed response : **200** * Changed content type : `application/json` From f89d0d4f2da7d0914fb82be10ce0aa58ea97c161 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Wed, 13 May 2026 19:52:56 +1200 Subject: [PATCH 36/62] Add 404 response handling to various search result endpoints --- .../Observations/Search_Observations_SearchResultsDbId_GET.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Specification/BrAPI-Phenotyping/Observations/Search_Observations_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Phenotyping/Observations/Search_Observations_SearchResultsDbId_GET.yaml index 196dfbb5..a2d348a9 100644 --- a/Specification/BrAPI-Phenotyping/Observations/Search_Observations_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Phenotyping/Observations/Search_Observations_SearchResultsDbId_GET.yaml @@ -30,5 +30,7 @@ paths: $ref: '#/components/responses/401Unauthorized' '403': $ref: '#/components/responses/403Forbidden' + '404': + $ref: '#/components/responses/404NotFound' tags: - Observations From 56a8dea8b0160fe7aeb356b11e55540a706c3d4c Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Wed, 13 May 2026 19:53:19 +1200 Subject: [PATCH 37/62] Add new parameter schemas --- .../ExternalReferencesParameters.json | 48 +++++++++++++++++++ .../Requests/Parameters/PagingParameters.json | 24 ++++++++++ .../Parameters/TokenPagingParameters.json | 30 ++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 Specification/BrAPI-Schema/Requests/Parameters/ExternalReferencesParameters.json create mode 100644 Specification/BrAPI-Schema/Requests/Parameters/PagingParameters.json create mode 100644 Specification/BrAPI-Schema/Requests/Parameters/TokenPagingParameters.json diff --git a/Specification/BrAPI-Schema/Requests/Parameters/ExternalReferencesParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/ExternalReferencesParameters.json new file mode 100644 index 00000000..26bde949 --- /dev/null +++ b/Specification/BrAPI-Schema/Requests/Parameters/ExternalReferencesParameters.json @@ -0,0 +1,48 @@ +{ + "$defs": { + "ExternalReferencesParameters": { + "type": "object", + "properties": { + "externalReferenceIDs": { + "deprecated": true, + "description": "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items": { + "type": "string" + }, + "type": "array", + "example": [ + "doi:10.155454/12341234", + "14a19841" + ] + }, + "externalReferenceIds": { + "description": "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items": { + "type": "string" + }, + "type": "array", + "example": [ + "doi:10.155454/12341234", + "14a19841" + ] + }, + "externalReferenceSources": { + "description": "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "items": { + "type": "string" + }, + "type": "array", + "example": [ + "DOI", + "Field App Name" + ] + } + }, + "brapi-metadata": { + "parameters": true + } + } + }, + "$id": "https://brapi.org/Specification/BrAPI-Schema/Requests/Parameters/ExternalReferencesParameters.json", + "$schema": "http://json-schema.org/draft/2020-12/schema" +} \ No newline at end of file diff --git a/Specification/BrAPI-Schema/Requests/Parameters/PagingParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/PagingParameters.json new file mode 100644 index 00000000..7df78add --- /dev/null +++ b/Specification/BrAPI-Schema/Requests/Parameters/PagingParameters.json @@ -0,0 +1,24 @@ +{ + "$defs": { + "PagingParameters": { + "type": "object", + "properties": { + "page": { + "description": "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "type": "integer", + "example": 0 + }, + "pageSize": { + "description": "The size of the pages to be returned. Default is `1000`.", + "example": 1000, + "type": "integer" + } + }, + "brapi-metadata": { + "parameters": true + } + } + }, + "$id": "https://brapi.org/Specification/BrAPI-Schema/Requests/Parameters/PagingParameters.json", + "$schema": "http://json-schema.org/draft/2020-12/schema" +} \ No newline at end of file diff --git a/Specification/BrAPI-Schema/Requests/Parameters/TokenPagingParameters.json b/Specification/BrAPI-Schema/Requests/Parameters/TokenPagingParameters.json new file mode 100644 index 00000000..01f2ecc3 --- /dev/null +++ b/Specification/BrAPI-Schema/Requests/Parameters/TokenPagingParameters.json @@ -0,0 +1,30 @@ +{ + "$defs": { + "TokenPagingParameters": { + "type": "object", + "properties": { + "pageToken": { + "deprecated": true, + "description": "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
Used to request a specific page of data to be returned.\n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. ", + "example": "33c27874", + "type": "string" + }, + "page": { + "description": "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "type": "integer", + "example": 0 + }, + "pageSize": { + "description": "The size of the pages to be returned. Default is `1000`.", + "example": 1000, + "type": "integer" + } + }, + "brapi-metadata": { + "parameters": true + } + } + }, + "$id": "https://brapi.org/Specification/BrAPI-Schema/Requests/Parameters/TokenPagingParameters.json", + "$schema": "http://json-schema.org/draft/2020-12/schema" +} \ No newline at end of file From f9cd4d99c04c36aadfe0bdddc22a38f640d3523a Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 15 May 2026 12:40:38 +1200 Subject: [PATCH 38/62] change nullables --- .../CallSets/CallSets_GET.yaml | 1 + .../ReferenceSets/ReferenceSets_GET.yaml | 1 + .../References/References_GET.yaml | 1 + .../Variants/Schemas/Variant.yaml | 2 +- .../Variants/Variants_GET.yaml | 1 + .../Germplasm/Schemas/GermplasmMCPD.yaml | 15 + .../Pedigree/Pedigree_GET_POST_PUT.yaml | 1 + .../BrAPI-Common/ExternalReference.json | 10 +- .../BrAPI-Schema/BrAPI-Core/Location.json | 33 +- .../BrAPI-Schema/BrAPI-Core/Person.json | 13 +- .../BrAPI-Schema/BrAPI-Core/Program.json | 24 +- .../BrAPI-Schema/BrAPI-Core/Study.json | 61 +- .../BrAPI-Schema/BrAPI-Core/Trial.json | 24 +- .../BrAPI-Schema/BrAPI-Genotyping/Call.json | 31 +- .../BrAPI-Genotyping/CallSet.json | 18 +- .../BrAPI-Schema/BrAPI-Genotyping/Plate.json | 46 +- .../BrAPI-Schema/BrAPI-Genotyping/Sample.json | 79 +- .../BrAPI-Genotyping/Variant.json | 33 +- .../BrAPI-Genotyping/VariantSet.json | 18 +- .../BrAPI-Schema/BrAPI-Germplasm/Cross.json | 66 +- .../BrAPI-Germplasm/CrossingProject.json | 24 +- .../BrAPI-Germplasm/Germplasm.json | 2015 +++++++++-------- .../GermplasmAttributeValue.json | 33 +- .../BrAPI-Germplasm/PlannedCross.json | 55 +- .../BrAPI-Schema/BrAPI-Germplasm/SeedLot.json | 53 +- .../BrAPI-Germplasm/SeedLotTransaction.json | 33 +- .../BrAPI-Schema/BrAPI-Phenotyping/Event.json | 36 +- .../BrAPI-Schema/BrAPI-Phenotyping/Image.json | 31 +- .../BrAPI-Phenotyping/Observation.json | 77 +- .../BrAPI-Phenotyping/ObservationUnit.json | 117 +- .../BrAPI-Phenotyping/Ontology.json | 13 +- .../BrAPI-Schema/Requests/ListRequest.json | 9 +- .../BrAPI-Schema/Requests/SeasonRequest.json | 6 +- .../BrAPI-Schema/Requests/TrialRequest.json | 26 - 34 files changed, 1766 insertions(+), 1240 deletions(-) diff --git a/Specification/BrAPI-Genotyping/CallSets/CallSets_GET.yaml b/Specification/BrAPI-Genotyping/CallSets/CallSets_GET.yaml index 719c426d..843f2ed9 100644 --- a/Specification/BrAPI-Genotyping/CallSets/CallSets_GET.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/CallSets_GET.yaml @@ -37,6 +37,7 @@ paths: - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/page' - $ref: '#/components/parameters/pageSize' + - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' - $ref: '#/components/parameters/authorizationHeader' diff --git a/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_GET.yaml b/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_GET.yaml index 652da770..02ef274f 100644 --- a/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_GET.yaml +++ b/Specification/BrAPI-Genotyping/ReferenceSets/ReferenceSets_GET.yaml @@ -32,6 +32,7 @@ paths: - $ref: '#/components/parameters/programDbId' - $ref: '#/components/parameters/trialDbId' - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' - $ref: '#/components/parameters/page' diff --git a/Specification/BrAPI-Genotyping/References/References_GET.yaml b/Specification/BrAPI-Genotyping/References/References_GET.yaml index d8b8a986..3a050ac5 100644 --- a/Specification/BrAPI-Genotyping/References/References_GET.yaml +++ b/Specification/BrAPI-Genotyping/References/References_GET.yaml @@ -55,6 +55,7 @@ paths: - $ref: '#/components/parameters/programDbId' - $ref: '#/components/parameters/trialDbId' - $ref: '#/components/parameters/studyDbId' + - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' - $ref: '#/components/parameters/page' diff --git a/Specification/BrAPI-Genotyping/Variants/Schemas/Variant.yaml b/Specification/BrAPI-Genotyping/Variants/Schemas/Variant.yaml index 69140b1a..0b6f94e1 100644 --- a/Specification/BrAPI-Genotyping/Variants/Schemas/Variant.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Schemas/Variant.yaml @@ -148,7 +148,7 @@ components: type: string nullable: true format: date-time - variantSetDbId: + variantSetDbIds: description: An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted. type: array nullable: true diff --git a/Specification/BrAPI-Genotyping/Variants/Variants_GET.yaml b/Specification/BrAPI-Genotyping/Variants/Variants_GET.yaml index 5f683b07..6d02a326 100644 --- a/Specification/BrAPI-Genotyping/Variants/Variants_GET.yaml +++ b/Specification/BrAPI-Genotyping/Variants/Variants_GET.yaml @@ -36,6 +36,7 @@ paths: - $ref: '#/components/parameters/pageToken' - $ref: '#/components/parameters/page' - $ref: '#/components/parameters/pageSize' + - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' - $ref: '#/components/parameters/authorizationHeader' diff --git a/Specification/BrAPI-Germplasm/Germplasm/Schemas/GermplasmMCPD.yaml b/Specification/BrAPI-Germplasm/Germplasm/Schemas/GermplasmMCPD.yaml index a2ee24ce..81a97069 100644 --- a/Specification/BrAPI-Germplasm/Germplasm/Schemas/GermplasmMCPD.yaml +++ b/Specification/BrAPI-Germplasm/Germplasm/Schemas/GermplasmMCPD.yaml @@ -111,6 +111,11 @@ components: items: type: object properties: + instituteAddress: + description: MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space. + type: string + nullable: true + example: 123 Main Street, Lima, Peru, 5555 instituteCode: description: MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. type: string @@ -243,6 +248,11 @@ components:
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available. type: object properties: + instituteAddress: + description: MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space. + type: string + nullable: true + example: 123 Main Street, Lima, Peru, 5555 instituteCode: description: MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard. type: string @@ -290,6 +300,11 @@ components: safetyDuplicateInstitutes: items: properties: + instituteAddress: + description: MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space. + type: string + nullable: true + example: 123 Main Street, Lima, Peru, 5555 instituteCode: description: MCPD (v2.1) (DUPLSITE) 25. FAO WIEWS code of the institute(s) where a safety duplicate of the accession is maintained. Follows INSTCODE standard. type: string diff --git a/Specification/BrAPI-Germplasm/Pedigree/Pedigree_GET_POST_PUT.yaml b/Specification/BrAPI-Germplasm/Pedigree/Pedigree_GET_POST_PUT.yaml index b5d65d47..0584f57d 100644 --- a/Specification/BrAPI-Germplasm/Pedigree/Pedigree_GET_POST_PUT.yaml +++ b/Specification/BrAPI-Germplasm/Pedigree/Pedigree_GET_POST_PUT.yaml @@ -96,6 +96,7 @@ paths: - $ref: '#/components/parameters/germplasmDbId' - $ref: '#/components/parameters/germplasmName' - $ref: '#/components/parameters/germplasmPUI' + - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceId' - $ref: '#/components/parameters/externalReferenceSource' - $ref: '#/components/parameters/page' diff --git a/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json b/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json index 37ac18c8..f6400696 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json @@ -5,14 +5,20 @@ "referenceId": { "description": "The external reference ID. Could be a simple string or a URI.", "type": [ - "null", "string" ] }, + "referenceID": { + "description": "**Deprecated in v2.1** Please use `referenceId`. Github issue number #460
The external reference ID. Could be a simple string or a URI.", + "type": [ + "string", + "null" + ], + "deprecated": true + }, "referenceSource": { "description": "An identifier for the source system or database of this reference", "type": [ - "null", "string" ] } diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Location.json b/Specification/BrAPI-Schema/BrAPI-Core/Location.json index e05e3d8d..801b4c81 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Location.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Location.json @@ -11,8 +11,15 @@ }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "coordinateDescription": { "description": "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)", @@ -31,7 +38,14 @@ "coordinates": { "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", "relationshipType": "one-to-one", - "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON" + "anyOf": [ + { + "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON" + }, + { + "type": "null" + } + ] }, "countryCode": { "description": "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec\n
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.'", @@ -112,10 +126,17 @@ ] }, "parentLocation": { - "$ref": "Location.json#/$defs/Location", "description": "The unique identifier for a Location\n
The Parent Location defines the encompassing Location that a smaller Location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", "referencedAttribute": "childLocations", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "Location.json#/$defs/Location" + }, + { + "type": "null" + } + ] }, "childLocations": { "title": "ChildLocations", @@ -209,4 +230,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Core/Location.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Person.json b/Specification/BrAPI-Schema/BrAPI-Core/Person.json index 929ccdff..3c6b6641 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Person.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Person.json @@ -4,8 +4,15 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "description": { "description": "description of this person", @@ -122,4 +129,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Core/Person.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Program.json b/Specification/BrAPI-Schema/BrAPI-Core/Program.json index 99c0877f..82efce6d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Program.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Program.json @@ -11,8 +11,15 @@ }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "commonCropName": { "description": "Common name for the crop which this program is for", @@ -50,10 +57,17 @@ ] }, "leadPerson": { - "$ref": "Person.json#/$defs/Person", "description": "The unique identifier of the program leader", "referencedAttribute": "programs", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "Person.json#/$defs/Person" + }, + { + "type": "null" + } + ] }, "objective": { "description": "The primary objective of the program", @@ -181,4 +195,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Core/Program.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index ed3a836d..86bbda43 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -1,4 +1,4 @@ - { +{ "$defs": { "Study": { "properties": { @@ -11,8 +11,15 @@ }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "commonCropName": { "description": "Common name for the crop associated with this study", @@ -81,7 +88,14 @@ "description": "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology", "relationshipType": "one-to-one", "referencedAttribute": "study", - "$ref": "../BrAPI-Core/Study.json#/$defs/ExperimentalDesign" + "anyOf": [ + { + "$ref": "../BrAPI-Core/Study.json#/$defs/ExperimentalDesign" + }, + { + "type": "null" + } + ] }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -100,13 +114,27 @@ "description": "Short description of the facility in which the study was carried out.", "relationshipType": "many-to-one", "referencedAttribute": "study", - "$ref": "../BrAPI-Core/Study.json#/$defs/GrowthFacility" + "anyOf": [ + { + "$ref": "../BrAPI-Core/Study.json#/$defs/GrowthFacility" + }, + { + "type": "null" + } + ] }, "lastUpdate": { "description": "The date and time when this study was last modified", "relationshipType": "one-to-one", "referencedAttribute": "study", - "$ref": "../BrAPI-Core/Study.json#/$defs/LastUpdate" + "anyOf": [ + { + "$ref": "../BrAPI-Core/Study.json#/$defs/LastUpdate" + }, + { + "type": "null" + } + ] }, "license": { "description": "The usage license associated with the study data", @@ -116,10 +144,17 @@ ] }, "location": { - "$ref": "Location.json#/$defs/Location", "description": "The unique identifier for a Location", "referencedAttribute": "studies", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "Location.json#/$defs/Location" + }, + { + "type": "null" + } + ] }, "observationLevels": { "description": "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", @@ -188,7 +223,10 @@ }, "studyName": { "description": "The human readable name for a study\n\nMIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study", - "type": "string" + "type": [ + "null", + "string" + ] }, "studyPUI": { "description": "A permanent unique identifier associated with this study data. For example, a URI or DOI", @@ -324,7 +362,7 @@ } }, "EnvironmentParameter": { - "description": "An environmental parameter that was kept constant throughout the study and did not change between observation units.\n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables.", + "description": "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below).", "properties": { "description": { "description": "Human-readable value of the environment parameter (defined above) constant within the experiment", @@ -386,7 +424,6 @@ "description" ], "title": "EnvironmentParameter", - "description": "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below).", "type": "object", "brapi-metadata": { "primaryModel": false @@ -493,4 +530,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Core/Study.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json index 76ae611f..76e8a644 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json @@ -11,8 +11,15 @@ }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "commonCropName": { "description": "Common name for the crop associated with this trial", @@ -75,10 +82,17 @@ ] }, "program": { - "$ref": "Program.json#/$defs/Program", "description": "A program identifier to search for", "referencedAttribute": "trials", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "Program.json#/$defs/Program" + }, + { + "type": "null" + } + ] }, "studies": { "title": "Studies", @@ -268,4 +282,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Core/Trial.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json index f86bcf47..ebd56cec 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json @@ -23,23 +23,16 @@ }, "title": "GenotypeMetadata", "type": [ - "null", "array" ] }, "genotypeValue": { "description": "The value of this genotype call", - "type": [ - "null", - "string" - ] + "type": "string" }, "phaseSet": { "description": "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string.", - "type": [ - "null", - "string" - ] + "type": "string" }, "variant": { "$ref": "Variant.json#/$defs/Variant", @@ -78,31 +71,19 @@ "boolean", null ], - "type": [ - "null", - "string" - ] + "type": "string" }, "fieldAbbreviation": { "description": "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard.", - "type": [ - "null", - "string" - ] + "type": "string" }, "fieldName": { "description": "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard.", - "type": [ - "null", - "string" - ] + "type": "string" }, "fieldValue": { "description": "The additional metadata value associated with this genotype call", - "type": [ - "null", - "string" - ] + "type": "string" }, "call": { "description": "Genotype metadata associated with a call", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json index d6096f23..a69ce7ef 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json @@ -68,13 +68,27 @@ ] }, "sample": { - "$ref": "Sample.json#/$defs/Sample", + "anyOf": [ + { + "$ref": "Sample.json#/$defs/Sample" + }, + { + "type": "null" + } + ], "description": "The Biosample entity the call set data was generated from.", "referencedAttribute": "callSets", "relationshipType": "many-to-one" }, "study": { - "$ref": "../BrAPI-Core/Study.json#/$defs/Study", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Study.json#/$defs/Study" + }, + { + "type": "null" + } + ], "description": "The ID which uniquely identifies a study within the given database server", "referencedAttribute": "callSets", "relationshipType": "many-to-one" diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json index 41512205..d260575d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json @@ -4,8 +4,15 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -48,10 +55,17 @@ "type": "string" }, "program": { - "$ref": "../BrAPI-Core/Program.json#/$defs/Program", "description": "The ID which uniquely identifies a `Program` within the given database server", "referencedAttribute": "plates", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Program.json#/$defs/Program" + }, + { + "type": "null" + } + ] }, "sampleType": { "description": "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", @@ -68,16 +82,30 @@ ] }, "study": { - "$ref": "../BrAPI-Core/Study.json#/$defs/Study", "description": "The ID which uniquely identifies a `Study` within the given database server", "referencedAttribute": "plates", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Study.json#/$defs/Study" + }, + { + "type": "null" + } + ] }, "trial": { - "$ref": "../BrAPI-Core/Trial.json#/$defs/Trial", "description": "The ID which uniquely identifies a `Trial` within the given database server", "referencedAttribute": "plates", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Trial.json#/$defs/Trial" + }, + { + "type": "null" + } + ] }, "samples": { "title": "samples", @@ -107,4 +135,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json index 408f6d35..e2c30e52 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json @@ -4,8 +4,15 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "callSets": { "title": "CallSets", @@ -44,28 +51,56 @@ ] }, "germplasm": { - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", "description": "The ID which uniquely identifies a `Germplasm`", "referencedAttribute": "samples", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm" + }, + { + "type": "null" + } + ] }, "observationUnit": { - "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/ObservationUnit", "description": "The ID which uniquely identifies an `ObservationUnit`", "referencedAttribute": "samples", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/ObservationUnit" + }, + { + "type": "null" + } + ] }, "plate": { - "$ref": "Plate.json#/$defs/Plate", "description": "The ID which uniquely identifies a `Plate` of `Sample`", "referencedAttribute": "samples", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "Plate.json#/$defs/Plate" + }, + { + "type": "null" + } + ] }, "program": { - "$ref": "../BrAPI-Core/Program.json#/$defs/Program", "description": "The ID which uniquely identifies a `Program` within the given database server", "referencedAttribute": "samples", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Program.json#/$defs/Program" + }, + { + "type": "null" + } + ] }, "row": { "description": "The Row identifier for this `Sample` location in the `Plate`", @@ -129,10 +164,17 @@ ] }, "study": { - "$ref": "../BrAPI-Core/Study.json#/$defs/Study", "description": "The ID which uniquely identifies a `Study` within the given database server", "referencedAttribute": "samples", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Study.json#/$defs/Study" + }, + { + "type": "null" + } + ] }, "takenBy": { "description": "The name or identifier of the entity which took the `Sample` from the field", @@ -149,10 +191,17 @@ ] }, "trial": { - "$ref": "../BrAPI-Core/Trial.json#/$defs/Trial", "description": "The ID which uniquely identifies a `Trial` within the given database server", "referencedAttribute": "samples", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Trial.json#/$defs/Trial" + }, + { + "type": "null" + } + ] }, "well": { "description": "The Well identifier for this `Sample` location in the `Plate`. Usually a concatenation of Row and Column, or just a number if the `Samples` are not part of an ordered `Plate`.", @@ -175,4 +224,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json index 8c064d57..736605c7 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json @@ -132,7 +132,14 @@ ] }, "reference": { - "$ref": "Reference.json#/$defs/Reference", + "anyOf": [ + { + "$ref": "Reference.json#/$defs/Reference" + }, + { + "type": "null" + } + ], "description": "The unique identifier for a Reference", "referencedAttribute": "variants", "relationshipType": "many-to-one" @@ -145,7 +152,14 @@ ] }, "referenceSet": { - "$ref": "ReferenceSet.json#/$defs/ReferenceSet", + "anyOf": [ + { + "$ref": "ReferenceSet.json#/$defs/ReferenceSet" + }, + { + "type": "null" + } + ], "description": "The unique identifier for a ReferenceSet", "referencedAttribute": "variants", "relationshipType": "many-to-one" @@ -174,7 +188,10 @@ }, "variantDbId": { "description": "The ID which uniquely identifies a `Variant`", - "type": "string" + "type": [ + "null", + "string" + ] }, "variantNames": { "description": "A human readable name associated with a `Variant`", @@ -187,10 +204,16 @@ ] }, "variantSet": { - "$ref": "VariantSet.json#/$defs/VariantSet", + "items": { + "$ref": "VariantSet.json#/$defs/VariantSet" + }, + "type": [ + "null", + "array" + ], "description": "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted.", "referencedAttribute": "variants", - "relationshipType": "many-to-one" + "relationshipType": "many-to-many" }, "variantType": { "description": "The \"variant_type\" is used to denote e.g. structural variants.\nExamples:\n DUP : duplication of sequence following \"start\"\n DEL : deletion of sequence following \"start\"", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json index 5c454ede..3e8872c3 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json @@ -108,13 +108,27 @@ ] }, "referenceSet": { - "$ref": "ReferenceSet.json#/$defs/ReferenceSet", + "anyOf": [ + { + "$ref": "ReferenceSet.json#/$defs/ReferenceSet" + }, + { + "type": "null" + } + ], "description": "The ID of the reference set that describes the sequences used by the variants in this set.", "referencedAttribute": "variantSets", "relationshipType": "many-to-one" }, "study": { - "$ref": "../BrAPI-Core/Study.json#/$defs/Study", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Study.json#/$defs/Study" + }, + { + "type": "null" + } + ], "description": "The ID of the dataset this variant set belongs to.", "referencedAttribute": "variantSets", "relationshipType": "many-to-one" diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json index 10b88eb0..20fa2483 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json @@ -4,8 +4,15 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "crossAttributes": { "description": "Set of custom attributes associated with a cross", @@ -34,13 +41,27 @@ }, "crossType": { "description": "the type of cross", - "$ref": "CrossType.json#/$defs/CrossType" + "anyOf": [ + { + "$ref": "CrossType.json#/$defs/CrossType" + }, + { + "type": "null" + } + ] }, "crossingProject": { - "$ref": "CrossingProject.json#/$defs/CrossingProject", "description": "the unique identifier for a crossing project", "referencedAttribute": "crosses", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "CrossingProject.json#/$defs/CrossingProject" + }, + { + "type": "null" + } + ] }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -56,18 +77,39 @@ ] }, "parent1": { - "$ref": "CrossParent.json#/$defs/CrossParent", - "description": "the first parent used in the cross" + "description": "the first parent used in the cross", + "anyOf": [ + { + "$ref": "CrossParent.json#/$defs/CrossParent" + }, + { + "type": "null" + } + ] }, "parent2": { - "$ref": "CrossParent.json#/$defs/CrossParent", - "description": "the second parent used in the cross" + "description": "the second parent used in the cross", + "anyOf": [ + { + "$ref": "CrossParent.json#/$defs/CrossParent" + }, + { + "type": "null" + } + ] }, "plannedCross": { - "$ref": "PlannedCross.json#/$defs/PlannedCross", "description": "The Cross that was used in the planning of this one.", "referencedAttribute": "crosses", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "PlannedCross.json#/$defs/PlannedCross" + }, + { + "type": "null" + } + ] }, "pollinationEvents": { "description": "The list of pollination events that occurred for this cross.", @@ -179,4 +221,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json index b8ad3b7a..69f4d513 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json @@ -4,8 +4,15 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "commonCropName": { "description": "the common name of a crop (for multi-crop systems)", @@ -53,10 +60,17 @@ ] }, "program": { - "$ref": "../BrAPI-Core/Program.json#/$defs/Program", "description": "the unique identifier for a program", "referencedAttribute": "crossingProjects", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Program.json#/$defs/Program" + }, + { + "type": "null" + } + ] }, "crosses": { "title": "crosses", @@ -115,4 +129,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index a792ec25..a033ac36 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -1,1021 +1,1026 @@ { - "$defs": { - "Germplasm": { - "properties": { - "accessionNumber": { - "description": "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", - "type": [ - "null", - "string" - ] - }, - "acquisitionDate": { - "description": "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", - "type": [ - "null", - "string" - ] - }, - "additionalInfo": { - "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" - }, - "biologicalStatusOfAccessionCode": { - "description": "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", - "enum": [ - "100", - "110", - "120", - "130", - "200", - "300", - "400", - "410", - "411", - "412", - "413", - "414", - "415", - "416", - "420", - "421", - "422", - "423", - "500", - "600", - "999", - null - ], - "type": [ - "null", - "string" - ] - }, - "biologicalStatusOfAccessionDescription": { - "description": "Supplemental text description for 'biologicalStatusOfAccessionCode'", - "type": [ - "null", - "string" - ] - }, - "breedingMethod": { - "$ref": "BreedingMethod.json#/$defs/BreedingMethod", - "description": "The unique identifier for the breeding method used to create this germplasm", - "referencedAttribute": "germplasm", - "relationshipType": "many-to-one" - }, - "collection": { - "description": "A specific panel/collection/population name this germplasm belongs to.", - "type": [ - "null", - "string" - ] - }, - "commonCropName": { - "description": "Common name for the crop \n\nMCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\".", - "type": "string" - }, - "countryOfOriginCode": { - "description": "3-letter ISO 3166-1 code of the country in which the sample was originally collected \n\nMCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", - "type": [ - "null", - "string" - ] - }, - "defaultDisplayName": { - "description": "Human readable name used for display purposes", - "type": [ - "null", - "string" - ] - }, - "documentationURL": { - "description": "A URL to the human readable documentation of an object", - "format": "uri", - "type": [ - "null", - "string" - ] - }, - "donors": { - "description": "List of donor institutes", - "relationshipType": "one-to-many", - "referencedAttribute": "germplasm", - "items": { - "$ref": "Germplasm.json#/$defs/Donor", - "description": "Donors" - }, - "title": "Donors", - "type": [ - "null", - "array" - ] - }, - "externalReferences": { - "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "relationshipType": "one-to-many", - "items": { - "$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference", - "description": "ExternalReferences" - }, - "title": "ExternalReferences", - "type": [ - "null", - "array" - ] - }, - "genus": { - "description": "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature.", - "type": [ - "null", - "string" - ] - }, - "germplasmDbId": { - "description": "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", - "type": "string" - }, - "germplasmName": { - "description": "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space.", - "type": "string" - }, - "germplasmOrigin": { - "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", - "relationshipType": "one-to-many", - "referencedAttribute": "germplasm", - "items": { - "$ref": "Germplasm.json#/$defs/GermplasmOrigin", - "description": "GermplasmOrigin" - }, - "title": "GermplasmOrigin", - "type": [ - "null", - "array" - ] - }, - "germplasmPUI": { - "description": "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties.", - "type": "string" - }, - "germplasmPreprocessing": { - "description": "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary.", - "type": [ - "null", - "string" - ] - }, - "instituteCode": { - "description": "The code for the institute that maintains the material. \n\nMCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", - "type": [ - "null", - "string" - ] - }, - "instituteName": { - "description": "The name of the institute that maintains the material", - "type": [ - "null", - "string" - ] - }, - "mcpd": { - "deprecated": true, - "$ref": "Germplasm.json#/$defs/GermplasmMCPD", - "description": "The mulit-crop passport descriptors (MCPD) for this germplasm", - "referencedAttribute": "germplasm", - "relationshipType": "one-to-one" - }, - "pedigree": { - "description": "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", - "type": [ - "null", - "string" - ] - }, - "seedSource": { - "description": "An identifier for the source of the biological material\n
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: \"mother_accession X father_accession\", or, if father is unknown, as \"mother_accession X UNKNOWN\". For in situ material, the region of provenance may be used when an accession is not available.", - "type": [ - "null", - "string" - ] - }, - "seedSourceDescription": { - "description": "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source", - "type": [ - "null", - "string" - ] - }, - "species": { - "description": "Specific epithet portion of the scientific name in lowercase letters.\n\nMCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" \n\nMIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature.", - "type": [ - "null", - "string" - ] - }, - "speciesAuthority": { - "description": "The authority organization responsible for tracking and maintaining the species name \n\nMCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", - "type": [ - "null", - "string" - ] - }, - "storageTypes": { - "description": "The type of storage this germplasm is kept in at a genebank.", - "relationshipType": "one-to-many", - "referencedAttribute": "germplasm", - "items": { - "$ref": "Germplasm.json#/$defs/StorageType", - "description": "StorageTypes" - }, - "title": "StorageTypes", - "type": [ - "null", - "array" - ] - }, - "subtaxa": { - "description": "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group).", - "type": [ - "null", - "string" - ] - }, - "subtaxaAuthority": { - "description": "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", - "type": [ - "null", - "string" - ] - }, - "synonyms": { - "description": "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon.", - "relationshipType": "one-to-many", - "items": { - "$ref": "Germplasm.json#/$defs/Synonym", - "description": "Synonyms" - }, - "title": "Synonyms", - "type": [ - "null", - "array" - ] - }, - "taxonIds": { - "description": "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species.\n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.", - "relationshipType": "one-to-many", - "referencedAttribute": "germplasm", - "items": { - "$ref": "Germplasm.json#/$defs/TaxonId", - "description": "TaxonIds" - }, - "type": [ - "null", - "array" - ] - }, - "samples": { - "title": "samples", - "description": "samples", - "referencedAttribute": "germplasm", - "relationshipType": "one-to-many", - "items": { - "$ref": "../BrAPI-Genotyping/Sample.json#/$defs/Sample", - "description": "Sample" - }, - "type": [ - "null", - "array" - ] - }, - "attributeValues": { - "title": "attributeValues", - "description": "attributeValues", - "referencedAttribute": "germplasm", - "relationshipType": "one-to-many", - "items": { - "$ref": "GermplasmAttributeValue.json#/$defs/GermplasmAttributeValue", - "description": "GermplasmAttributeValue" - }, - "type": [ - "null", - "array" - ] - }, - "progenyPedigreeNodes": { - "title": "progenyPedigreeNodes", - "description": "progenyPedigreeNodes", - "relationshipType": "one-to-many", - "items": { - "$ref": "PedigreeNode.json#/$defs/PedigreeNode", - "description": "PedigreeNode" - }, - "type": [ - "null", - "array" - ] - }, - "parentPedigreeNodes": { - "title": "parentPedigreeNodes", - "description": "parentPedigreeNodes", - "relationshipType": "one-to-many", - "items": { - "$ref": "PedigreeNode.json#/$defs/PedigreeNode", - "description": "PedigreeNode" - }, - "type": [ - "null", - "array" - ] - }, - "siblingPedigreeNodes": { - "title": "SiblingPedigreeNodes", - "description": "siblingPedigreeNodes", - "relationshipType": "one-to-many", - "items": { - "$ref": "PedigreeNode.json#/$defs/PedigreeNode", - "description": "PedigreeNode" - }, - "type": [ - "null", - "array" - ] - }, - "observations": { - "title": "observations", - "description": "observations", - "referencedAttribute": "germplasm", - "relationshipType": "one-to-many", - "items": { - "$ref": "../BrAPI-Phenotyping/Observation.json#/$defs/Observation", - "description": "Observation" - }, - "type": [ - "null", - "array" - ] - }, - "observationUnits": { - "title": "observationUnits", - "description": "observationUnits", - "referencedAttribute": "germplasm", - "relationshipType": "one-to-many", - "items": { - "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/ObservationUnit", - "description": "ObservationUnit" - }, - "type": [ - "null", - "array" - ] - }, - "reference": { - "description": "Germplasm associated with a reference", - "$ref": "../BrAPI-Genotyping/Reference.json#/$defs/Reference", - "relationshipType": "many-to-one", - "referencedAttribute": "sourceGermplasm" - }, - "referenceSet": { - "description": "Germplasm associated with a reference", - "$ref": "../BrAPI-Genotyping/ReferenceSet.json#/$defs/ReferenceSet", - "relationshipType": "many-to-one", - "referencedAttribute": "sourceGermplasm" - } - }, - "required": [ - "germplasmName", - "germplasmDbId", - "germplasmPUI", - "commonCropName" - ], - "title": "Germplasm", - "description": "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy.", - "type": "object", - "brapi-metadata": { - "primaryModel": true - } - }, - "GermplasmMCPD": { - "deprecated": true, - "properties": { - "accessionNames": { - "description": "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered names or other designations given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase.", - "items": { - "type": "string" - }, - "type": [ - "null", - "array" - ], - "examples": [ - "Symphony", - "Emma" - ] - }, - "accessionNumber": { - "description": "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", - "type": [ - "null", - "string" - ], - "example": "A0000003" - }, - "acquisitionDate": { - "description": "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", - "type": [ - "null", - "string" - ], - "format": "date" - }, - "acquisitionSourceCode": { - "description": "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)", - "enum": [ - "10", - "11", - "12", - "13", - "14", - "15", - "20", - "21", - "22", - "23", - "24", - "25", - "26", - "27", - "28", - "30", - "40", - "50", - "60", - "61", - "62", - "99" - ], - "type": [ - "null", - "string" - ], - "example": "26" - }, - "alternateIDs": { - "description": "MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. ", - "items": { - "type": "string" - }, - "type": [ - "null", - "array" - ], - "examples": [ - "PER001:3", - "PER001:http://pui.per/accession/A0000003", - "USA001:A0000003" - ] - }, - "ancestralData": { - "description": "MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", - "type": [ - "null", - "string" - ], - "example": "A0000001/A0000002" - }, - "biologicalStatusOfAccessionCode": { - "description": "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", - "enum": [ - "100", - "110", - "120", - "130", - "200", - "300", - "400", - "410", - "411", - "412", - "413", - "414", - "415", - "416", - "420", - "421", - "422", - "423", - "500", - "600", - "999" - ], - "type": [ - "null", - "string" - ], - "example": "421" - }, - "breedingInstitutes": { - "description": "A list of institutes that were involved with breeding a material/germplasm\n
MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard.\n
MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available.", - "type": [ - "null", - "array" - ], - "items": { - "$ref": "Germplasm.json#/$defs/Institute" - } - }, - "collectingInfo": { - "description": "Information about the collection of a germplasm", - "title": "CollectingInfo", - "properties": { - "collectingDate": { - "description": "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", - "type": [ - "null", - "string" - ], - "format": "date" + "$defs": { + "Germplasm": { + "properties": { + "accessionNumber": { + "description": "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "type": [ + "null", + "string" + ] + }, + "acquisitionDate": { + "description": "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "type": [ + "null", + "string" + ] + }, + "additionalInfo": { + "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] + }, + "biologicalStatusOfAccessionCode": { + "description": "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "enum": [ + "100", + "110", + "120", + "130", + "200", + "300", + "400", + "410", + "411", + "412", + "413", + "414", + "415", + "416", + "420", + "421", + "422", + "423", + "500", + "600", + "999", + null + ], + "type": [ + "null", + "string" + ] + }, + "biologicalStatusOfAccessionDescription": { + "description": "Supplemental text description for 'biologicalStatusOfAccessionCode'", + "type": [ + "null", + "string" + ] + }, + "breedingMethod": { + "description": "The unique identifier for the breeding method used to create this germplasm", + "referencedAttribute": "germplasm", + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "BreedingMethod.json#/$defs/BreedingMethod" + }, + { + "type": "null" + } + ] + }, + "collection": { + "description": "A specific panel/collection/population name this germplasm belongs to.", + "type": [ + "null", + "string" + ] + }, + "commonCropName": { + "description": "Common name for the crop \n\nMCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\".", + "type": "string" + }, + "countryOfOriginCode": { + "description": "3-letter ISO 3166-1 code of the country in which the sample was originally collected \n\nMCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", + "type": [ + "null", + "string" + ] + }, + "defaultDisplayName": { + "description": "Human readable name used for display purposes", + "type": [ + "null", + "string" + ] + }, + "documentationURL": { + "description": "A URL to the human readable documentation of an object", + "format": "uri", + "type": [ + "null", + "string" + ] + }, + "donors": { + "description": "List of donor institutes", + "relationshipType": "one-to-many", + "referencedAttribute": "germplasm", + "items": { + "$ref": "Germplasm.json#/$defs/Donor", + "description": "Donors" + }, + "title": "Donors", + "type": [ + "null", + "array" + ] + }, + "externalReferences": { + "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", + "relationshipType": "one-to-many", + "items": { + "$ref": "../BrAPI-Common/ExternalReference.json#/$defs/ExternalReference", + "description": "ExternalReferences" + }, + "title": "ExternalReferences", + "type": [ + "null", + "array" + ] + }, + "genus": { + "description": "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature.", + "type": [ + "null", + "string" + ] + }, + "germplasmDbId": { + "description": "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", + "type": "string" + }, + "germplasmName": { + "description": "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space.", + "type": "string" + }, + "germplasmOrigin": { + "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", + "relationshipType": "one-to-many", + "referencedAttribute": "germplasm", + "items": { + "$ref": "Germplasm.json#/$defs/GermplasmOrigin", + "description": "GermplasmOrigin" + }, + "title": "GermplasmOrigin", + "type": [ + "null", + "array" + ] + }, + "germplasmPUI": { + "description": "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties.", + "type": "string" + }, + "germplasmPreprocessing": { + "description": "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary.", + "type": [ + "null", + "string" + ] + }, + "instituteCode": { + "description": "The code for the institute that maintains the material. \n\nMCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "type": [ + "null", + "string" + ] + }, + "instituteName": { + "description": "The name of the institute that maintains the material", + "type": [ + "null", + "string" + ] + }, + "mcpd": { + "deprecated": true, + "$ref": "Germplasm.json#/$defs/GermplasmMCPD", + "description": "The mulit-crop passport descriptors (MCPD) for this germplasm", + "referencedAttribute": "germplasm", + "relationshipType": "one-to-one" + }, + "pedigree": { + "description": "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", + "type": [ + "null", + "string" + ] + }, + "seedSource": { + "description": "An identifier for the source of the biological material\n
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: \"mother_accession X father_accession\", or, if father is unknown, as \"mother_accession X UNKNOWN\". For in situ material, the region of provenance may be used when an accession is not available.", + "type": [ + "null", + "string" + ] + }, + "seedSourceDescription": { + "description": "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source", + "type": [ + "null", + "string" + ] + }, + "species": { + "description": "Specific epithet portion of the scientific name in lowercase letters.\n\nMCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" \n\nMIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature.", + "type": [ + "null", + "string" + ] + }, + "speciesAuthority": { + "description": "The authority organization responsible for tracking and maintaining the species name \n\nMCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", + "type": [ + "null", + "string" + ] + }, + "storageTypes": { + "description": "The type of storage this germplasm is kept in at a genebank.", + "relationshipType": "one-to-many", + "referencedAttribute": "germplasm", + "items": { + "$ref": "Germplasm.json#/$defs/StorageType", + "description": "StorageTypes" + }, + "title": "StorageTypes", + "type": [ + "null", + "array" + ] + }, + "subtaxa": { + "description": "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group).", + "type": [ + "null", + "string" + ] + }, + "subtaxaAuthority": { + "description": "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", + "type": [ + "null", + "string" + ] + }, + "synonyms": { + "description": "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon.", + "relationshipType": "one-to-many", + "items": { + "$ref": "Germplasm.json#/$defs/Synonym", + "description": "Synonyms" + }, + "title": "Synonyms", + "type": [ + "null", + "array" + ] + }, + "taxonIds": { + "description": "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species.\n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.", + "relationshipType": "one-to-many", + "referencedAttribute": "germplasm", + "items": { + "$ref": "Germplasm.json#/$defs/TaxonId", + "description": "TaxonIds" + }, + "type": [ + "null", + "array" + ] + }, + "samples": { + "title": "samples", + "description": "samples", + "referencedAttribute": "germplasm", + "relationshipType": "one-to-many", + "items": { + "$ref": "../BrAPI-Genotyping/Sample.json#/$defs/Sample", + "description": "Sample" + }, + "type": [ + "null", + "array" + ] + }, + "attributeValues": { + "title": "attributeValues", + "description": "attributeValues", + "referencedAttribute": "germplasm", + "relationshipType": "one-to-many", + "items": { + "$ref": "GermplasmAttributeValue.json#/$defs/GermplasmAttributeValue", + "description": "GermplasmAttributeValue" + }, + "type": [ + "null", + "array" + ] + }, + "progenyPedigreeNodes": { + "title": "progenyPedigreeNodes", + "description": "progenyPedigreeNodes", + "relationshipType": "one-to-many", + "items": { + "$ref": "PedigreeNode.json#/$defs/PedigreeNode", + "description": "PedigreeNode" + }, + "type": [ + "null", + "array" + ] + }, + "parentPedigreeNodes": { + "title": "parentPedigreeNodes", + "description": "parentPedigreeNodes", + "relationshipType": "one-to-many", + "items": { + "$ref": "PedigreeNode.json#/$defs/PedigreeNode", + "description": "PedigreeNode" + }, + "type": [ + "null", + "array" + ] + }, + "siblingPedigreeNodes": { + "title": "SiblingPedigreeNodes", + "description": "siblingPedigreeNodes", + "relationshipType": "one-to-many", + "items": { + "$ref": "PedigreeNode.json#/$defs/PedigreeNode", + "description": "PedigreeNode" + }, + "type": [ + "null", + "array" + ] + }, + "observations": { + "title": "observations", + "description": "observations", + "referencedAttribute": "germplasm", + "relationshipType": "one-to-many", + "items": { + "$ref": "../BrAPI-Phenotyping/Observation.json#/$defs/Observation", + "description": "Observation" + }, + "type": [ + "null", + "array" + ] + }, + "observationUnits": { + "title": "observationUnits", + "description": "observationUnits", + "referencedAttribute": "germplasm", + "relationshipType": "one-to-many", + "items": { + "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/ObservationUnit", + "description": "ObservationUnit" + }, + "type": [ + "null", + "array" + ] + }, + "reference": { + "description": "Germplasm associated with a reference", + "$ref": "../BrAPI-Genotyping/Reference.json#/$defs/Reference", + "relationshipType": "many-to-one", + "referencedAttribute": "sourceGermplasm" + }, + "referenceSet": { + "description": "Germplasm associated with a reference", + "$ref": "../BrAPI-Genotyping/ReferenceSet.json#/$defs/ReferenceSet", + "relationshipType": "many-to-one", + "referencedAttribute": "sourceGermplasm" + } }, - "collectingInstitutes": { - "description": "Institutes which collected the sample", - "type": [ - "null", - "array" - ], - "items": { - "$ref": "Germplasm.json#/$defs/Institute" - } + "required": [ + "germplasmName", + "germplasmDbId", + "germplasmPUI", + "commonCropName" + ], + "title": "Germplasm", + "description": "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy.", + "type": "object", + "brapi-metadata": { + "primaryModel": true + } + }, + "GermplasmMCPD": { + "deprecated": true, + "properties": { + "accessionNames": { + "description": "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered names or other designations given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase.", + "items": { + "type": "string" + }, + "type": [ + "null", + "array" + ], + "examples": [ + "Symphony", + "Emma" + ] + }, + "accessionNumber": { + "description": "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "type": [ + "null", + "string" + ], + "example": "A0000003" + }, + "acquisitionDate": { + "description": "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "type": [ + "null", + "string" + ], + "format": "date" + }, + "acquisitionSourceCode": { + "description": "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)", + "enum": [ + "10", + "11", + "12", + "13", + "14", + "15", + "20", + "21", + "22", + "23", + "24", + "25", + "26", + "27", + "28", + "30", + "40", + "50", + "60", + "61", + "62", + "99" + ], + "type": [ + "null", + "string" + ], + "example": "26" + }, + "alternateIDs": { + "description": "MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. ", + "items": { + "type": "string" + }, + "type": [ + "null", + "array" + ], + "examples": [ + "PER001:3", + "PER001:http://pui.per/accession/A0000003", + "USA001:A0000003" + ] + }, + "ancestralData": { + "description": "MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", + "type": [ + "null", + "string" + ], + "example": "A0000001/A0000002" + }, + "biologicalStatusOfAccessionCode": { + "description": "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "enum": [ + "100", + "110", + "120", + "130", + "200", + "300", + "400", + "410", + "411", + "412", + "413", + "414", + "415", + "416", + "420", + "421", + "422", + "423", + "500", + "600", + "999" + ], + "type": [ + "null", + "string" + ], + "example": "421" + }, + "breedingInstitutes": { + "description": "A list of institutes that were involved with breeding a material/germplasm\n
MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard.\n
MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available.", + "type": [ + "null", + "array" + ], + "items": { + "$ref": "Germplasm.json#/$defs/Institute" + } + }, + "collectingInfo": { + "description": "Information about the collection of a germplasm", + "title": "CollectingInfo", + "properties": { + "collectingDate": { + "description": "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero].", + "type": [ + "null", + "string" + ], + "format": "date" + }, + "collectingInstitutes": { + "description": "Institutes which collected the sample", + "type": [ + "null", + "array" + ], + "items": { + "$ref": "Germplasm.json#/$defs/Institute" + } + }, + "collectingMissionIdentifier": { + "description": "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\").", + "type": [ + "null", + "string" + ], + "example": "CIATFOR_052" + }, + "collectingNumber": { + "description": "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections.", + "type": [ + "null", + "string" + ], + "example": "ab109909" + }, + "collectingSite": { + "description": "Information about the location where the sample was collected", + "properties": { + "coordinateUncertainty": { + "description": "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown.", + "type": [ + "null", + "string" + ], + "example": "20" + }, + "elevation": { + "description": "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed.", + "type": [ + "null", + "string" + ], + "example": "35" + }, + "georeferencingMethod": { + "description": "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known.", + "type": [ + "null", + "string" + ], + "example": "WGS84" + }, + "latitudeDecimal": { + "description": "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975).", + "type": [ + "null", + "string" + ], + "example": "+42.445295" + }, + "latitudeDegrees": { + "description": "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10", + "type": [ + "null", + "string" + ], + "example": "42 26 43.1 N" + }, + "locationDescription": { + "description": "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville).", + "type": [ + "null", + "string" + ], + "example": "South east hill near institute buildings" + }, + "longitudeDecimal": { + "description": "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123).", + "type": [ + "null", + "string" + ], + "example": "-076.471934" + }, + "longitudeDegrees": { + "description": "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076", + "type": [ + "null", + "string" + ], + "example": "76 28 19.0 W" + }, + "spatialReferenceSystem": { + "description": "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum.", + "type": [ + "null", + "string" + ], + "example": "WGS84" + } + }, + "type": [ + "null", + "object" + ] + } + }, + "type": "object" + }, + "commonCropName": { + "description": "MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\". ", + "type": [ + "null", + "string" + ], + "example": "malting barley" + }, + "countryOfOrigin": { + "description": "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers\" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", + "type": [ + "null", + "string" + ], + "example": "Peru" + }, + "donorInfo": { + "type": "object", + "description": "Information about an accession donor", + "properties": { + "donorAccessionPui": { + "description": "PUI (DOI mostly) of the accession in the donor system.", + "type": [ + "null", + "string" + ], + "example": "http://pui.per/accession/A0010025" + }, + "donorAccessionNumber": { + "description": "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", + "type": [ + "null", + "string" + ], + "example": "A0090204" + }, + "donorInstitute": { + "description": "The identifying information for the entity acting as an accession donor\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.\n
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.", + "$ref": "Germplasm.json#/$defs/Institute" + } + } + }, + "genus": { + "description": "MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.", + "type": [ + "null", + "string" + ], + "example": "Aspergillus" + }, + "germplasm": { + "description": "donors associated with a germplasm", + "$ref": "Germplasm.json#/$defs/Germplasm", + "relationshipType": "one-to-one", + "referencedAttribute": "mcpd" + }, + "instituteCode": { + "description": "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "type": [ + "null", + "string" + ], + "example": "PER001" + }, + "mlsStatus": { + "description": "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")", + "enum": [ + "", + "0", + "1", + "99" + ], + "type": [ + "null", + "string" + ], + "example": "0" + }, + "remarks": { + "description": "MCPD (v2.1) (REMARKS) 28. The remarks field is used to add notes or to elaborate on descriptors with value 99 or 999 (= Other). Prefix remarks with the field name they refer to and a colon (:) without space (e.g. COLLSRC:riverside). Distinct remarks referring to different fields are separated by semi-colons without space.", + "type": [ + "null", + "string" + ], + "example": "This is an example remark to demonstrate that any notable information can be put here" + }, + "safetyDuplicateInstitutes": { + "items": { + "$ref": "Germplasm.json#/$defs/Institute" + }, + "type": [ + "null", + "array" + ] + }, + "species": { + "description": "MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" ", + "type": [ + "null", + "string" + ], + "example": "fructus" + }, + "speciesAuthority": { + "description": "MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", + "type": [ + "null", + "string" + ], + "example": "Smith, 1822" + }, + "storageTypeCodes": { + "description": "MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) 10) Seed collection 11) Short term 12) Medium term 13) Long term 20) Field collection 30) In vitro collection 40) Cryo-preserved collection 50) DNA collection 99) Other (elaborate in REMARKS field)", + "items": { + "enum": [ + "10", + "11", + "12", + "13", + "20", + "30", + "40", + "50", + "99" + ], + "type": "string" + }, + "type": [ + "null", + "array" + ], + "examples": [ + "11", + "13" + ] + }, + "subtaxon": { + "description": "MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").", + "type": [ + "null", + "string" + ], + "example": "Aspergillus fructus A" + }, + "subtaxonAuthority": { + "description": "MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", + "type": [ + "null", + "string" + ], + "example": "Smith, 1822" + } }, - "collectingMissionIdentifier": { - "description": "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\").", - "type": [ - "null", - "string" - ], - "example": "CIATFOR_052" + "title": "GermplasmMCPD", + "description": "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } + }, + "Institute": { + "properties": { + "instituteAddress": { + "description": "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "type": [ + "null", + "string" + ], + "example": "123 Main Street, Lima, Peru, 5555" + }, + "instituteCode": { + "description": "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space.", + "type": [ + "null", + "string" + ], + "example": "PER001" + }, + "instituteName": { + "description": "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "type": [ + "null", + "string" + ], + "example": "The BrAPI Institute" + } }, - "collectingNumber": { - "description": "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections.", - "type": [ - "null", - "string" - ], - "example": "ab109909" + "title": "Institute", + "description": "The details of an Institute or other simular entity.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } + }, + "Donor": { + "properties": { + "donorAccessionNumber": { + "description": "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", + "type": [ + "null", + "string" + ] + }, + "donorInstituteCode": { + "description": "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", + "type": [ + "null", + "string" + ] + }, + "germplasm": { + "description": "donors associated with a germplasm", + "$ref": "Germplasm.json#/$defs/Germplasm", + "relationshipType": "many-to-one", + "referencedAttribute": "donors" + } }, - "collectingSite": { - "description": "Information about the location where the sample was collected", - "properties": { + "title": "Donor", + "description": "Identifier assigned to an accession by the material donor.", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } + }, + "GermplasmOrigin": { + "properties": { "coordinateUncertainty": { - "description": "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown.", - "type": [ - "null", - "string" - ], - "example": "20" - }, - "elevation": { - "description": "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed.", - "type": [ - "null", - "string" - ], - "example": "35" - }, - "georeferencingMethod": { - "description": "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known.", - "type": [ - "null", - "string" - ], - "example": "WGS84" - }, - "latitudeDecimal": { - "description": "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975).", - "type": [ - "null", - "string" - ], - "example": "+42.445295" - }, - "latitudeDegrees": { - "description": "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10", - "type": [ - "null", - "string" - ], - "example": "42 26 43.1 N" - }, - "locationDescription": { - "description": "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville).", - "type": [ - "null", - "string" - ], - "example": "South east hill near institute buildings" - }, - "longitudeDecimal": { - "description": "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123).", - "type": [ - "null", - "string" - ], - "example": "-076.471934" - }, - "longitudeDegrees": { - "description": "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076", - "type": [ - "null", - "string" - ], - "example": "76 28 19.0 W" - }, - "spatialReferenceSystem": { - "description": "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum.", - "type": [ - "null", - "string" - ], - "example": "WGS84" + "description": "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.", + "type": [ + "null", + "string" + ] + }, + "coordinates": { + "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "anyOf": [ + { + "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON" + }, + { + "type": "null" + } + ] + }, + "germplasm": { + "description": "associated germplasm", + "$ref": "Germplasm.json#/$defs/Germplasm", + "relationshipType": "many-to-one", + "referencedAttribute": "germplasmOrigin" } - }, - "type": [ - "null", - "object" - ] + }, + "title": "GermplasmOrigin", + "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", + "type": "object", + "brapi-metadata": { + "primaryModel": false } - }, - "type": "object" - }, - "commonCropName": { - "description": "MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\". ", - "type": [ - "null", - "string" - ], - "example": "malting barley" }, - "countryOfOrigin": { - "description": "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers\" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\".", - "type": [ - "null", - "string" - ], - "example": "Peru" - }, - "donorInfo": { - "type": "object", - "description": "Information about an accession donor", - "properties": { - "donorAccessionPui": { - "description": "PUI (DOI mostly) of the accession in the donor system.", - "type": [ - "null", - "string" - ], - "example": "http://pui.per/accession/A0010025" - }, - "donorAccessionNumber": { - "description": "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", - "type": [ - "null", - "string" - ], - "example": "A0090204" + "StorageType": { + "properties": { + "code": { + "description": "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", + "enum": [ + "10", + "11", + "12", + "13", + "20", + "30", + "40", + "50", + "99", + null + ], + "type": [ + "null", + "string" + ], + "title": "StorageTypeCode" + }, + "description": { + "description": "A supplemental text description of the storage type", + "type": [ + "null", + "string" + ] + }, + "germplasm": { + "description": "associated germplasm", + "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", + "relationshipType": "many-to-one", + "referencedAttribute": "storageTypes" + } }, - "donorInstitute": { - "description": "The identifying information for the entity acting as an accession donor\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.\n
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.", - "$ref": "Germplasm.json#/$defs/Institute" + "title": "StorageType", + "description": "The type of storage this germplasm is kept in at a genebank.", + "type": "object", + "brapi-metadata": { + "primaryModel": false } - } - }, - "genus": { - "description": "MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.", - "type": [ - "null", - "string" - ], - "example": "Aspergillus" - }, - "germplasm": { - "description": "donors associated with a germplasm", - "$ref": "Germplasm.json#/$defs/Germplasm", - "relationshipType": "one-to-one", - "referencedAttribute": "mcpd" - }, - "instituteCode": { - "description": "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", - "type": [ - "null", - "string" - ], - "example": "PER001" }, - "mlsStatus": { - "description": "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")", - "enum": [ - "", - "0", - "1", - "99" - ], - "type": [ - "null", - "string" - ], - "example": "0" - }, - "remarks": { - "description": "MCPD (v2.1) (REMARKS) 28. The remarks field is used to add notes or to elaborate on descriptors with value 99 or 999 (= Other). Prefix remarks with the field name they refer to and a colon (:) without space (e.g. COLLSRC:riverside). Distinct remarks referring to different fields are separated by semi-colons without space.", - "type": [ - "null", - "string" - ], - "example": "This is an example remark to demonstrate that any notable information can be put here" - }, - "safetyDuplicateInstitutes": { - "items": { - "$ref": "Germplasm.json#/$defs/Institute" - }, - "type": [ - "null", - "array" - ] - }, - "species": { - "description": "MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" ", - "type": [ - "null", - "string" - ], - "example": "fructus" - }, - "speciesAuthority": { - "description": "MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name.", - "type": [ - "null", - "string" - ], - "example": "Smith, 1822" + "Synonym": { + "description": "Alternative names or IDs used to reference this germplasm", + "properties": { + "synonym": { + "description": "Alternative name or ID used to reference this germplasm", + "type": [ + "null", + "string" + ] + }, + "type": { + "description": "A descriptive classification for this synonym", + "type": [ + "null", + "string" + ] + }, + "germplasm": { + "description": "associated germplasm", + "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", + "relationshipType": "many-to-one", + "referencedAttribute": "synonyms" + } + }, + "title": "Synonym", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } }, - "storageTypeCodes": { - "description": "MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) 10) Seed collection 11) Short term 12) Medium term 13) Long term 20) Field collection 30) In vitro collection 40) Cryo-preserved collection 50) DNA collection 99) Other (elaborate in REMARKS field)", - "items": { - "enum": [ - "10", - "11", - "12", - "13", - "20", - "30", - "40", - "50", - "99" + "TaxonId": { + "description": "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.", + "properties": { + "taxonId": { + "description": "The identifier (name, ID, URI) of a particular taxonomy within the source provider", + "type": "string" + }, + "sourceName": { + "description": "The human readable name of the taxonomy provider", + "type": "string" + }, + "germplasm": { + "description": "associated germplasm", + "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", + "relationshipType": "many-to-one", + "referencedAttribute": "taxonIds" + } + }, + "required": [ + "sourceName", + "taxonId" ], - "type": "string" - }, - "type": [ - "null", - "array" - ], - "examples": [ - "11", - "13" - ] - }, - "subtaxon": { - "description": "MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").", - "type": [ - "null", - "string" - ], - "example": "Aspergillus fructus A" - }, - "subtaxonAuthority": { - "description": "MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level.", - "type": [ - "null", - "string" - ], - "example": "Smith, 1822" - } - }, - "required": [ - "germplasm", - "commonCropName" - ], - "title": "GermplasmMCPD", - "description": "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy.", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } - }, - "Institute": { - "properties": { - "instituteAddress": { - "description": "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", - "type": [ - "null", - "string" - ], - "example": "123 Main Street, Lima, Peru, 5555" - }, - "instituteCode": { - "description": "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space.", - "type": [ - "null", - "string" - ], - "example": "PER001" - }, - "instituteName": { - "description": "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", - "type": [ - "null", - "string" - ], - "example": "The BrAPI Institute" - } - }, - "title": "Institute", - "description": "The details of an Institute or other simular entity.", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } - }, - "Donor": { - "properties": { - "donorAccessionNumber": { - "description": "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", - "type": [ - "null", - "string" - ] - }, - "donorInstituteCode": { - "description": "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", - "type": [ - "null", - "string" - ] - }, - "germplasm": { - "description": "donors associated with a germplasm", - "$ref": "Germplasm.json#/$defs/Germplasm", - "relationshipType": "many-to-one", - "referencedAttribute": "donors" - } - }, - "title": "Donor", - "description": "Identifier assigned to an accession by the material donor.", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } - }, - "GermplasmOrigin": { - "properties": { - "coordinateUncertainty": { - "description": "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown.", - "type": [ - "null", - "string" - ] - }, - "coordinates": { - "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", - "relationshipType": "one-to-many", - "referencedAttribute": "germplasmOrigin", - "items": { - "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON", - "description": "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed." - }, - "title": "GeoJSON", - "type": [ - "null", - "array" - ] - }, - "germplasm": { - "description": "associated germplasm", - "$ref": "Germplasm.json#/$defs/Germplasm", - "relationshipType": "many-to-one", - "referencedAttribute": "germplasmOrigin" - } - }, - "title": "GermplasmOrigin", - "description": "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm.", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } - }, - "StorageType": { - "properties": { - "code": { - "description": "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", - "enum": [ - "10", - "11", - "12", - "13", - "20", - "30", - "40", - "50", - "99", - null - ], - "type": [ - "null", - "string" - ], - "title": "StorageTypeCode" - }, - "description": { - "description": "A supplemental text description of the storage type", - "type": [ - "null", - "string" - ] - }, - "germplasm": { - "description": "associated germplasm", - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", - "relationshipType": "many-to-one", - "referencedAttribute": "storageTypes" - } - }, - "title": "StorageType", - "description": "The type of storage this germplasm is kept in at a genebank.", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } - }, - "Synonym": { - "description": "Alternative way to refer to a Germplasm, Cultivar of Variety", - "properties": { - "synonym": { - "description": "Alternative name or ID used to reference this germplasm", - "type": [ - "null", - "string" - ] - }, - "type": { - "description": "A descriptive classification for this synonym", - "type": [ - "null", - "string" - ] - }, - "germplasm": { - "description": "associated germplasm", - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", - "relationshipType": "many-to-one", - "referencedAttribute": "synonyms" + "title": "TaxonId", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } } - }, - "title": "Synonym", - "description": "Alternative names or IDs used to reference this germplasm", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } }, - "TaxonId": { - "description": "The Taxon of the Germplasm", - "properties": { - "taxonId": { - "description": "The identifier (name, ID, URI) of a particular taxonomy within the source provider", - "type": "string" - }, - "sourceName": { - "description": "The human readable name of the taxonomy provider", - "type": "string" - }, - "germplasm": { - "description": "associated germplasm", - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", - "relationshipType": "many-to-one", - "referencedAttribute": "taxonIds" - } - }, - "required": [ - "sourceName", - "taxonId" - ], - "title": "TaxonId", - "description": "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended.", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } - } - }, - "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json", - "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file + "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json", + "$schema": "http://json-schema.org/draft/2020-12/schema" +} diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json index c5ba60cf..d1ee0dbb 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json @@ -5,13 +5,27 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "relationshipType": "one-to-one", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "attribute": { - "$ref": "GermplasmAttribute.json#/$defs/GermplasmAttribute", "description": "The ID which uniquely identifies this attribute within the given database server", "referencedAttribute": "attributeValues", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "GermplasmAttribute.json#/$defs/GermplasmAttribute" + }, + { + "type": "null" + } + ] }, "attributeValueDbId": { "description": "The ID which uniquely identifies this attribute value within the given database server", @@ -39,10 +53,17 @@ ] }, "germplasm": { - "$ref": "Germplasm.json#/$defs/Germplasm", "description": "The ID which uniquely identifies a germplasm within the given database server", "referencedAttribute": "attributeValues", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "Germplasm.json#/$defs/Germplasm" + }, + { + "type": "null" + } + ] }, "value": { "description": "The value of this attribute for a given germplasm", @@ -65,4 +86,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json index 900996ce..1f4efa1d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json @@ -4,18 +4,39 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "crossType": { "description": "the type of cross", - "$ref": "CrossType.json#/$defs/CrossType" + "anyOf": [ + { + "$ref": "CrossType.json#/$defs/CrossType" + }, + { + "type": "null" + } + ] }, "crossingProject": { - "$ref": "CrossingProject.json#/$defs/CrossingProject", "description": "the unique identifier for a crossing project", "referencedAttribute": "plannedCrosses", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "CrossingProject.json#/$defs/CrossingProject" + }, + { + "type": "null" + } + ] }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -31,12 +52,26 @@ ] }, "parent1": { - "$ref": "CrossParent.json#/$defs/CrossParent", - "description": "the first parent used in the cross" + "description": "the first parent used in the cross", + "anyOf": [ + { + "$ref": "CrossParent.json#/$defs/CrossParent" + }, + { + "type": "null" + } + ] }, "parent2": { - "$ref": "CrossParent.json#/$defs/CrossParent", - "description": "the second parent used in the cross" + "description": "the second parent used in the cross", + "anyOf": [ + { + "$ref": "CrossParent.json#/$defs/CrossParent" + }, + { + "type": "null" + } + ] }, "plannedCrossDbId": { "description": "the unique identifier for a planned cross", @@ -91,4 +126,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json index 8a040568..b80b4969 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json @@ -4,8 +4,15 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "amount": { "description": "The current balance of the amount of material in a SeedLot. Could be a count (seeds, bulbs, etc) or a weight (kg of seed).", @@ -58,16 +65,30 @@ ] }, "location": { - "$ref": "../BrAPI-Core/Location.json#/$defs/Location", "description": "The unique identifier for a Location", "referencedAttribute": "seedLots", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Location.json#/$defs/Location" + }, + { + "type": "null" + } + ] }, "program": { - "$ref": "../BrAPI-Core/Program.json#/$defs/Program", "description": "The unique DbId of the breeding program this Seed Lot belongs to", "referencedAttribute": "seedLots", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Program.json#/$defs/Program" + }, + { + "type": "null" + } + ] }, "seedLotDbId": { "description": "Unique DbId for the Seed Lot", @@ -147,12 +168,26 @@ "ContentMixture": { "properties": { "cross": { - "$ref": "Cross.json#/$defs/Cross", + "anyOf": [ + { + "$ref": "Cross.json#/$defs/Cross" + }, + { + "type": "null" + } + ], "description": "The cross for the germplasm using in this content mixture", "relationshipType": "many-to-one" }, "germplasm": { - "$ref": "Germplasm.json#/$defs/Germplasm", + "anyOf": [ + { + "$ref": "Germplasm.json#/$defs/Germplasm" + }, + { + "type": "null" + } + ], "description": "The germplasm using in this content mixture", "relationshipType": "many-to-one" }, @@ -180,4 +215,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json index a1b03084..ff553b85 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json @@ -5,7 +5,14 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "relationshipType": "one-to-one", - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + "anyOf": [ + { + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" + }, + { + "type": "null" + } + ] }, "amount": { "description": "The number of units being transferred between SeedLots. Could be a count (seeds, bulbs, etc) or a weight (kg of seed).", @@ -28,14 +35,28 @@ ] }, "fromSeedLot": { - "$ref": "SeedLot.json#/$defs/SeedLot", "description": "The identifier for the Seed Lot being transferred out of", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "SeedLot.json#/$defs/SeedLot" + }, + { + "type": "null" + } + ] }, "toSeedLot": { - "$ref": "SeedLot.json#/$defs/SeedLot", "description": "The identifier for the Seed Lot being transferred into", - "relationshipType": "many-to-one" + "relationshipType": "many-to-one", + "anyOf": [ + { + "$ref": "SeedLot.json#/$defs/SeedLot" + }, + { + "type": "null" + } + ] }, "transactionDbId": { "description": "Unique DbId for the Seed Lot Transaction", @@ -77,4 +98,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json index 1f61935f..44fbf5a7 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json @@ -9,16 +9,13 @@ }, "eventDateRange": { "description": "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)", - "relationshipType": "one-to-many", - "referencedAttribute": "event", - "items": { - "$ref": "../BrAPI-Phenotyping/Event.json#/$defs/EventDateRange", - "description": "EventDateRange" - }, - "title": "EventDateRange", - "type": [ - "null", - "array" + "anyOf": [ + { + "$ref": "../BrAPI-Phenotyping/Event.json#/$defs/EventDateRange" + }, + { + "type": "null" + } ] }, "eventDbId": { @@ -48,10 +45,7 @@ }, "eventType": { "description": "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology).", - "type": [ - "null", - "string" - ] + "type": "string" }, "eventTypeDbId": { "description": "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology).", @@ -174,6 +168,20 @@ "string" ] }, + "key": { + "deprecated": true, + "description": "**Deprecated in v2.1** Please use `name`. Github issue number #440 \n
Specifies the relationship between the event and the given property. E.g. fertilizer, operator", + "type": "string", + "nullable": true, + "example": "operator" + }, + "rdfValue": { + "deprecated": true, + "description": "**Deprecated in v2.1** Please use `code`. Github issue number #440 \n Date: Fri, 15 May 2026 12:44:06 +1200 Subject: [PATCH 39/62] change non-nullable for external refs --- .../BrAPI-Schema/BrAPI-Common/Variable.json | 11 ++++------- Specification/BrAPI-Schema/BrAPI-Core/List.json | 9 +++------ .../BrAPI-Schema/BrAPI-Core/Location.json | 5 +---- Specification/BrAPI-Schema/BrAPI-Core/Person.json | 5 +---- .../BrAPI-Schema/BrAPI-Core/Program.json | 5 +---- Specification/BrAPI-Schema/BrAPI-Core/Study.json | 5 +---- Specification/BrAPI-Schema/BrAPI-Core/Trial.json | 5 +---- .../BrAPI-Schema/BrAPI-Genotyping/CallSet.json | 9 +++------ .../BrAPI-Schema/BrAPI-Genotyping/Plate.json | 5 +---- .../BrAPI-Schema/BrAPI-Genotyping/Reference.json | 11 ++++------- .../BrAPI-Genotyping/ReferenceSet.json | 15 ++++++--------- .../BrAPI-Schema/BrAPI-Genotyping/Sample.json | 5 +---- .../BrAPI-Schema/BrAPI-Genotyping/Variant.json | 9 +++------ .../BrAPI-Schema/BrAPI-Genotyping/VariantSet.json | 9 +++------ .../BrAPI-Schema/BrAPI-Germplasm/Cross.json | 5 +---- .../BrAPI-Germplasm/CrossingProject.json | 5 +---- .../BrAPI-Schema/BrAPI-Germplasm/Germplasm.json | 5 +---- .../BrAPI-Germplasm/GermplasmAttributeValue.json | 5 +---- .../BrAPI-Germplasm/PedigreeNode.json | 9 +++------ .../BrAPI-Germplasm/PlannedCross.json | 5 +---- .../BrAPI-Schema/BrAPI-Germplasm/SeedLot.json | 5 +---- .../BrAPI-Germplasm/SeedLotTransaction.json | 5 +---- .../BrAPI-Schema/BrAPI-Phenotyping/Image.json | 5 +---- .../BrAPI-Schema/BrAPI-Phenotyping/Method.json | 9 +++------ .../BrAPI-Phenotyping/Observation.json | 5 +---- .../BrAPI-Phenotyping/ObservationUnit.json | 5 +---- .../BrAPI-Schema/BrAPI-Phenotyping/Scale.json | 15 +++++---------- .../BrAPI-Schema/BrAPI-Phenotyping/Trait.json | 9 +++------ 28 files changed, 57 insertions(+), 143 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json index a8bd778a..f814886f 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json @@ -5,7 +5,7 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one" }, "commonCropName": { "description": "Crop name (examples: \"Maize\", \"Wheat\")", @@ -47,10 +47,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "growthStage": { "description": "Growth stage at which measurement is made (examples: \"flowering\")", @@ -75,7 +72,7 @@ }, "method": { "description": "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". ", - "relationshipType": "one-to-one", + "relationshipType": "one-to-one", "$ref": "../BrAPI-Phenotyping/Method.json#/$defs/Method" }, "ontologyReference": { @@ -141,4 +138,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/Variable.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Core/List.json b/Specification/BrAPI-Schema/BrAPI-Core/List.json index 78806be7..b75270ec 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/List.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/List.json @@ -5,7 +5,7 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one" }, "data": { "description": "The array of DbIds of the BrAPI objects contained in a List", @@ -42,10 +42,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "listDbId": { "description": "The unique identifier for a List", @@ -112,4 +109,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Core/List.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Location.json b/Specification/BrAPI-Schema/BrAPI-Core/Location.json index 801b4c81..43ce5824 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Location.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Location.json @@ -91,10 +91,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "instituteAddress": { "description": "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Person.json b/Specification/BrAPI-Schema/BrAPI-Core/Person.json index 3c6b6641..b9879db2 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Person.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Person.json @@ -36,10 +36,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "firstName": { "description": "Persons first name", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Program.json b/Specification/BrAPI-Schema/BrAPI-Core/Program.json index 82efce6d..25b8f012 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Program.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Program.json @@ -44,10 +44,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "fundingInformation": { "description": "Information describing the grant or funding source for this program", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index 86bbda43..842a02dd 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -105,10 +105,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "growthFacility": { "description": "Short description of the facility in which the study was carried out.", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json index 76e8a644..82bc818d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json @@ -76,10 +76,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "program": { "description": "A program identifier to search for", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json index a69ce7ef..10993bbd 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json @@ -5,7 +5,7 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one" }, "alleleMatrices": { "title": "AlleleMatrices", @@ -62,10 +62,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "sample": { "anyOf": [ @@ -124,4 +121,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json index d260575d..0d8563ab 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json @@ -22,10 +22,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "plateBarcode": { "description": "A unique identifier physically attached to a `Plate`", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json index f6f7dcc2..a423a065 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json @@ -5,7 +5,7 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one" }, "commonCropName": { "description": "Common name for the crop", @@ -27,10 +27,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "isDerived": { "description": "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", @@ -109,7 +106,7 @@ "description": "An ontology term describing an attribute.", "relationshipType": "one-to-one", "referencedAttribute": "reference", - "$ref": "../BrAPI-Common/OntologyTerm.json#/$defs/OntologyTerm" + "$ref": "../BrAPI-Common/OntologyTerm.json#/$defs/OntologyTerm" }, "variants": { "title": "variants", @@ -174,4 +171,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json index 16650470..addf018d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json @@ -5,7 +5,7 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one" }, "assemblyPUI": { "description": "The remaining information is about the source of the sequences Public id of this reference set, such as `GRCH_37`.", @@ -36,10 +36,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "isDerived": { "description": "A reference set may be derived from a source if it contains additional sequences, or some of the sequences within it are derived (see the definition of `isDerived` in `Reference`).", @@ -94,18 +91,18 @@ "string" ] }, - "species": { + "species": { "description": "An ontology term describing an attribute.", "relationshipType": "one-to-one", "referencedAttribute": "referenceSet", - "$ref": "../BrAPI-Common/OntologyTerm.json#/$defs/OntologyTerm" + "$ref": "../BrAPI-Common/OntologyTerm.json#/$defs/OntologyTerm" }, "references": { "title": "references", "description": "references", "referencedAttribute": "referenceSet", "relationshipType": "one-to-one", - "$ref": "Reference.json#/$defs/Reference" + "$ref": "Reference.json#/$defs/Reference" }, "variants": { "title": "variants", @@ -150,4 +147,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json index e2c30e52..5f75c92f 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json @@ -45,10 +45,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "germplasm": { "description": "The ID which uniquely identifies a `Germplasm`", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json index 736605c7..abd58af8 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json @@ -5,7 +5,7 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one" }, "markerPositions": { "title": "markerPositions", @@ -102,10 +102,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "filtersApplied": { "description": "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value.", @@ -236,4 +233,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json index 3e8872c3..2aa3efe2 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json @@ -5,7 +5,7 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one" }, "alleleMatrices": { "title": "AlleleMatrices", @@ -90,10 +90,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "metadataFields": { "description": "The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard ", @@ -378,4 +375,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json index 20fa2483..19d2420c 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json @@ -71,10 +71,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "parent1": { "description": "the first parent used in the cross", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json index 69f4d513..66d780d7 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json @@ -44,10 +44,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "potentialParents": { "description": "A list of all the potential parents in the crossing block, available in the crossing project\n
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object.", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index a033ac36..d9e1a195 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -134,10 +134,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "genus": { "description": "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature.", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json index d1ee0dbb..e81ea55d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json @@ -47,10 +47,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "germplasm": { "description": "The ID which uniquely identifies a germplasm within the given database server", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json index 7f41b3fe..3b54ef90 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json @@ -41,10 +41,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "familyCode": { "description": "The code representing the family of this germplasm", @@ -72,7 +69,7 @@ "array" ] }, - "pedigreeNodeDbId": { + "pedigreeNodeDbId": { "description": "The ID which uniquely identifies a pedigree node", "type": [ "null", @@ -187,4 +184,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json index 1f4efa1d..c088395d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json @@ -46,10 +46,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "parent1": { "description": "the first parent used in the cross", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json index b80b4969..8fc6e028 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json @@ -51,10 +51,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "lastUpdated": { "description": "The timestamp for the last update to this Seed Lot (including transactions)", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json index ff553b85..6dde7d1f 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json @@ -29,10 +29,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "fromSeedLot": { "description": "The identifier for the Seed Lot being transferred out of", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json index d2077ec5..6a7da613 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json @@ -45,10 +45,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "imageContent": { "description": "The content of the image", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json index 12b70fb7..b3e1fe10 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json @@ -5,7 +5,7 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one" }, "bibliographicalReference": { "description": "Bibliographical reference describing the method.\n
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method.", @@ -29,10 +29,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "formula": { "description": "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation", @@ -86,4 +83,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json index e38eaa2a..b9ffdc2d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json @@ -29,10 +29,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "geoCoordinates": { "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json index cd97eb2e..323b64c9 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json @@ -35,10 +35,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "germplasm": { "description": "The ID which uniquely identifies a germplasm", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json index 9cc0342c..001c9a94 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json @@ -5,7 +5,7 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one" }, "dataType": { "description": "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", @@ -39,10 +39,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "ontologyReference": { "description": "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", @@ -94,7 +91,7 @@ } }, "ValidValues": { - "description": "Defines the valid values for a Scale, which can be restricted to a list of categorical values, or a minimum and/or a maximum value.", + "description": "Metadata describing the acceptable values for this Scale", "properties": { "categories": { "description": "List of possible values with optional labels", @@ -132,14 +129,13 @@ } }, "title": "ValidValues", - "description": "Metadata describing the acceptable values for this Scale", "type": "object", "brapi-metadata": { "primaryModel": false } }, "ValidValuesCategory": { - "description": "A categorical value for a Scale.", + "description": "If the Scale is a categorical type, these objects define the valid options", "properties": { "label": { "description": "A text label for a category", @@ -163,7 +159,6 @@ } }, "title": "ValidValuesCategory", - "description": "If the Scale is a categorical type, these objects define the valid options", "type": "object", "brapi-metadata": { "primaryModel": false @@ -172,4 +167,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json index 10d25d49..6b967065 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json @@ -5,7 +5,7 @@ "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", - "relationshipType": "one-to-one" + "relationshipType": "one-to-one" }, "alternativeAbbreviations": { "description": "A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention.", @@ -53,10 +53,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "mainAbbreviation": { "description": "A shortened version of the human readable name for a Trait", @@ -133,4 +130,4 @@ }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json", "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file +} From 1dcccdfbd178cbbb7eca3e521284f075794255c1 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 15 May 2026 18:22:17 +1200 Subject: [PATCH 40/62] change non-nullable for external refs --- .../CallSets/Schemas/CallSet.yaml | 1 - .../BrAPI-Common/AdditionalInfo.json | 1 + .../BrAPI-Schema/BrAPI-Common/Variable.json | 5 +- .../BrAPI-Schema/BrAPI-Core/List.json | 5 +- .../BrAPI-Schema/BrAPI-Core/Location.json | 16 +++---- .../BrAPI-Schema/BrAPI-Core/Person.json | 16 +++---- .../BrAPI-Schema/BrAPI-Core/Program.json | 16 +++---- .../BrAPI-Schema/BrAPI-Core/Study.json | 16 +++---- .../BrAPI-Schema/BrAPI-Core/Trial.json | 16 +++---- .../BrAPI-Genotyping/AlleleMatrix.json | 5 +- .../BrAPI-Genotyping/CallSet.json | 5 +- .../BrAPI-Schema/BrAPI-Genotyping/Plate.json | 16 +++---- .../BrAPI-Genotyping/Reference.json | 5 +- .../BrAPI-Genotyping/ReferenceSet.json | 5 +- .../BrAPI-Schema/BrAPI-Genotyping/Sample.json | 16 +++---- .../BrAPI-Genotyping/Variant.json | 5 +- .../BrAPI-Genotyping/VariantSet.json | 5 +- .../BrAPI-Schema/BrAPI-Germplasm/Cross.json | 47 +++++-------------- .../BrAPI-Germplasm/CrossType.json | 3 +- .../BrAPI-Germplasm/CrossingProject.json | 16 +++---- .../BrAPI-Germplasm/Germplasm.json | 16 +++---- .../GermplasmAttributeValue.json | 16 +++---- .../BrAPI-Germplasm/ParentType.json | 3 +- .../BrAPI-Germplasm/PedigreeNode.json | 5 +- .../BrAPI-Germplasm/PlannedCross.json | 16 +++---- .../BrAPI-Schema/BrAPI-Germplasm/SeedLot.json | 16 +++---- .../BrAPI-Germplasm/SeedLotTransaction.json | 16 +++---- .../BrAPI-Schema/BrAPI-Phenotyping/Image.json | 15 +++--- .../BrAPI-Phenotyping/Method.json | 5 +- .../BrAPI-Phenotyping/Observation.json | 16 +++---- .../BrAPI-Phenotyping/ObservationUnit.json | 16 +++---- .../BrAPI-Phenotyping/Ontology.json | 11 +---- .../BrAPI-Schema/BrAPI-Phenotyping/Scale.json | 5 +- .../BrAPI-Schema/BrAPI-Phenotyping/Trait.json | 5 +- 34 files changed, 161 insertions(+), 220 deletions(-) diff --git a/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSet.yaml b/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSet.yaml index 4e6026dc..9e0d1f7c 100644 --- a/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSet.yaml +++ b/Specification/BrAPI-Genotyping/CallSets/Schemas/CallSet.yaml @@ -23,7 +23,6 @@ components: nullable: true externalReferences: $ref: '#/components/schemas/ExternalReferences' - nullable: true sampleDbId: description: The Biosample entity the call set data was generated from. type: string diff --git a/Specification/BrAPI-Schema/BrAPI-Common/AdditionalInfo.json b/Specification/BrAPI-Schema/BrAPI-Common/AdditionalInfo.json index b4bab73e..73acfa8d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/AdditionalInfo.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/AdditionalInfo.json @@ -1,6 +1,7 @@ { "$defs": { "AdditionalInfo": { + "nullable": true, "additionalProperties": { "description": "A free space containing any additional information related to a particular object.", "type": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json index f814886f..59e0a822 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json @@ -47,7 +47,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "growthStage": { "description": "Growth stage at which measurement is made (examples: \"flowering\")", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/List.json b/Specification/BrAPI-Schema/BrAPI-Core/List.json index b75270ec..3bec2ab1 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/List.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/List.json @@ -42,7 +42,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "listDbId": { "description": "The unique identifier for a List", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Location.json b/Specification/BrAPI-Schema/BrAPI-Core/Location.json index 43ce5824..ab5f1cb8 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Location.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Location.json @@ -11,15 +11,8 @@ }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "coordinateDescription": { "description": "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)", @@ -91,7 +84,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "instituteAddress": { "description": "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Person.json b/Specification/BrAPI-Schema/BrAPI-Core/Person.json index b9879db2..9b561fea 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Person.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Person.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "description": { "description": "description of this person", @@ -36,7 +29,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "firstName": { "description": "Persons first name", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Program.json b/Specification/BrAPI-Schema/BrAPI-Core/Program.json index 25b8f012..130c4604 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Program.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Program.json @@ -11,15 +11,8 @@ }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "commonCropName": { "description": "Common name for the crop which this program is for", @@ -44,7 +37,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "fundingInformation": { "description": "Information describing the grant or funding source for this program", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index 842a02dd..92e4e735 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -11,15 +11,8 @@ }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "commonCropName": { "description": "Common name for the crop associated with this study", @@ -105,7 +98,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "growthFacility": { "description": "Short description of the facility in which the study was carried out.", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json index 82bc818d..0c08e91d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json @@ -11,15 +11,8 @@ }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "commonCropName": { "description": "Common name for the crop associated with this trial", @@ -76,7 +69,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "program": { "description": "A program identifier to search for", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json index 87ed0582..d3d4ee97 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json @@ -83,7 +83,10 @@ }, "referencedAttribute": "alleleMatrices", "relationshipType": "many-to-many", - "type": "array" + "type": [ + "null", + "array" + ] } }, "required": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json index 10993bbd..ca811dc4 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json @@ -62,7 +62,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "sample": { "anyOf": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json index 0d8563ab..4aa88513 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Plate.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "externalReferences": { "description": "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -22,7 +15,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "plateBarcode": { "description": "A unique identifier physically attached to a `Plate`", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json index a423a065..74f78810 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json @@ -27,7 +27,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "isDerived": { "description": "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json index addf018d..fc6fb133 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json @@ -36,7 +36,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "isDerived": { "description": "A reference set may be derived from a source if it contains additional sequences, or some of the sequences within it are derived (see the definition of `isDerived` in `Reference`).", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json index 5f75c92f..e1474253 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "callSets": { "title": "CallSets", @@ -45,7 +38,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "germplasm": { "description": "The ID which uniquely identifies a `Germplasm`", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json index abd58af8..9a681b97 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json @@ -102,7 +102,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "filtersApplied": { "description": "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value.", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json index 2aa3efe2..b2987c88 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json @@ -90,7 +90,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "metadataFields": { "description": "The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard ", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json index 19d2420c..4544ce5b 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "crossAttributes": { "description": "Set of custom attributes associated with a cross", @@ -41,14 +34,7 @@ }, "crossType": { "description": "the type of cross", - "anyOf": [ - { - "$ref": "CrossType.json#/$defs/CrossType" - }, - { - "type": "null" - } - ] + "$ref": "CrossType.json#/$defs/CrossType" }, "crossingProject": { "description": "the unique identifier for a crossing project", @@ -71,29 +57,18 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "parent1": { - "description": "the first parent used in the cross", - "anyOf": [ - { - "$ref": "CrossParent.json#/$defs/CrossParent" - }, - { - "type": "null" - } - ] + "$ref": "CrossParent.json#/$defs/CrossParent", + "description": "the first parent used in the cross" }, "parent2": { - "description": "the second parent used in the cross", - "anyOf": [ - { - "$ref": "CrossParent.json#/$defs/CrossParent" - }, - { - "type": "null" - } - ] + "$ref": "CrossParent.json#/$defs/CrossParent", + "description": "the second parent used in the cross" }, "plannedCross": { "description": "The Cross that was used in the planning of this one.", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json index a971b749..000f55ee 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json @@ -11,7 +11,8 @@ "BULK_OPEN_POLLINATED", "DOUBLE_HAPLOID" ], - "type": "string" + "type": "string", + "nullable": true } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossType.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json index 66d780d7..580aa041 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossingProject.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "commonCropName": { "description": "the common name of a crop (for multi-crop systems)", @@ -44,7 +37,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "potentialParents": { "description": "A list of all the potential parents in the crossing block, available in the crossing project\n
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object.", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index d9e1a195..8e690ca5 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -18,15 +18,8 @@ }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "biologicalStatusOfAccessionCode": { "description": "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", @@ -134,7 +127,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "genus": { "description": "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature.", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json index e81ea55d..3b0ae156 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttributeValue.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "attribute": { "description": "The ID which uniquely identifies this attribute within the given database server", @@ -47,7 +40,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "germplasm": { "description": "The ID which uniquely identifies a germplasm within the given database server", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/ParentType.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/ParentType.json index 4651dca7..e3e0a490 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/ParentType.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/ParentType.json @@ -6,8 +6,7 @@ "MALE", "FEMALE", "SELF", - "POPULATION", - "CLONAL" + "POPULATION" ], "type": "string" } diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json index 3b54ef90..c20173d4 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json @@ -41,7 +41,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "familyCode": { "description": "The code representing the family of this germplasm", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json index c088395d..d03674f1 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "crossType": { "description": "the type of cross", @@ -46,7 +39,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "parent1": { "description": "the first parent used in the cross", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json index 8fc6e028..412956a2 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "amount": { "description": "The current balance of the amount of material in a SeedLot. Could be a count (seeds, bulbs, etc) or a weight (kg of seed).", @@ -51,7 +44,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "lastUpdated": { "description": "The timestamp for the last update to this Seed Lot (including transactions)", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json index 6dde7d1f..c124d11d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "amount": { "description": "The number of units being transferred between SeedLots. Could be a count (seeds, bulbs, etc) or a weight (kg of seed).", @@ -29,7 +22,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "fromSeedLot": { "description": "The identifier for the Seed Lot being transferred out of", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json index 6a7da613..613a1642 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json @@ -4,14 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "copyright": { "description": "The copyright information of this image. Example 'Copyright 2018 Bob Robertson'", @@ -45,7 +39,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "imageContent": { "description": "The content of the image", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json index b3e1fe10..e7ccea2e 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Method.json @@ -29,7 +29,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "formula": { "description": "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json index b9ffdc2d..f877913a 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "collector": { "description": "The name or identifier of the entity which collected the observation", @@ -29,7 +22,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "geoCoordinates": { "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json index 323b64c9..e6e3bda3 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "cross": { "description": "the unique identifier for a cross", @@ -35,7 +28,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "germplasm": { "description": "The ID which uniquely identifies a germplasm", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json index f6a4e098..fe2fe699 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Ontology.json @@ -4,15 +4,8 @@ "properties": { "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", + "relationshipType": "one-to-one" }, "authors": { "description": "Ontology's list of authors (no specific format)", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json index 001c9a94..f4b72da5 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json @@ -39,7 +39,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "ontologyReference": { "description": "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json index 6b967065..a3c2e200 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Trait.json @@ -53,7 +53,10 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": "array" + "type": [ + "null", + "array" + ] }, "mainAbbreviation": { "description": "A shortened version of the human readable name for a Trait", From e2a92e2545f0abc4df99410ca2aa69231ebf8f69 Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Fri, 15 May 2026 06:26:12 +0000 Subject: [PATCH 41/62] Generate specifications (manually triggered) --- Specification/Generated/BrAPI-Core.yaml | 183 +- Specification/Generated/BrAPI-Genotyping.yaml | 159 +- Specification/Generated/BrAPI-Germplasm.yaml | 153 +- .../Generated/BrAPI-Phenotyping.yaml | 178 +- .../Generated/brapi_generated.graphqls | 55 +- Specification/Generated/brapi_generated.json | 604 +++---- Specification/Generated/brapi_generated.ttl | 796 ++++----- Specification/Generated/brapi_openapi.json | 86 +- .../Generated/brapi_openapi_comparison.md | 1478 ++++------------- 9 files changed, 1577 insertions(+), 2115 deletions(-) diff --git a/Specification/Generated/BrAPI-Core.yaml b/Specification/Generated/BrAPI-Core.yaml index b560e8d6..f466fad5 100644 --- a/Specification/Generated/BrAPI-Core.yaml +++ b/Specification/Generated/BrAPI-Core.yaml @@ -485,10 +485,11 @@ paths: type: string - name: year in: query - description: The 4 digit year of a season. Example "2017" + description: The 4 digit year of a season. Example 2017 required: false schema: - type: string + type: integer + format: int32 - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" - $ref: "#/components/parameters/authorizationHeader" @@ -787,33 +788,6 @@ paths: required: false schema: type: string - - name: sortBy - in: query - description: Name of the field to sort by. - required: false - schema: - type: string - description: Name of the field to sort by. - enum: - - trialDbId - - trialName - - programDbId - - programName - - locationDbId - - startDate - - endDate - - name: sortOrder - in: query - description: Sort order direction. Ascending/Descending. - required: false - schema: - type: string - description: Sort order direction. Ascending/Descending. - enum: - - asc - - ASC - - desc - - DESC - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" @@ -2606,14 +2580,41 @@ components: ExternalReference: type: object properties: + referenceID: + type: string + description: "**Deprecated in v2.1** Please use `referenceId`. Github issue\ + \ number #460
The external reference ID. Could be a simple string\ + \ or a URI." + nullable: true referenceId: type: string description: The external reference ID. Could be a simple string or a URI. - nullable: true referenceSource: type: string description: An identifier for the source system or database of this reference - nullable: true + ExternalReferencesParameters: + type: object + properties: + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string GenomeMapRequest: type: object properties: @@ -3782,8 +3783,10 @@ components: nullable: true locationDbId: type: string + nullable: true locationName: type: string + nullable: true locationType: type: string description: "A short description of a type of Location (ex. Field Station,\ @@ -4764,6 +4767,20 @@ components: schema or its resource implementation. nullable: true description: A pointer to an ontology used by a genomic reference + PagingParameters: + type: object + properties: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 PedigreeNodeRequest: type: object properties: @@ -5369,6 +5386,7 @@ components: nullable: true personDbId: type: string + nullable: true programName: type: string description: Human readable name of the program @@ -5999,9 +6017,10 @@ components: type: string years: type: array - description: The 4 digit year of a season. Example "2017" + description: The 4 digit year of a season. Example 2017 items: - type: string + type: integer + format: int32 SeedLotRequest: type: object properties: @@ -6169,8 +6188,10 @@ components: nullable: true locationDbId: type: string + nullable: true locationName: type: string + nullable: true observationLevels: type: array description: "Observation levels indicate the granularity level at which\ @@ -6221,6 +6242,7 @@ components: The human readable name for a study MIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study + nullable: true studyPUI: type: string description: "A permanent unique identifier associated with this study data.\ @@ -6545,6 +6567,29 @@ components: location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies. + TokenPagingParameters: + type: object + properties: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + pageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
Used to request a specific page of data to be returned.\n\ +
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken from\ + \ a prior response to construct a query and move to the next or previous\ + \ page respectively. " + example: 33c27874 TraitDataType: type: string description: |- @@ -6676,8 +6721,10 @@ components: $ref: "#/components/schemas/ExternalReference" programDbId: type: string + nullable: true programName: type: string + nullable: true publications: type: array description: MIAPPE V1.1 (DM-9) Associated publication - An identifier for @@ -6764,22 +6811,6 @@ components: description: A human readable names to search for items: type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -6820,25 +6851,6 @@ components: \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ \ is before `trial.endDate`" format: date - sortBy: - type: string - description: Name of the field to sort by. - enum: - - trialDbId - - trialName - - programDbId - - programName - - locationDbId - - startDate - - endDate - sortOrder: - type: string - description: Sort order direction. Ascending/Descending. - enum: - - asc - - ASC - - desc - - DESC studyDbIds: type: array description: List of study identifiers to search for @@ -6922,12 +6934,6 @@ components: \ on a server." items: type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string trialDbIds: type: array description: The ID which uniquely identifies a trial to search for @@ -6949,40 +6955,11 @@ components: formatted identifier. items: type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string studyNames: type: array description: List of study names to filter search results items: type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - sortOrder: - type: string - description: Sort order direction. Ascending/Descending. - enum: - - asc - - ASC - - desc - - DESC - sortBy: - type: string - description: Name of the field to sort by. - enum: - - trialDbId - - trialName - - programDbId - - programName - - locationDbId - - startDate - - endDate contactDbIds: type: array description: List of contact entities associated with this trial diff --git a/Specification/Generated/BrAPI-Genotyping.yaml b/Specification/Generated/BrAPI-Genotyping.yaml index 1a314080..93734846 100644 --- a/Specification/Generated/BrAPI-Genotyping.yaml +++ b/Specification/Generated/BrAPI-Genotyping.yaml @@ -2622,19 +2622,16 @@ components: type: array description: Genotype Metadata are additional layers of metadata associated with each genotype. - nullable: true items: $ref: "#/components/schemas/GenotypeMetadata" genotypeValue: type: string description: The value of this genotype call - nullable: true phaseSet: type: string description: "If this field is populated, this variant call's genotype ordering\ \ implies the phase of the bases and \nis consistent with any other variant\ \ calls on the same contig which have the same phase set string." - nullable: true variantDbId: type: string variantSetDbId: @@ -2772,16 +2769,22 @@ components: $ref: "#/components/schemas/ExternalReference" sampleDbId: type: string + nullable: true sampleName: type: string + nullable: true samplePUI: type: string + nullable: true studyDbId: type: string + nullable: true studyName: type: string + nullable: true studyPUI: type: string + nullable: true updated: type: string description: The time at which this call set was last updated @@ -3228,14 +3231,41 @@ components: ExternalReference: type: object properties: + referenceID: + type: string + description: "**Deprecated in v2.1** Please use `referenceId`. Github issue\ + \ number #460
The external reference ID. Could be a simple string\ + \ or a URI." + nullable: true referenceId: type: string description: The external reference ID. Could be a simple string or a URI. - nullable: true referenceSource: type: string description: An identifier for the source system or database of this reference - nullable: true + ExternalReferencesParameters: + type: object + properties: + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string FileFormat: type: string description: "fileFormat defines the MIME type of the file (ie text/csv, application/excel,\ @@ -3390,7 +3420,6 @@ components: type: string description: The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON. - nullable: true enum: - string - integer @@ -3401,18 +3430,15 @@ components: description: |- The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: "GQ", "RD", and "HQ"
This maps to a FORMAT field in the VCF file standard. - nullable: true fieldName: type: string description: |- The name of the field represented in this Genotype Field. Examples include: "Genotype Quality", "Read Depth", and "Haplotype Quality"
This maps to a FORMAT field in the VCF file standard. - nullable: true fieldValue: type: string description: The additional metadata value associated with this genotype call - nullable: true description: Genotype Metadata are additional layers of metadata associated with each genotype. GeoJSON: @@ -5206,6 +5232,20 @@ components: format: int32 nullable: true description: Pagination info for the matrix + PagingParameters: + type: object + properties: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 PedigreeNodeRequest: type: object properties: @@ -5558,8 +5598,10 @@ components: description: A human readable name for a `Plate` programDbId: type: string + nullable: true programName: type: string + nullable: true sampleType: type: string description: "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" @@ -5571,16 +5613,22 @@ components: - MIXED studyDbId: type: string + nullable: true studyName: type: string + nullable: true studyPUI: type: string + nullable: true trialDbId: type: string + nullable: true trialName: type: string + nullable: true trialPUI: type: string + nullable: true description: "A Plate represents the metadata for a collection of Samples. The\ \ physical Plate being represented might be a plastic tray full of Samples,\ \ or a group of Samples stored in individual containers ie bags, test tubes,\ @@ -6580,24 +6628,34 @@ components: $ref: "#/components/schemas/ExternalReference" germplasmDbId: type: string + nullable: true germplasmName: type: string + nullable: true germplasmPUI: type: string + nullable: true observationUnitDbId: type: string + nullable: true observationUnitName: type: string + nullable: true observationUnitPUI: type: string + nullable: true plateDbId: type: string + nullable: true plateName: type: string + nullable: true programDbId: type: string + nullable: true programName: type: string + nullable: true row: type: string description: The Row identifier for this `Sample` location in the `Plate` @@ -6641,10 +6699,13 @@ components: nullable: true studyDbId: type: string + nullable: true studyName: type: string + nullable: true studyPUI: type: string + nullable: true takenBy: type: string description: The name or identifier of the entity which took the `Sample` @@ -6658,10 +6719,13 @@ components: nullable: true trialDbId: type: string + nullable: true trialName: type: string + nullable: true trialPUI: type: string + nullable: true well: type: string description: "The Well identifier for this `Sample` location in the `Plate`.\ @@ -6958,9 +7022,10 @@ components: type: string years: type: array - description: The 4 digit year of a season. Example "2017" + description: The 4 digit year of a season. Example 2017 items: - type: string + type: integer + format: int32 SeedLotRequest: type: object properties: @@ -7199,6 +7264,29 @@ components: description: The human readable name of a trial to search for items: type: string + TokenPagingParameters: + type: object + properties: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + pageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
Used to request a specific page of data to be returned.\n\ +
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken from\ + \ a prior response to construct a query and move to the next or previous\ + \ page respectively. " + example: 33c27874 TraitDataType: type: string description: |- @@ -7313,22 +7401,6 @@ components: description: A human readable names to search for items: type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -7369,25 +7441,6 @@ components: \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ \ is before `trial.endDate`" format: date - sortBy: - type: string - description: Name of the field to sort by. - enum: - - trialDbId - - trialName - - programDbId - - programName - - locationDbId - - startDate - - endDate - sortOrder: - type: string - description: Sort order direction. Ascending/Descending. - enum: - - asc - - ASC - - desc - - DESC studyDbIds: type: array description: List of study identifiers to search for @@ -7743,12 +7796,16 @@ components: nullable: true referenceDbId: type: string + nullable: true referenceName: type: string + nullable: true referenceSetDbId: type: string + nullable: true referenceSetName: type: string + nullable: true start: type: integer description: "This field is optional and may be ignored if there is no relevant\ @@ -7774,16 +7831,13 @@ components: variantDbId: type: string description: The ID which uniquely identifies a `Variant` + nullable: true variantNames: type: array description: A human readable name associated with a `Variant` nullable: true items: type: string - variantSetDbId: - type: string - variantSetName: - type: string variantType: type: string description: |- @@ -8036,14 +8090,19 @@ components: $ref: "#/components/schemas/MetadataField" referenceSetDbId: type: string + nullable: true referenceSetName: type: string + nullable: true studyDbId: type: string + nullable: true studyName: type: string + nullable: true studyPUI: type: string + nullable: true variantCount: type: integer description: The number of Variants included in this VariantSet diff --git a/Specification/Generated/BrAPI-Germplasm.yaml b/Specification/Generated/BrAPI-Germplasm.yaml index 293761af..2013039a 100644 --- a/Specification/Generated/BrAPI-Germplasm.yaml +++ b/Specification/Generated/BrAPI-Germplasm.yaml @@ -2396,14 +2396,19 @@ components: properties: crossDbId: type: string + nullable: true crossName: type: string + nullable: true germplasmDbId: type: string + nullable: true germplasmName: type: string + nullable: true germplasmPUI: type: string + nullable: true mixturePercentage: type: integer description: The percentage of the given germplasm in the seed lot mixture. @@ -2490,8 +2495,10 @@ components: $ref: "#/components/schemas/CrossType" crossingProjectDbId: type: string + nullable: true crossingProjectName: type: string + nullable: true externalReferences: type: array description: An array of external reference ids. These are references to @@ -2506,8 +2513,10 @@ components: $ref: "#/components/schemas/CrossParent" plannedCrossDbId: type: string + nullable: true plannedCrossName: type: string + nullable: true pollinationEvents: type: array description: The list of pollination events that occurred for this cross. @@ -2661,8 +2670,10 @@ components: $ref: "#/components/schemas/CrossParent" programDbId: type: string + nullable: true programName: type: string + nullable: true description: "A project structure where a list of PlannedCrosses is generated,\ \ the crossing events occur in the field, and the resulting actual Crosses\ \ can documented." @@ -2792,14 +2803,41 @@ components: ExternalReference: type: object properties: + referenceID: + type: string + description: "**Deprecated in v2.1** Please use `referenceId`. Github issue\ + \ number #460
The external reference ID. Could be a simple string\ + \ or a URI." + nullable: true referenceId: type: string description: The external reference ID. Could be a simple string or a URI. - nullable: true referenceSource: type: string description: An identifier for the source system or database of this reference - nullable: true + ExternalReferencesParameters: + type: object + properties: + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string GenomeMapRequest: type: object properties: @@ -3562,10 +3600,13 @@ components: $ref: "#/components/schemas/AdditionalInfo" attributeDbId: type: string + nullable: true attributeName: type: string + nullable: true attributePUI: type: string + nullable: true determinedDate: type: string description: The date the value of this attribute was determined for a given @@ -3582,10 +3623,13 @@ components: $ref: "#/components/schemas/ExternalReference" germplasmDbId: type: string + nullable: true germplasmName: type: string + nullable: true germplasmPUI: type: string + nullable: true value: type: string description: The value of this attribute for a given germplasm @@ -3817,11 +3861,6 @@ components: description: "A germplasm reference that is a direct child of this germplasm.\ \ These represent edges in the tree, connecting to other nodes." GermplasmMCPD: - required: - - commonCropName - - germplasmDbId - - germplasmName - - germplasmPUI type: object properties: accessionNames: @@ -4282,8 +4321,10 @@ components: nullable: true breedingMethodDbId: type: string + nullable: true breedingMethodName: type: string + nullable: true collection: type: string description: A specific panel/collection/population name this germplasm @@ -4478,17 +4519,7 @@ components: the value empty if the uncertainty is unknown. nullable: true coordinates: - type: array - description: |- - One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - - Copied from RFC 7946 Section 3.1.1 - - A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. - nullable: true - items: - $ref: "#/components/schemas/GeoJSON" + $ref: "#/components/schemas/GeoJSON" germplasmDbId: type: string germplasmName: @@ -5928,6 +5959,20 @@ components: schema or its resource implementation. nullable: true description: A pointer to an ontology used by a genomic reference + PagingParameters: + type: object + properties: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 ParentType: type: string description: "The type of parent used during crossing. Accepted values for this\ @@ -5945,7 +5990,6 @@ components: - FEMALE - SELF - POPULATION - - CLONAL PedigreeNode: required: - germplasmDbId @@ -6444,8 +6488,10 @@ components: $ref: "#/components/schemas/CrossType" crossingProjectDbId: type: string + nullable: true crossingProjectName: type: string + nullable: true externalReferences: type: array description: An array of external reference ids. These are references to @@ -7164,9 +7210,10 @@ components: type: string years: type: array - description: The 4 digit year of a season. Example "2017" + description: The 4 digit year of a season. Example 2017 items: - type: string + type: integer + format: int32 SeedLot: allOf: - $ref: "#/components/schemas/SeedLotNewRequest" @@ -7228,12 +7275,16 @@ components: nullable: true locationDbId: type: string + nullable: true locationName: type: string + nullable: true programDbId: type: string + nullable: true programName: type: string + nullable: true seedLotDescription: type: string description: A general description of this Seed Lot @@ -7349,8 +7400,10 @@ components: $ref: "#/components/schemas/ExternalReference" seedLotDbId: type: string + nullable: true seedLotName: type: string + nullable: true transactionDbId: type: string description: Unique DbId for the Seed Lot Transaction @@ -7645,6 +7698,29 @@ components: \ The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism\ \ - An identifier for the organism at the species level. Use of the NCBI taxon\ \ ID is recommended." + TokenPagingParameters: + type: object + properties: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + pageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
Used to request a specific page of data to be returned.\n\ +
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken from\ + \ a prior response to construct a query and move to the next or previous\ + \ page respectively. " + example: 33c27874 TraitDataType: type: string description: |- @@ -7759,22 +7835,6 @@ components: description: A human readable names to search for items: type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -7815,25 +7875,6 @@ components: \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ \ is before `trial.endDate`" format: date - sortBy: - type: string - description: Name of the field to sort by. - enum: - - trialDbId - - trialName - - programDbId - - programName - - locationDbId - - startDate - - endDate - sortOrder: - type: string - description: Sort order direction. Ascending/Descending. - enum: - - asc - - ASC - - desc - - DESC studyDbIds: type: array description: List of study identifiers to search for diff --git a/Specification/Generated/BrAPI-Phenotyping.yaml b/Specification/Generated/BrAPI-Phenotyping.yaml index 857506ff..443b6a1f 100644 --- a/Specification/Generated/BrAPI-Phenotyping.yaml +++ b/Specification/Generated/BrAPI-Phenotyping.yaml @@ -679,11 +679,11 @@ paths: $ref: "#/components/schemas/ObservationUnitNewRequest" example: "{_1={additionalInfo={}, cross={}, externalReferences=[{}],\ \ germplasm={}, location={}, observationUnitDbId=59ce1af8, observationUnitName=5a5b18e6,\ - \ observationUnitPUI=491c6d6d, observationUnitPosition=[{}], program={},\ + \ observationUnitPUI=491c6d6d, observationUnitPosition={}, program={},\ \ seedLot={}, study={}, treatments=[{}], trial={}, samples=[{}], events=[{}],\ \ images=[{}], observations=[{}]}, _2={additionalInfo={},\ \ cross={}, externalReferences=[{}], germplasm={}, location={}, observationUnitDbId=59ce1af9,\ - \ observationUnitName=5a5b18e7, observationUnitPUI=491c6d6e, observationUnitPosition=[{}],\ + \ observationUnitName=5a5b18e7, observationUnitPUI=491c6d6e, observationUnitPosition={},\ \ program={}, seedLot={}, study={}, treatments=[{}], trial={}, samples=[{}],\ \ events=[{}], images=[{}], observations=[{}]}}" responses: @@ -2415,14 +2415,7 @@ components: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" eventDateRange: - type: array - description: "An object describing when a particular Event has taken place.\ - \ An Event can occur at one or more discrete time points (`discreteDates`)\ - \ or an event can happen continuously over a longer period of time (`startDate`,\ - \ `endDate`)" - nullable: true - items: - $ref: "#/components/schemas/EventDateRange" + $ref: "#/components/schemas/EventDateRange" eventDbId: type: string description: Internal database identifier @@ -2445,7 +2438,6 @@ components: An identifier for this event type, in the form of an ontology class reference
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology). - nullable: true eventTypeDbId: type: string description: |- @@ -2514,12 +2506,23 @@ components: nullable: true eventDbId: type: string + key: + type: string + description: "**Deprecated in v2.1** Please use `name`. Github issue number\ + \ #440 \n
Specifies the relationship between the event\ + \ and the given property. E.g. fertilizer, operator" + example: operator name: type: string description: |- The full name of an event parameter
ICASA "Variable_Name" nullable: true + rdfValue: + type: string + description: "**Deprecated in v2.1** Please use `code`. Github issue number\ + \ #440 \nIf the 'value'\ @@ -2592,14 +2595,41 @@ components: ExternalReference: type: object properties: + referenceID: + type: string + description: "**Deprecated in v2.1** Please use `referenceId`. Github issue\ + \ number #460
The external reference ID. Could be a simple string\ + \ or a URI." + nullable: true referenceId: type: string description: The external reference ID. Could be a simple string or a URI. - nullable: true referenceSource: type: string description: An identifier for the source system or database of this reference - nullable: true + ExternalReferencesParameters: + type: object + properties: + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string GenomeMapRequest: type: object properties: @@ -3337,10 +3367,13 @@ components: nullable: true observationUnitDbId: type: string + nullable: true observationUnitName: type: string + nullable: true observationUnitPUI: type: string + nullable: true description: The metadata for an image file that is connected to some phenotypic observation data. ImageRequest: @@ -3958,10 +3991,13 @@ components: $ref: "#/components/schemas/GeoJSON" germplasmDbId: type: string + nullable: true germplasmName: type: string + nullable: true germplasmPUI: type: string + nullable: true observationTimeStamp: type: string description: The date and time when this observation was made @@ -3969,26 +4005,37 @@ components: nullable: true observationUnitDbId: type: string + nullable: true observationUnitName: type: string + nullable: true observationUnitPUI: type: string + nullable: true observationVariableDbId: type: string + nullable: true observationVariableName: type: string + nullable: true observationVariablePUI: type: string + nullable: true seasonDbId: type: string + nullable: true seasonName: type: string + nullable: true studyDbId: type: string + nullable: true studyName: type: string + nullable: true studyPUI: type: string + nullable: true uploadedBy: type: string description: The name or id of the user who uploaded the observation to @@ -4498,8 +4545,10 @@ components: $ref: "#/components/schemas/AdditionalInfo" crossDbId: type: string + nullable: true crossName: type: string + nullable: true externalReferences: type: array description: An array of external reference ids. These are references to @@ -4510,14 +4559,19 @@ components: $ref: "#/components/schemas/ExternalReference" germplasmDbId: type: string + nullable: true germplasmName: type: string + nullable: true germplasmPUI: type: string + nullable: true locationDbId: type: string + nullable: true locationName: type: string + nullable: true observationUnitName: type: string description: A human readable name for an observation unit @@ -4530,30 +4584,28 @@ components: MIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible. nullable: true observationUnitPosition: - type: array - description: "All positional and layout information related to this Observation\ - \ Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of\ - \ a spatial coordinate (georeference or relative) \nor level of observation\ - \ (plot 45, subblock 7, block 2) provided as a key-value pair of the form\ - \ type:value. \nLevels of observation must be consistent with those listed\ - \ in the Study section." - nullable: true - items: - $ref: "#/components/schemas/ObservationUnitPosition" + $ref: "#/components/schemas/ObservationUnitPosition" programDbId: type: string + nullable: true programName: type: string + nullable: true seedLotDbId: type: string + nullable: true seedLotName: type: string + nullable: true studyDbId: type: string + nullable: true studyName: type: string + nullable: true studyPUI: type: string + nullable: true treatments: type: array description: |- @@ -4565,10 +4617,13 @@ components: $ref: "#/components/schemas/ObservationTreatment" trialDbId: type: string + nullable: true trialName: type: string + nullable: true trialPUI: type: string + nullable: true description: "A representation of the physical entity being observed during\ \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ \ but it could include things like Fields, Blocks, or Samples." @@ -5563,6 +5618,20 @@ components: schema or its resource implementation. nullable: true description: A pointer to an ontology used by a genomic reference + PagingParameters: + type: object + properties: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 PedigreeNodeRequest: type: object properties: @@ -6559,9 +6628,10 @@ components: type: string years: type: array - description: The 4 digit year of a season. Example "2017" + description: The 4 digit year of a season. Example 2017 items: - type: string + type: integer + format: int32 SeedLotRequest: type: object properties: @@ -6800,6 +6870,29 @@ components: description: The human readable name of a trial to search for items: type: string + TokenPagingParameters: + type: object + properties: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + pageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
Used to request a specific page of data to be returned.\n\ +
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken from\ + \ a prior response to construct a query and move to the next or previous\ + \ page respectively. " + example: 33c27874 Trait: allOf: - $ref: "#/components/schemas/TraitNewRequest" @@ -7018,22 +7111,6 @@ components: description: A human readable names to search for items: type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -7074,25 +7151,6 @@ components: \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ \ is before `trial.endDate`" format: date - sortBy: - type: string - description: Name of the field to sort by. - enum: - - trialDbId - - trialName - - programDbId - - programName - - locationDbId - - startDate - - endDate - sortOrder: - type: string - description: Sort order direction. Ascending/Descending. - enum: - - asc - - ASC - - desc - - DESC studyDbIds: type: array description: List of study identifiers to search for diff --git a/Specification/Generated/brapi_generated.graphqls b/Specification/Generated/brapi_generated.graphqls index 17105737..459fe2c8 100644 --- a/Specification/Generated/brapi_generated.graphqls +++ b/Specification/Generated/brapi_generated.graphqls @@ -760,7 +760,7 @@ type Event { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" - eventDateRange: [EventDateRange] + eventDateRange: EventDateRange "Internal database identifier" eventDbId: String """ @@ -826,11 +826,21 @@ type EventParameter { "associated event" eventDbIds: ID """ + **Deprecated in v2.1** Please use `name`. Github issue number #440 +
Specifies the relationship between the event and the given property. E.g. fertilizer, operator + """ + key: String + """ The full name of an event parameter
ICASA "Variable_Name" """ name: String """ + **Deprecated in v2.1** Please use `code`. Github issue number #440 + If the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'.
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. @@ -862,6 +872,8 @@ type ExperimentalDesign { } type ExternalReference { + "**Deprecated in v2.1** Please use `referenceId`. Github issue number #460
The external reference ID. Could be a simple string or a URI." + referenceID: String "The external reference ID. Could be a simple string or a URI." referenceId: String "An identifier for the source system or database of this reference" @@ -1398,7 +1410,7 @@ type GermplasmOrigin { A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. """ - coordinates: [GeoJSON] + coordinates: GeoJSON "associated germplasm" germplasmDbIds: ID } @@ -1955,7 +1967,7 @@ type ObservationUnit { or level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. Levels of observation must be consistent with those listed in the Study section. """ - observationUnitPosition: [ObservationUnitPosition] + observationUnitPosition: ObservationUnitPosition "The ID which uniquely identifies a program" programDbIds: ID "The unique identifier for the originating Seed Lot" @@ -3288,7 +3300,7 @@ type Variant { "A human readable name associated with a `Variant`" variantNames: [String] "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted." - variantSetDbIds: ID + variantSet(paging: PageInput, variantSetsInput: VariantSetsInput): VariantSetListResponse """ The "variant_type" is used to denote e.g. structural variants. Examples: @@ -3543,7 +3555,6 @@ enum MlsStatus { "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. " enum ParentType { - CLONAL FEMALE MALE POPULATION @@ -4277,7 +4288,7 @@ input EventInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" - eventDateRange: [EventDateRangeInput] + eventDateRange: EventDateRangeInput "Internal database identifier" eventDbId: String """ @@ -4317,11 +4328,21 @@ input EventParameterInput { "associated event" event: EventInput """ + **Deprecated in v2.1** Please use `name`. Github issue number #440 +
Specifies the relationship between the event and the given property. E.g. fertilizer, operator + """ + key: String + """ The full name of an event parameter
ICASA "Variable_Name" """ name: String """ + **Deprecated in v2.1** Please use `code`. Github issue number #440 + If the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'.
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. @@ -4365,6 +4386,8 @@ input ExperimentalDesignInput { } input ExternalReferenceInput { + "**Deprecated in v2.1** Please use `referenceId`. Github issue number #460
The external reference ID. Could be a simple string or a URI." + referenceID: String "The external reference ID. Could be a simple string or a URI." referenceId: String "An identifier for the source system or database of this reference" @@ -5099,7 +5122,7 @@ input GermplasmOriginInput { A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. """ - coordinates: [GeoJSONInput] + coordinates: GeoJSONInput "associated germplasm" germplasm: GermplasmInput } @@ -5734,7 +5757,7 @@ input ObservationUnitInput { or level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. Levels of observation must be consistent with those listed in the Study section. """ - observationUnitPosition: [ObservationUnitPositionInput] + observationUnitPosition: ObservationUnitPositionInput "observations" observations: [ObservationInput] "The ID which uniquely identifies a program" @@ -7164,8 +7187,8 @@ input SeasonsInput { seasonNames: [String] "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\"." seasons: [String] - "The 4 digit year of a season. Example \"2017\"" - years: [String] + "The 4 digit year of a season. Example 2017" + years: [Int] } "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program." @@ -7654,12 +7677,6 @@ input TrialsInput { locationDbIds: [String] "A human readable names to search for" locationNames: [String] - "The DbIds of Variables to search for" - observationVariableDbIds: [String] - "The names of Variables to search for" - observationVariableNames: [String] - "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI" - observationVariablePUIs: [String] """ A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. @@ -7702,10 +7719,6 @@ input TrialsInput { - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate` """ searchDateRangeStart: String - "Name of the field to sort by." - sortBy: SortBy - "Sort order direction. Ascending/Descending." - sortOrder: SortOrder "List of study identifiers to search for" studyDbIds: [String] "List of study names to filter search results" @@ -7798,7 +7811,7 @@ input VariantInput { "A human readable name associated with a `Variant`" variantNames: [String] "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted." - variantSet: VariantSetInput + variantSet: [VariantSetInput] """ The "variant_type" is used to denote e.g. structural variants. Examples: diff --git a/Specification/Generated/brapi_generated.json b/Specification/Generated/brapi_generated.json index 1b763f4e..f4f58ac8 100644 --- a/Specification/Generated/brapi_generated.json +++ b/Specification/Generated/brapi_generated.json @@ -2435,7 +2435,7 @@ "additionalProperties" : { "$ref" : "#/components/schemas/ObservationUnitNewRequest" }, - "example" : "{_1={additionalInfo={}, cross={}, externalReferences=[{}], germplasm={}, location={}, observationUnitDbId=59ce1af8, observationUnitName=5a5b18e6, observationUnitPUI=491c6d6d, observationUnitPosition=[{}], program={}, seedLot={}, study={}, treatments=[{}], trial={}, samples=[{}], events=[{}], images=[{}], observations=[{}]}, _2={additionalInfo={}, cross={}, externalReferences=[{}], germplasm={}, location={}, observationUnitDbId=59ce1af9, observationUnitName=5a5b18e7, observationUnitPUI=491c6d6e, observationUnitPosition=[{}], program={}, seedLot={}, study={}, treatments=[{}], trial={}, samples=[{}], events=[{}], images=[{}], observations=[{}]}}" + "example" : "{_1={additionalInfo={}, cross={}, externalReferences=[{}], germplasm={}, location={}, observationUnitDbId=59ce1af8, observationUnitName=5a5b18e6, observationUnitPUI=491c6d6d, observationUnitPosition={}, program={}, seedLot={}, study={}, treatments=[{}], trial={}, samples=[{}], events=[{}], images=[{}], observations=[{}]}, _2={additionalInfo={}, cross={}, externalReferences=[{}], germplasm={}, location={}, observationUnitDbId=59ce1af9, observationUnitName=5a5b18e7, observationUnitPUI=491c6d6e, observationUnitPosition={}, program={}, seedLot={}, study={}, treatments=[{}], trial={}, samples=[{}], events=[{}], images=[{}], observations=[{}]}}" } } } @@ -4367,10 +4367,11 @@ { "name" : "year", "in" : "query", - "description" : "The 4 digit year of a season. Example \"2017\"", + "description" : "The 4 digit year of a season. Example 2017", "required" : false, "schema" : { - "type" : "string" + "type" : "integer", + "format" : "int32" } }, { @@ -5051,41 +5052,6 @@ "type" : "string" } }, - { - "name" : "sortBy", - "in" : "query", - "description" : "Name of the field to sort by.", - "required" : false, - "schema" : { - "type" : "string", - "description" : "Name of the field to sort by.", - "enum" : [ - "trialDbId", - "trialName", - "programDbId", - "programName", - "locationDbId", - "startDate", - "endDate" - ] - } - }, - { - "name" : "sortOrder", - "in" : "query", - "description" : "Sort order direction. Ascending/Descending.", - "required" : false, - "schema" : { - "type" : "string", - "description" : "Sort order direction. Ascending/Descending.", - "enum" : [ - "asc", - "ASC", - "desc", - "DESC" - ] - } - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -10776,20 +10742,17 @@ "genotypeMetadata" : { "type" : "array", "description" : "Genotype Metadata are additional layers of metadata associated with each genotype.", - "nullable" : true, "items" : { "$ref" : "#/components/schemas/GenotypeMetadata" } }, "genotypeValue" : { "type" : "string", - "description" : "The value of this genotype call", - "nullable" : true + "description" : "The value of this genotype call" }, "phaseSet" : { "type" : "string", - "description" : "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string.", - "nullable" : true + "description" : "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string." }, "variantDbId" : { "type" : "string" @@ -10943,22 +10906,28 @@ } }, "sampleDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "sampleName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "samplePUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "updated" : { "type" : "string", @@ -11397,19 +11366,24 @@ "type" : "object", "properties" : { "crossDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "crossName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "mixturePercentage" : { "type" : "integer", @@ -11512,10 +11486,12 @@ "$ref" : "#/components/schemas/CrossType" }, "crossingProjectDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "crossingProjectName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "externalReferences" : { "type" : "array", @@ -11532,10 +11508,12 @@ "$ref" : "#/components/schemas/CrossParent" }, "plannedCrossDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "plannedCrossName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "pollinationEvents" : { "type" : "array", @@ -11716,10 +11694,12 @@ } }, "programDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "programName" : { - "type" : "string" + "type" : "string", + "nullable" : true } }, "description" : "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented." @@ -12071,12 +12051,7 @@ "$ref" : "#/components/schemas/AdditionalInfo" }, "eventDateRange" : { - "type" : "array", - "description" : "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)", - "nullable" : true, - "items" : { - "$ref" : "#/components/schemas/EventDateRange" - } + "$ref" : "#/components/schemas/EventDateRange" }, "eventDbId" : { "type" : "string", @@ -12097,8 +12072,7 @@ }, "eventType" : { "type" : "string", - "description" : "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology).", - "nullable" : true + "description" : "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology)." }, "eventTypeDbId" : { "type" : "string", @@ -12163,11 +12137,21 @@ "eventDbId" : { "type" : "string" }, + "key" : { + "type" : "string", + "description" : "**Deprecated in v2.1** Please use `name`. Github issue number #440 \n
Specifies the relationship between the event and the given property. E.g. fertilizer, operator", + "example" : "operator" + }, "name" : { "type" : "string", "description" : "The full name of an event parameter\n
ICASA \"Variable_Name\"", "nullable" : true }, + "rdfValue" : { + "type" : "string", + "description" : "**Deprecated in v2.1** Please use `code`. Github issue number #440 \nIf the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'. \n
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. \n
If the value IS a number, then 'unit' should specify the units used eg. 'ml', 'cm', etc\n
ICASA \"Unit_or_type\"", @@ -12272,15 +12256,44 @@ "ExternalReference" : { "type" : "object", "properties" : { - "referenceId" : { + "referenceID" : { "type" : "string", - "description" : "The external reference ID. Could be a simple string or a URI.", + "description" : "**Deprecated in v2.1** Please use `referenceId`. Github issue number #460
The external reference ID. Could be a simple string or a URI.", "nullable" : true }, + "referenceId" : { + "type" : "string", + "description" : "The external reference ID. Could be a simple string or a URI." + }, "referenceSource" : { "type" : "string", - "description" : "An identifier for the source system or database of this reference", - "nullable" : true + "description" : "An identifier for the source system or database of this reference" + } + } + }, + "ExternalReferencesParameters" : { + "type" : "object", + "properties" : { + "externalReferenceIDs" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items" : { + "type" : "string" + } + }, + "externalReferenceIds" : { + "type" : "array", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items" : { + "type" : "string" + } + }, + "externalReferenceSources" : { + "type" : "array", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "items" : { + "type" : "string" + } } } }, @@ -12458,7 +12471,6 @@ "dataType" : { "type" : "string", "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", - "nullable" : true, "enum" : [ "string", "integer", @@ -12468,18 +12480,15 @@ }, "fieldAbbreviation" : { "type" : "string", - "description" : "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard.", - "nullable" : true + "description" : "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard." }, "fieldName" : { "type" : "string", - "description" : "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard.", - "nullable" : true + "description" : "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard." }, "fieldValue" : { "type" : "string", - "description" : "The additional metadata value associated with this genotype call", - "nullable" : true + "description" : "The additional metadata value associated with this genotype call" } }, "description" : "Genotype Metadata are additional layers of metadata associated with each genotype." @@ -13279,13 +13288,16 @@ "$ref" : "#/components/schemas/AdditionalInfo" }, "attributeDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "attributeName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "attributePUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "determinedDate" : { "type" : "string", @@ -13302,13 +13314,16 @@ } }, "germplasmDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "value" : { "type" : "string", @@ -13575,12 +13590,6 @@ "description" : "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes." }, "GermplasmMCPD" : { - "required" : [ - "commonCropName", - "germplasmDbId", - "germplasmName", - "germplasmPUI" - ], "type" : "object", "properties" : { "accessionNames" : { @@ -13958,10 +13967,12 @@ "nullable" : true }, "breedingMethodDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "breedingMethodName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "collection" : { "type" : "string", @@ -14119,12 +14130,7 @@ "nullable" : true }, "coordinates" : { - "type" : "array", - "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", - "nullable" : true, - "items" : { - "$ref" : "#/components/schemas/GeoJSON" - } + "$ref" : "#/components/schemas/GeoJSON" }, "germplasmDbId" : { "type" : "string" @@ -14624,13 +14630,16 @@ "nullable" : true }, "observationUnitDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true } }, "description" : "The metadata for an image file that is connected to some phenotypic observation data." @@ -15365,10 +15374,12 @@ "nullable" : true }, "locationDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "locationName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "locationType" : { "type" : "string", @@ -15956,13 +15967,16 @@ "$ref" : "#/components/schemas/GeoJSON" }, "germplasmDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationTimeStamp" : { "type" : "string", @@ -15971,37 +15985,48 @@ "nullable" : true }, "observationUnitDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationVariableDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationVariableName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationVariablePUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "seasonDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "seasonName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "uploadedBy" : { "type" : "string", @@ -16490,10 +16515,12 @@ "$ref" : "#/components/schemas/AdditionalInfo" }, "crossDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "crossName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "externalReferences" : { "type" : "array", @@ -16504,19 +16531,24 @@ } }, "germplasmDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "locationDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "locationName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitName" : { "type" : "string", @@ -16529,33 +16561,35 @@ "nullable" : true }, "observationUnitPosition" : { - "type" : "array", - "description" : "All positional and layout information related to this Observation Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) \nor level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. \nLevels of observation must be consistent with those listed in the Study section.", - "nullable" : true, - "items" : { - "$ref" : "#/components/schemas/ObservationUnitPosition" - } + "$ref" : "#/components/schemas/ObservationUnitPosition" }, "programDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "programName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "seedLotDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "seedLotName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "treatments" : { "type" : "array", @@ -16566,13 +16600,16 @@ } }, "trialDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "trialName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "trialPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true } }, "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." @@ -17724,6 +17761,23 @@ }, "description" : "Pagination info for the matrix" }, + "PagingParameters" : { + "type" : "object", + "properties" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + } + } + }, "ParentType" : { "type" : "string", "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", @@ -17731,8 +17785,7 @@ "MALE", "FEMALE", "SELF", - "POPULATION", - "CLONAL" + "POPULATION" ] }, "PedigreeNode" : { @@ -18431,10 +18484,12 @@ "$ref" : "#/components/schemas/CrossType" }, "crossingProjectDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "crossingProjectName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "externalReferences" : { "type" : "array", @@ -18608,10 +18663,12 @@ "description" : "A human readable name for a `Plate`" }, "programDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "programName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "sampleType" : { "type" : "string", @@ -18625,22 +18682,28 @@ ] }, "studyDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "trialDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "trialName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "trialPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true } }, "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." @@ -19004,7 +19067,8 @@ "nullable" : true }, "personDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "programName" : { "type" : "string", @@ -19955,34 +20019,44 @@ } }, "germplasmDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "germplasmPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationUnitPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "plateDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "plateName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "programDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "programName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "row" : { "type" : "string", @@ -20025,13 +20099,16 @@ "nullable" : true }, "studyDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "takenBy" : { "type" : "string", @@ -20044,13 +20121,16 @@ "nullable" : true }, "trialDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "trialName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "trialPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "well" : { "type" : "string", @@ -20484,9 +20564,10 @@ }, "years" : { "type" : "array", - "description" : "The 4 digit year of a season. Example \"2017\"", + "description" : "The 4 digit year of a season. Example 2017", "items" : { - "type" : "string" + "type" : "integer", + "format" : "int32" } } } @@ -20554,16 +20635,20 @@ "nullable" : true }, "locationDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "locationName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "programDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "programName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "seedLotDescription" : { "type" : "string", @@ -20686,10 +20771,12 @@ } }, "seedLotDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "seedLotName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "transactionDbId" : { "type" : "string", @@ -20885,10 +20972,12 @@ "nullable" : true }, "locationDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "locationName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "observationLevels" : { "type" : "array", @@ -20929,7 +21018,8 @@ }, "studyName" : { "type" : "string", - "description" : "The human readable name for a study\n\nMIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study" + "description" : "The human readable name for a study\n\nMIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study", + "nullable" : true }, "studyPUI" : { "type" : "string", @@ -21365,6 +21455,28 @@ }, "description" : "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended." }, + "TokenPagingParameters" : { + "type" : "object", + "properties" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "pageToken" : { + "type" : "string", + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
Used to request a specific page of data to be returned.\n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. ", + "example" : "33c27874" + } + } + }, "Trait" : { "allOf" : [ { @@ -21606,10 +21718,12 @@ } }, "programDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "programName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "publications" : { "type" : "array", @@ -21704,27 +21818,6 @@ "type" : "string" } }, - "observationVariableDbIds" : { - "type" : "array", - "description" : "The DbIds of Variables to search for", - "items" : { - "type" : "string" - } - }, - "observationVariableNames" : { - "type" : "array", - "description" : "The names of Variables to search for", - "items" : { - "type" : "string" - } - }, - "observationVariablePUIs" : { - "type" : "array", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "items" : { - "type" : "string" - } - }, "programDbIds" : { "type" : "array", "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", @@ -21749,29 +21842,6 @@ "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", "format" : "date" }, - "sortBy" : { - "type" : "string", - "description" : "Name of the field to sort by.", - "enum" : [ - "trialDbId", - "trialName", - "programDbId", - "programName", - "locationDbId", - "startDate", - "endDate" - ] - }, - "sortOrder" : { - "type" : "string", - "description" : "Sort order direction. Ascending/Descending.", - "enum" : [ - "asc", - "ASC", - "desc", - "DESC" - ] - }, "studyDbIds" : { "type" : "array", "description" : "List of study identifiers to search for", @@ -21857,13 +21927,6 @@ "type" : "string" } }, - "observationVariablePUIs" : { - "type" : "array", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "items" : { - "type" : "string" - } - }, "trialDbIds" : { "type" : "array", "description" : "The ID which uniquely identifies a trial to search for", @@ -21892,13 +21955,6 @@ "type" : "string" } }, - "observationVariableNames" : { - "type" : "array", - "description" : "The names of Variables to search for", - "items" : { - "type" : "string" - } - }, "studyNames" : { "type" : "array", "description" : "List of study names to filter search results", @@ -21906,36 +21962,6 @@ "type" : "string" } }, - "observationVariableDbIds" : { - "type" : "array", - "description" : "The DbIds of Variables to search for", - "items" : { - "type" : "string" - } - }, - "sortOrder" : { - "type" : "string", - "description" : "Sort order direction. Ascending/Descending.", - "enum" : [ - "asc", - "ASC", - "desc", - "DESC" - ] - }, - "sortBy" : { - "type" : "string", - "description" : "Name of the field to sort by.", - "enum" : [ - "trialDbId", - "trialName", - "programDbId", - "programName", - "locationDbId", - "startDate", - "endDate" - ] - }, "contactDbIds" : { "type" : "array", "description" : "List of contact entities associated with this trial", @@ -22369,16 +22395,20 @@ "nullable" : true }, "referenceDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "referenceName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "referenceSetDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "referenceSetName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "start" : { "type" : "integer", @@ -22400,7 +22430,8 @@ }, "variantDbId" : { "type" : "string", - "description" : "The ID which uniquely identifies a `Variant`" + "description" : "The ID which uniquely identifies a `Variant`", + "nullable" : true }, "variantNames" : { "type" : "array", @@ -22410,12 +22441,6 @@ "type" : "string" } }, - "variantSetDbId" : { - "type" : "string" - }, - "variantSetName" : { - "type" : "string" - }, "variantType" : { "type" : "string", "description" : "The \"variant_type\" is used to denote e.g. structural variants.\nExamples:\n DUP : duplication of sequence following \"start\"\n DEL : deletion of sequence following \"start\"", @@ -22677,19 +22702,24 @@ } }, "referenceSetDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "referenceSetName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "variantCount" : { "type" : "integer", diff --git a/Specification/Generated/brapi_generated.ttl b/Specification/Generated/brapi_generated.ttl index 572ccd7d..21f6decd 100644 --- a/Specification/Generated/brapi_generated.ttl +++ b/Specification/Generated/brapi_generated.ttl @@ -3,6 +3,10 @@ PREFIX rdf: PREFIX rdfs: PREFIX xsd: +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; @@ -39,10 +43,6 @@ PREFIX xsd: rdfs:label "slope"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; @@ -174,13 +174,6 @@ PREFIX xsd: rdfs:label "seedSourceDescription"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable description of a trial\n\nMIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail."@en; - rdfs:domain ; - rdfs:label "trialDescription"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "If the event parameter 'unit' field is 'code', then use 'valueDescription' to add a human readable description to the value."@en; @@ -188,6 +181,13 @@ PREFIX xsd: rdfs:label "valueDescription"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable description of a trial\n\nMIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail."@en; + rdfs:domain ; + rdfs:label "trialDescription"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -266,13 +266,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "The child germplasm"@en; - rdfs:domain ; - rdfs:label "childGermplasm"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "Zero or more filters that failed for this variant. VCF column 7 \"FILTER\" shared across all alleles in the same VCF record."@en; @@ -285,6 +278,13 @@ PREFIX xsd: rdfs:comment "Links to various ontology documentation"@en; rdfs:label "DocumentationLink"@en . + + rdf:type owl:ObjectProperty; + rdfs:comment "The child germplasm"@en; + rdfs:domain ; + rdfs:label "childGermplasm"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The name or identifier of the entity which took the `Sample` from the field"@en; @@ -550,10 +550,6 @@ PREFIX xsd: rdfs:label "commonCropName"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; @@ -691,6 +687,13 @@ PREFIX xsd: rdf:type , owl:NamedIndividual , . + + rdf:type owl:ObjectProperty; + rdfs:comment "All known corresponding Germplasm"@en; + rdfs:domain ; + rdfs:label "sourceGermplasm"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "observationUnits"@en; @@ -708,13 +711,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "All known corresponding Germplasm"@en; - rdfs:domain ; - rdfs:label "sourceGermplasm"@en; - rdfs:range . - rdf:type owl:Class; rdfs:comment "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier."@en; @@ -806,10 +802,6 @@ PREFIX xsd: rdfs:label "crossType"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -954,6 +946,10 @@ PREFIX xsd: rdfs:label "publicationReference"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The Uniquely Identifiable name of a `LinkageGroup`
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable."@en; @@ -975,11 +971,6 @@ PREFIX xsd: rdfs:label "sampleType"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "All positional and layout information related to this Observation Unit"@en; - rdfs:label "ObservationUnitPosition"@en . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -987,6 +978,11 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . + + rdf:type owl:Class; + rdfs:comment "All positional and layout information related to this Observation Unit"@en; + rdfs:label "ObservationUnitPosition"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)"@en; @@ -1074,6 +1070,10 @@ PREFIX xsd: rdfs:label "acquisitionDate"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable."@en; @@ -1082,6 +1082,11 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . + + rdf:type owl:Class; + rdfs:comment "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\""@en; + rdfs:label "EntryType"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; @@ -1089,10 +1094,9 @@ PREFIX xsd: rdfs:label "submissionTimestamp"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\""@en; - rdfs:label "EntryType"@en . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -1158,10 +1162,6 @@ PREFIX xsd: rdfs:comment "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy."@en; rdfs:label "Germplasm"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy."@en; @@ -1238,6 +1238,13 @@ PREFIX xsd: rdfs:label "collector"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name or id of the user who uploaded the observation to the database system"@en; + rdfs:domain ; + rdfs:label "uploadedBy"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The unique identifier for a `Reference`"@en; @@ -1259,13 +1266,6 @@ PREFIX xsd: rdfs:label "documentationURL"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name or id of the user who uploaded the observation to the database system"@en; - rdfs:domain ; - rdfs:label "uploadedBy"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -1302,10 +1302,6 @@ PREFIX xsd: rdfs:label "germplasmOrigin"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "Supplemental text description for 'biologicalStatusOfAccessionCode'"@en; @@ -1353,6 +1349,10 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -1521,6 +1521,10 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The X position coordinate for an observation unit. Different systems may use different coordinate systems."@en; @@ -1651,13 +1655,6 @@ PREFIX xsd: rdfs:label "mapPUI"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; - rdfs:domain ; - rdfs:label "trait"@en; - rdfs:range . - rdf:type owl:NamedIndividual , . @@ -1671,6 +1668,13 @@ PREFIX xsd: rdfs:label "mimeType"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; + rdfs:domain ; + rdfs:label "trait"@en; + rdfs:range . + rdf:type owl:NamedIndividual , . @@ -1723,10 +1727,6 @@ PREFIX xsd: rdfs:label "siblingPedigreeNodes"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit"@en; @@ -1892,10 +1892,6 @@ PREFIX xsd: rdfs:comment "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard "@en; rdfs:label "MetadataField"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; @@ -1915,13 +1911,6 @@ PREFIX xsd: rdfs:label "crosses"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "the description for a crossing project"@en; - rdfs:domain ; - rdfs:label "crossingProjectDescription"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The string used as a separator for unphased allele calls."@en; @@ -1929,6 +1918,13 @@ PREFIX xsd: rdfs:label "sepUnphased"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "the description for a crossing project"@en; + rdfs:domain ; + rdfs:label "crossingProjectDescription"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The time stamp for when this seed lot was created"@en; @@ -2026,6 +2022,10 @@ PREFIX xsd: rdfs:label "donorInfo"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:label "ObservationVariable"@en . @@ -2086,6 +2086,13 @@ PREFIX xsd: rdfs:label "filtersPassed"@en; rdfs:range xsd:boolean . + + rdf:type owl:DatatypeProperty; + rdfs:comment "**Deprecated in v2.1** Please use `code`. Github issue number #440 \n; + rdfs:label "rdfValue"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "A unique identifier physically attached to the `Sample`"@en; @@ -2093,6 +2100,10 @@ PREFIX xsd: rdfs:label "sampleBarcode"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:Class; rdfs:comment "Identifier assigned to an accession by the material donor."@en; @@ -2145,10 +2156,6 @@ PREFIX xsd: rdfs:label "variantNames"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "parentPedigreeNodes"@en; @@ -2321,12 +2328,9 @@ PREFIX xsd: rdfs:label "observations"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of scientist submitting the variable."@en; - rdfs:domain ; - rdfs:label "scientist"@en; - rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -2349,6 +2353,13 @@ PREFIX xsd: rdfs:label "publicReleaseDate"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of scientist submitting the variable."@en; + rdfs:domain ; + rdfs:label "scientist"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "Information about the location where the sample was collected"@en; @@ -2394,6 +2405,10 @@ PREFIX xsd: rdfs:label "alternateIDs"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "General category for the attribute. very similar to Trait class."@en; @@ -2467,12 +2482,9 @@ PREFIX xsd: rdfs:label "programDbId"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:DatatypeProperty; @@ -2481,6 +2493,13 @@ PREFIX xsd: rdfs:label "expandHomozygotes"@en; rdfs:range xsd:boolean . + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "The unique identifier for the breeding method used to create this germplasm"@en; @@ -2569,13 +2588,6 @@ PREFIX xsd: rdfs:label "germplasm"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "the human readable name of a cross attribute"@en; - rdfs:domain ; - rdfs:label "crossAttributeName"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; @@ -2586,6 +2598,13 @@ PREFIX xsd: rdfs:comment "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; rdfs:label "GeoJSONPoint"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "the human readable name of a cross attribute"@en; + rdfs:domain ; + rdfs:label "crossAttributeName"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required."@en; @@ -2621,10 +2640,6 @@ PREFIX xsd: rdfs:label "study"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "the human readable name for a planned cross"@en; @@ -2724,10 +2739,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:NamedIndividual , . @@ -2878,13 +2889,6 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated \nby `start + referenceBases.length`."@en; - rdfs:domain ; - rdfs:label "end"@en; - rdfs:range xsd:integer . - rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; @@ -2892,6 +2896,13 @@ PREFIX xsd: rdfs:label "study"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated \nby `start + referenceBases.length`."@en; + rdfs:domain ; + rdfs:label "end"@en; + rdfs:range xsd:integer . + rdf:type owl:DatatypeProperty; rdfs:comment "phone number of this person"@en; @@ -2913,6 +2924,10 @@ PREFIX xsd: rdfs:label "variants"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; @@ -3079,6 +3094,10 @@ PREFIX xsd: rdfs:label "metadataFields"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "List of donor institutes"@en; @@ -3127,10 +3146,6 @@ PREFIX xsd: rdfs:label "dataMatrixAbbreviation"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; @@ -3296,20 +3311,20 @@ PREFIX xsd: rdfs:comment "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')."@en; rdfs:label "PlannedCrossStatus"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature."@en; - rdfs:domain ; - rdfs:label "genus"@en; - rdfs:range xsd:string . - - + rdf:type owl:DatatypeProperty; rdfs:comment "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation"@en; rdfs:domain ; rdfs:label "methodName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature."@en; + rdfs:domain ; + rdfs:label "genus"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of institution submitting the variable"@en; @@ -3701,13 +3716,6 @@ PREFIX xsd: rdfs:label "genotypeMetadata"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology's list of authors (no specific format)"@en; - rdfs:domain ; - rdfs:label "authors"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; @@ -3715,10 +3723,12 @@ PREFIX xsd: rdfs:label "biologicalStatusOfAccessionCode"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; - rdfs:label "StorageTypeCode"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The value of this attribute for a given germplasm"@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -3727,11 +3737,16 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . - + + rdf:type owl:Class; + rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; + rdfs:label "StorageTypeCode"@en . + + rdf:type owl:DatatypeProperty; - rdfs:comment "The value of this attribute for a given germplasm"@en; - rdfs:domain ; - rdfs:label "value"@en; + rdfs:comment "Ontology's list of authors (no specific format)"@en; + rdfs:domain ; + rdfs:label "authors"@en; rdfs:range xsd:string . @@ -3790,13 +3805,6 @@ PREFIX xsd: rdfs:comment "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis."@en; rdfs:label "Plate"@en . - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The 4 digit year of the season."@en; @@ -3804,6 +3812,13 @@ PREFIX xsd: rdfs:label "year"@en; rdfs:range xsd:integer . + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; @@ -3825,6 +3840,9 @@ PREFIX xsd: rdfs:label "md5checksum"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -3832,9 +3850,6 @@ PREFIX xsd: rdfs:label "externalReferences"@en; rdfs:range . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "The type of analysis."@en; @@ -3854,13 +3869,6 @@ PREFIX xsd: rdfs:label "url"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "Species associated with a referenceSet"@en; - rdfs:domain ; - rdfs:label "referenceSet"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "Alternative name or ID used to reference this germplasm"@en; @@ -3868,6 +3876,13 @@ PREFIX xsd: rdfs:label "synonym"@en; rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "Species associated with a referenceSet"@en; + rdfs:domain ; + rdfs:label "referenceSet"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of scientist submitting the variable."@en; @@ -3903,13 +3918,6 @@ PREFIX xsd: rdfs:label "callSets"@en; rdfs:range . - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Siblings share at least one parent with the given germplasm. \n
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response."@en; - rdfs:domain ; - rdfs:label "siblings"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "associated scale"@en; @@ -3917,6 +3925,13 @@ PREFIX xsd: rdfs:label "scale"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Siblings share at least one parent with the given germplasm. \n
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response."@en; + rdfs:domain ; + rdfs:label "siblings"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; @@ -3924,10 +3939,6 @@ PREFIX xsd: rdfs:label "additionalInfo"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:Class; rdfs:comment "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100."@en; @@ -3983,10 +3994,6 @@ PREFIX xsd: rdfs:label "crossingProject"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:ObjectProperty; rdfs:comment "the Observation Unit of the cross parent"@en; @@ -4020,13 +4027,6 @@ PREFIX xsd: rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. "@en; rdfs:label "ParentType"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "The current balance of the amount of material in a SeedLot. Could be a count (seeds, bulbs, etc) or a weight (kg of seed)."@en; @@ -4034,6 +4034,13 @@ PREFIX xsd: rdfs:label "amount"@en; rdfs:range xsd:double . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")"@en; @@ -4053,10 +4060,6 @@ PREFIX xsd: rdfs:label "parent2"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; @@ -4095,6 +4098,10 @@ PREFIX xsd: rdfs:label "synonyms"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:NamedIndividual , . @@ -4213,12 +4220,9 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The value of the data collected as an observation"@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . rdf:type owl:ObjectProperty; @@ -4227,6 +4231,13 @@ PREFIX xsd: rdfs:label "plannedCrosses"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The value of the data collected as an observation"@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Other variable names"@en; @@ -4320,14 +4331,12 @@ PREFIX xsd: rdfs:label "commonCropName"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:Class; - rdfs:comment "A persons contact information"@en; - rdfs:label "Contact"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of CallSets included in this VariantSet"@en; + rdfs:domain ; + rdfs:label "callSetCount"@en; + rdfs:range xsd:integer . rdf:type owl:DatatypeProperty; @@ -4336,12 +4345,10 @@ PREFIX xsd: rdfs:label "unit"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of CallSets included in this VariantSet"@en; - rdfs:domain ; - rdfs:label "callSetCount"@en; - rdfs:range xsd:integer . + + rdf:type owl:Class; + rdfs:comment "A persons contact information"@en; + rdfs:label "Contact"@en . rdf:type owl:DatatypeProperty; @@ -4418,6 +4425,10 @@ PREFIX xsd: rdfs:label "publications"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The MIME type of the file (ie text/csv, application/excel, application/zip).\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; @@ -4430,13 +4441,6 @@ PREFIX xsd: rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; rdfs:label "ObservationUnitLevel"@en . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\""@en; @@ -4444,6 +4448,9 @@ PREFIX xsd: rdfs:label "attribute"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -4513,6 +4520,10 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "The child locations that belong to this Location. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; @@ -4546,10 +4557,6 @@ PREFIX xsd: rdfs:label "listDbId"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "A URL to the human readable documentation of an object"@en; @@ -4565,13 +4572,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; - rdfs:domain ; - rdfs:label "donorAccessionNumber"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a `Variant` within the given database server\n
A `Variant` can also represent a Marker "@en; @@ -4579,6 +4579,13 @@ PREFIX xsd: rdfs:label "variant"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; + rdfs:domain ; + rdfs:label "donorAccessionNumber"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Full scientific binomial format name. This includes Genus, Species, and Sub-species"@en; @@ -4655,6 +4662,10 @@ PREFIX xsd: rdfs:label "donorAccessionNumber"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study."@en; @@ -4723,10 +4734,6 @@ PREFIX xsd: rdfs:label "sepUnphased"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard."@en; @@ -4816,13 +4823,6 @@ PREFIX xsd: rdfs:label "callSetName"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -4849,6 +4849,10 @@ PREFIX xsd: rdfs:label "ontologyReference"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "events"@en; @@ -4877,6 +4881,13 @@ PREFIX xsd: rdfs:label "levelOrder"@en; rdfs:range xsd:integer . + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + rdf:type owl:ObjectProperty; rdfs:comment "images"@en; @@ -4908,13 +4919,6 @@ PREFIX xsd: rdfs:label "coordinateUncertainty"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The units used to describe the data in a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "unit"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The date and time when this study was last modified"@en; @@ -4922,6 +4926,13 @@ PREFIX xsd: rdfs:label "lastUpdate"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The units used to describe the data in a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "unit"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; @@ -4943,6 +4954,10 @@ PREFIX xsd: rdfs:label "eventDateRange"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The full name of an event parameter\n
ICASA \"Variable_Name\""@en; @@ -4960,13 +4975,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of markers present in a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "markerCount"@en; - rdfs:range xsd:integer . - rdf:type owl:ObjectProperty; rdfs:comment "the second parent used in the cross"@en; @@ -4974,24 +4982,26 @@ PREFIX xsd: rdfs:label "parent2"@en; rdfs:range . - - rdf:type owl:DatatypeProperty; - rdfs:comment "A short human readable code for a study"@en; - rdfs:domain ; - rdfs:label "studyCode"@en; - rdfs:range xsd:string . - - + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of markers present in a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "markerCount"@en; + rdfs:range xsd:integer . + + rdf:type owl:DatatypeProperty; rdfs:comment "the unique identifier for a planned cross"@en; rdfs:domain ; rdfs:label "plannedCrossDbId"@en; rdfs:range xsd:string . - - rdf:type owl:Class; - rdfs:comment "Alternative names or IDs used to reference this germplasm"@en; - rdfs:label "Synonym"@en . + + rdf:type owl:DatatypeProperty; + rdfs:comment "A short human readable code for a study"@en; + rdfs:domain ; + rdfs:label "studyCode"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -5000,6 +5010,11 @@ PREFIX xsd: rdfs:label "exposure"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "Alternative names or IDs used to reference this germplasm"@en; + rdfs:label "Synonym"@en . + rdf:type owl:Class; rdfs:comment "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology"@en; @@ -5062,9 +5077,12 @@ PREFIX xsd: rdfs:label "fieldValue"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The content of the image"@en; + rdfs:domain ; + rdfs:label "imageContent"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -5073,13 +5091,6 @@ PREFIX xsd: rdfs:label "coordinateUncertainty"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The content of the image"@en; - rdfs:domain ; - rdfs:label "imageContent"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; @@ -5157,6 +5168,10 @@ PREFIX xsd: rdfs:label "alleleMatrices"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The date and time the image was taken"@en; @@ -5199,13 +5214,6 @@ PREFIX xsd: rdfs:label "samplePUI"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The season for this Observation"@en; @@ -5220,6 +5228,13 @@ PREFIX xsd: rdfs:label "position"@en; rdfs:range xsd:integer . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; + rdfs:domain ; + rdfs:label "growthStage"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. "@en; @@ -5234,11 +5249,11 @@ PREFIX xsd: rdfs:label "toSeedLot"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; - rdfs:domain ; - rdfs:label "growthStage"@en; + rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; + rdfs:domain ; + rdfs:label "type"@en; rdfs:range xsd:string . @@ -5396,18 +5411,18 @@ PREFIX xsd: rdfs:label "datasetAuthorships"@en; rdfs:range . - + rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\")."@en; + rdfs:comment "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group)."@en; rdfs:domain ; - rdfs:label "accessionNumber"@en; + rdfs:label "subtaxa"@en; rdfs:range xsd:string . - + rdf:type owl:DatatypeProperty; - rdfs:comment "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group)."@en; + rdfs:comment "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\")."@en; rdfs:domain ; - rdfs:label "subtaxa"@en; + rdfs:label "accessionNumber"@en; rdfs:range xsd:string . @@ -5458,6 +5473,10 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:DatatypeProperty; rdfs:comment "The type of map this represents, usually \"Genetic\" or \"Physical\""@en; @@ -5498,9 +5517,12 @@ PREFIX xsd: rdfs:label "term"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The DOI or other permanent unique identifier for this published dataset"@en; + rdfs:domain ; + rdfs:label "datasetPUI"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -5509,16 +5531,12 @@ PREFIX xsd: rdfs:label "growthStage"@en; rdfs:range xsd:string . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The DOI or other permanent unique identifier for this published dataset"@en; - rdfs:domain ; - rdfs:label "datasetPUI"@en; - rdfs:range xsd:string . + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies an `ObservationUnit`"@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . rdf:type owl:Class; @@ -5530,13 +5548,6 @@ PREFIX xsd: rdfs:comment "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present."@en; rdfs:label "Cross"@en . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name used for display purposes"@en; - rdfs:domain ; - rdfs:label "defaultDisplayName"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the entity was last updated"@en; @@ -5544,12 +5555,12 @@ PREFIX xsd: rdfs:label "dateModified"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies an `ObservationUnit`"@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name used for display purposes"@en; + rdfs:domain ; + rdfs:label "defaultDisplayName"@en; + rdfs:range xsd:string . rdf:type owl:DatatypeProperty; @@ -5615,10 +5626,6 @@ PREFIX xsd: rdf:type owl:NamedIndividual , . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - rdf:type owl:DatatypeProperty; rdfs:comment "The Permanent Unique Identifier of a Method, usually in the form of a URI"@en; @@ -5633,6 +5640,10 @@ PREFIX xsd: rdfs:label "units"@en; rdfs:range xsd:string . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + rdf:type owl:ObjectProperty; rdfs:comment "The study in which the event occurred"@en; @@ -5664,13 +5675,6 @@ PREFIX xsd: rdfs:label "description"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."@en; - rdfs:domain ; - rdfs:label "orcid"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. "@en; @@ -5706,6 +5710,13 @@ PREFIX xsd: rdfs:label "accessionNumber"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."@en; + rdfs:domain ; + rdfs:label "orcid"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "Method unique identifier"@en; @@ -5734,9 +5745,12 @@ PREFIX xsd: rdfs:label "trial"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:DatatypeProperty; + rdfs:comment "**Deprecated in v2.1** Please use `name`. Github issue number #440 \n
Specifies the relationship between the event and the given property. E.g. fertilizer, operator"@en; + rdfs:domain ; + rdfs:label "key"@en; + rdfs:range xsd:string . rdf:type owl:ObjectProperty; @@ -5780,11 +5794,6 @@ PREFIX xsd: rdfs:label "geoCoordinates"@en; rdfs:range . - - rdf:type owl:Class; - rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; - rdfs:label "ObservationUnitHierarchyLevel"@en . - rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this Seed Lot"@en; @@ -5792,6 +5801,11 @@ PREFIX xsd: rdfs:label "seedLotName"@en; rdfs:range xsd:string . + + rdf:type owl:Class; + rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; + rdfs:label "ObservationUnitHierarchyLevel"@en . + rdf:type owl:DatatypeProperty; rdfs:comment "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation"@en; @@ -5957,13 +5971,6 @@ PREFIX xsd: rdfs:label "entityPUI"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a VariantSet"@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - rdf:type owl:ObjectProperty; rdfs:comment "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; @@ -5971,6 +5978,13 @@ PREFIX xsd: rdfs:label "observationLevels"@en; rdfs:range . + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a VariantSet"@en; + rdfs:domain ; + rdfs:label "variantSet"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The width of the image in Pixels."@en; @@ -6052,9 +6066,12 @@ PREFIX xsd: rdfs:label "dataType"@en; rdfs:range . -[ rdf:type owl:Class; - owl:oneOf ( ) -] . + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. \n
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response."@en; + rdfs:domain ; + rdfs:label "parents"@en; + rdfs:range . rdf:type owl:DatatypeProperty; @@ -6063,13 +6080,6 @@ PREFIX xsd: rdfs:label "contextOfUse"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. \n
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response."@en; - rdfs:domain ; - rdfs:label "parents"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "A human readable name for this attribute"@en; @@ -6164,6 +6174,17 @@ PREFIX xsd: rdfs:label "study"@en; rdfs:range . +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "programs"@en; + rdfs:range . + rdf:type owl:DatatypeProperty; rdfs:comment "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\""@en; @@ -6178,13 +6199,6 @@ PREFIX xsd: rdfs:label "bibliographicalReference"@en; rdfs:range xsd:string . - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "programs"@en; - rdfs:range . - rdf:type owl:DatatypeProperty; rdfs:comment "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)"@en; @@ -6282,6 +6296,13 @@ PREFIX xsd: rdfs:label "parameterPUI"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "mapDbId"@en; + rdfs:range xsd:string . + rdf:type owl:Class; rdfs:comment "a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group."@en; @@ -6294,13 +6315,6 @@ PREFIX xsd: rdfs:label "startDate"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name used for display purposes"@en; - rdfs:domain ; - rdfs:label "defaultDisplayName"@en; - rdfs:range xsd:string . - rdf:type owl:DatatypeProperty; rdfs:comment "A human readable description of this attribute"@en; @@ -6308,11 +6322,11 @@ PREFIX xsd: rdfs:label "attributeDescription"@en; rdfs:range xsd:string . - + rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "mapDbId"@en; + rdfs:comment "Human readable name used for display purposes"@en; + rdfs:domain ; + rdfs:label "defaultDisplayName"@en; rdfs:range xsd:string . @@ -6322,13 +6336,6 @@ PREFIX xsd: rdfs:label "defaultValue"@en; rdfs:range xsd:string . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The timestamp when this variant was created."@en; - rdfs:domain ; - rdfs:label "created"@en; - rdfs:range xsd:string . - rdf:type owl:ObjectProperty; rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; @@ -6336,6 +6343,13 @@ PREFIX xsd: rdfs:label "study"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The timestamp when this variant was created."@en; + rdfs:domain ; + rdfs:label "created"@en; + rdfs:range xsd:string . + rdf:type owl:DatatypeProperty; rdfs:comment "The size of the image in Bytes."@en; @@ -6375,9 +6389,6 @@ PREFIX xsd: rdfs:comment "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)."@en; rdfs:label "EnvironmentParameter"@en . - - rdf:type owl:NamedIndividual , . - rdf:type owl:DatatypeProperty; rdfs:comment "Name of scientist submitting the variable."@en; @@ -6385,6 +6396,9 @@ PREFIX xsd: rdfs:label "scientist"@en; rdfs:range xsd:string . + + rdf:type owl:NamedIndividual , . + rdf:type owl:DatatypeProperty; rdfs:comment "Timestamp when the entity was first created"@en; @@ -6399,6 +6413,13 @@ PREFIX xsd: rdfs:label "imageFileName"@en; rdfs:range xsd:string . + + rdf:type owl:DatatypeProperty; + rdfs:comment "**Deprecated in v2.1** Please use `referenceId`. Github issue number #460
The external reference ID. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "referenceID"@en; + rdfs:range xsd:string . + rdf:type owl:ObjectProperty; rdfs:comment "List of contact entities associated with this study"@en; @@ -6503,6 +6524,13 @@ PREFIX xsd: rdfs:label "dataType"@en; rdfs:range . + + rdf:type owl:DatatypeProperty; + rdfs:comment "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; + rdfs:domain ; + rdfs:label "instituteAddress"@en; + rdfs:range xsd:string . + rdf:type , , owl:NamedIndividual , . @@ -6513,13 +6541,6 @@ PREFIX xsd: rdfs:label "filtersApplied"@en; rdfs:range xsd:boolean . - - rdf:type owl:DatatypeProperty; - rdfs:comment "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; - rdfs:domain ; - rdfs:label "instituteAddress"@en; - rdfs:range xsd:string . - rdf:type owl:Class; rdfs:comment "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples."@en; @@ -6530,9 +6551,6 @@ PREFIX xsd: rdfs:comment "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies."@en; rdfs:label "Program"@en . - - rdf:type owl:NamedIndividual , . - rdf:type owl:NamedIndividual , . diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index 4cfb3ca5..0a52c98f 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -2039,6 +2039,17 @@ "type" : "integer" }, "style" : "form" + }, { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "explode" : true, + "in" : "query", + "name" : "externalReferenceID", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" }, { "description" : "An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", "explode" : true, @@ -9540,6 +9551,17 @@ "type" : "string" }, "style" : "form" + }, { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "explode" : true, + "in" : "query", + "name" : "externalReferenceID", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" }, { "description" : "An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", "explode" : true, @@ -11761,6 +11783,17 @@ "type" : "string" }, "style" : "form" + }, { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "explode" : true, + "in" : "query", + "name" : "externalReferenceID", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" }, { "description" : "An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", "explode" : true, @@ -12150,6 +12183,17 @@ "type" : "string" }, "style" : "form" + }, { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "explode" : true, + "in" : "query", + "name" : "externalReferenceID", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" }, { "description" : "An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", "explode" : true, @@ -15588,6 +15632,17 @@ } }, "description" : "Forbidden" + }, + "404" : { + "content" : { + "application/json" : { + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found", + "schema" : { + "type" : "string" + } + } + }, + "description" : "Not Found" } }, "summary" : "Get the results of a `Observations` search request", @@ -21722,6 +21777,17 @@ "type" : "integer" }, "style" : "form" + }, { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "explode" : true, + "in" : "query", + "name" : "externalReferenceID", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" }, { "description" : "An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", "explode" : true, @@ -36722,7 +36788,7 @@ "nullable" : true, "type" : "array" }, - "variantSetDbId" : { + "variantSetDbIds" : { "description" : "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted.", "example" : [ "c8ae400b", "ef2c204b" ], "items" : { @@ -41505,6 +41571,12 @@ }, "GermplasmMCPD_breedingInstitutes_inner" : { "properties" : { + "instituteAddress" : { + "description" : "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "example" : "123 Main Street, Lima, Peru, 5555", + "nullable" : true, + "type" : "string" + }, "instituteCode" : { "description" : "MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard.", "example" : "PER001", @@ -41642,6 +41714,12 @@ "GermplasmMCPD_donorInfo_donorInstitute" : { "description" : "The identifying information for the entity acting as an accession donor\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.\n
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.", "properties" : { + "instituteAddress" : { + "description" : "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "example" : "123 Main Street, Lima, Peru, 5555", + "nullable" : true, + "type" : "string" + }, "instituteCode" : { "description" : "MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", "example" : "PER001", @@ -41680,6 +41758,12 @@ }, "GermplasmMCPD_safetyDuplicateInstitutes_inner" : { "properties" : { + "instituteAddress" : { + "description" : "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", + "example" : "123 Main Street, Lima, Peru, 5555", + "nullable" : true, + "type" : "string" + }, "instituteCode" : { "description" : "MCPD (v2.1) (DUPLSITE) 25. FAO WIEWS code of the institute(s) where a safety duplicate of the accession is maintained. Follows INSTCODE standard.", "example" : "PER001", diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index c2453225..37f2977e 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -72,13 +72,6 @@ Changed response : **200** Deleted properties: `variantName` -##### `GET` /referencesets - - -###### Parameters: - -Added: `externalReferenceID` in `query` - ##### `POST` /search/allelematrix @@ -285,6 +278,8 @@ Deleted: `Accept` in `header` Deleted response : **202** +Deleted response : **404** + ##### `GET` /search/observationunits/{searchResultsDbId} @@ -415,8 +410,6 @@ Deleted response : **404** * Changed content type : `application/json` - New properties: `observationVariablePUIs`, `observationVariableNames`, `observationVariableDbIds`, `sortOrder`, `sortBy` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` ##### `GET` /search/trials/{searchResultsDbId} @@ -449,14 +442,6 @@ Deleted response : **202** Deleted response : **404** -##### `GET` /seasons - - -###### Parameters: - -Changed: `year` in `query`: - - Type changed: `integer` -> `string` - ##### `POST` /attributevalues @@ -468,29 +453,12 @@ Changed: `year` in `query`: New properties: `attributePUI`, `germplasmPUI` - * Changed property `attributeDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `attributeName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `PUT` /attributevalues/{attributeValueDbId} @@ -501,29 +469,12 @@ Changed: `year` in `query`: New properties: `attributePUI`, `germplasmPUI` - * Changed property `attributeDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `attributeName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /calls @@ -544,36 +495,9 @@ Changed response : **200** Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - * Changed property `genotypeValue` (string): - - Nullable changed: `null` -> `true` - - * Changed property `phaseSet` (string): - - Nullable changed: `null` -> `true` - - * Changed property `genotypeMetadata` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `dataType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldAbbreviation` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldName` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldValue` (string): - - Nullable changed: `null` -> `true` - ##### `GET` /callsets -###### Parameters: - -Added: `externalReferenceID` in `query` - ###### Return Type: Changed response : **200** @@ -590,24 +514,13 @@ Changed response : **200** Deleted properties: `variantSetDbIds` - * Changed property `sampleDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /callsets/{callSetDbId} @@ -624,24 +537,13 @@ Changed response : **200** Deleted properties: `variantSetDbIds` - * Changed property `sampleDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /callsets/{callSetDbId}/calls @@ -662,29 +564,6 @@ Changed response : **200** Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - * Changed property `genotypeValue` (string): - - Nullable changed: `null` -> `true` - - * Changed property `phaseSet` (string): - - Nullable changed: `null` -> `true` - - * Changed property `genotypeMetadata` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `dataType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldAbbreviation` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldName` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldValue` (string): - - Nullable changed: `null` -> `true` - ##### `POST` /crosses @@ -699,18 +578,6 @@ Changed response : **200** * Changed property `crossType` (string): - Nullable changed: `true` -> `null` - * Changed property `crossingProjectDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossingProjectName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `plannedCrossDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `plannedCrossName` (string): - - Nullable changed: `true` -> `null` - * Changed property `crossAttributes` (array) Changed items (array): @@ -722,22 +589,14 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `parent1` (object): - Nullable changed: `true` -> `null` New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `parentType` (string): - - Added enum values: [CLONAL] - * Changed property `pollinationEvents` (array) Changed items (array): @@ -753,23 +612,12 @@ Changed response : **200** Changed items (array): - * Changed property `programDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `programName` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `potentialParents` (array) @@ -777,9 +625,6 @@ Changed response : **200** New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `parentType` (string): - - Added enum values: [CLONAL] - ##### `PUT` /crossingprojects/{crossingProjectDbId} @@ -787,23 +632,12 @@ Changed response : **200** * Changed content type : `application/json` - * Changed property `programDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `programName` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `potentialParents` (array) @@ -811,9 +645,6 @@ Changed response : **200** New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `parentType` (string): - - Added enum values: [CLONAL] - ##### `GET` /events @@ -833,147 +664,30 @@ Changed response : **200** Deleted properties: `date`, `observationUnitDbIds` - * Changed property `eventDateRange` (object -> array): - - Type changed: `object` -> `array` - - * Changed property `eventType` (string): - - Nullable changed: `null` -> `true` - * Changed property `studyDbId` (string): - Nullable changed: `true` -> `null` * Changed property `studyName` (string): - Nullable changed: `true` -> `null` + * Changed property `eventDateRange` (object): + - Nullable changed: `true` -> `null` + + New properties: `eventDbId` + * Changed property `eventParameters` (array) Changed items (array): New properties: `eventDbId` - Deleted properties: `key`, `rdfValue` - -##### `POST` /germplasm - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `sampleDbIds` - - * Changed property `breedingMethodDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `breedingMethodName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `donors` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` - - * Changed property `germplasmOrigin` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `coordinates` (object -> array): - - Type changed: `object` -> `array` - - * Changed property `storageTypes` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `synonyms` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `taxonIds` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - -##### `PUT` /germplasm/{germplasmDbId} - - -###### Request: - -* Changed content type : `application/json` - - New properties: `sampleDbIds` - - * Changed property `breedingMethodDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `breedingMethodName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `donors` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` - - * Changed property `germplasmOrigin` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `coordinates` (object -> array): - - Type changed: `object` -> `array` - - * Changed property `storageTypes` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `synonyms` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `taxonIds` (array) - - Changed items (array): + * Changed property `key` (string): + - Nullable changed: `true` -> `null` + - Deprecated status changed - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + * Changed property `rdfValue` (string): + - Nullable changed: `true` -> `null` + - Deprecated status changed ##### `GET` /germplasm/{germplasmDbId}/mcpd @@ -988,21 +702,9 @@ Changed response : **200** New properties: `germplasmName` - New required properties: - - `commonCropName` - - `germplasmDbId` - - `germplasmName` - - `germplasmPUI` - * Changed property `germplasmPUI` (string): - Nullable changed: `true` -> `null` - * Changed property `breedingInstitutes` (array) - - Changed items (array): - - New properties: `instituteAddress` - ##### `POST` /lists @@ -1020,13 +722,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `PUT` /lists/{listDbId} @@ -1043,87 +740,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` - -##### `POST` /observationunits - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `germplasmPUI`, `studyPUI`, `trialPUI` - - * Changed property `crossDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `locationDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `locationName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitPosition` (object -> array): - - Type changed: `object` -> `array` - - * Changed property `programDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `programName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `seedLotDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `seedLotName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `studyName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `trialDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `trialName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array) - - Changed items (array): - - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` - - * Changed property `treatments` (array) - - Changed items (array): - - New properties: `observationUnitDbId`, `observationUnitName`, `observationUnitPUI` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `POST` /people @@ -1138,13 +756,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `PUT` /people/{personDbId} @@ -1157,13 +770,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /plannedcrosses @@ -1183,32 +791,18 @@ Changed response : **200** * Changed property `crossType` (string): - Nullable changed: `true` -> `null` - * Changed property `crossingProjectDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossingProjectName` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `parent1` (object): - Nullable changed: `true` -> `null` New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `parentType` (string): - - Added enum values: [CLONAL] - ##### `PUT` /plannedcrosses @@ -1227,32 +821,18 @@ Changed response : **200** * Changed property `crossType` (string): - Nullable changed: `true` -> `null` - * Changed property `crossingProjectDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossingProjectName` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `parent1` (object): - Nullable changed: `true` -> `null` New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `parentType` (string): - - Added enum values: [CLONAL] - ##### `POST` /plannedcrosses @@ -1270,32 +850,18 @@ Changed response : **200** * Changed property `crossType` (string): - Nullable changed: `true` -> `null` - * Changed property `crossingProjectDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossingProjectName` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `parent1` (object): - Nullable changed: `true` -> `null` New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `parentType` (string): - - Added enum values: [CLONAL] - ###### Return Type: Changed response : **200** @@ -1311,32 +877,18 @@ Changed response : **200** * Changed property `crossType` (string): - Nullable changed: `true` -> `null` - * Changed property `crossingProjectDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossingProjectName` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `parent1` (object): - Nullable changed: `true` -> `null` New properties: `germplasmPUI`, `observationUnitPUI` - * Changed property `parentType` (string): - - Added enum values: [CLONAL] - ##### `POST` /plates @@ -1348,26 +900,12 @@ Changed response : **200** New properties: `programName`, `studyName`, `studyPUI`, `trialName`, `trialPUI` - * Changed property `programDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `trialDbId` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /programs @@ -1398,13 +936,8 @@ Changed: `programType` in `query`: Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `PUT` /programs/{programDbId} @@ -1424,21 +957,12 @@ Changed: `programType` in `query`: Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /references -###### Parameters: - -Added: `externalReferenceID` in `query` - ###### Return Type: Changed response : **200** @@ -1466,13 +990,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /references/{referenceDbId} @@ -1500,13 +1019,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `PUT` /samples @@ -1528,39 +1042,13 @@ Deleted response : **404** Deleted properties: `sampleGroupDbId` - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `plateDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `plateName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `programDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `trialDbId` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `POST` /search/calls @@ -1587,29 +1075,6 @@ Changed response : **200** Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - * Changed property `genotypeValue` (string): - - Nullable changed: `null` -> `true` - - * Changed property `phaseSet` (string): - - Nullable changed: `null` -> `true` - - * Changed property `genotypeMetadata` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `dataType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldAbbreviation` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldName` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldValue` (string): - - Nullable changed: `null` -> `true` - ##### `GET` /search/calls/{searchResultsDbId} @@ -1631,34 +1096,11 @@ Changed response : **200** Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` - * Changed property `data` (array) - - Changed items (array): - - Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - - * Changed property `genotypeValue` (string): - - Nullable changed: `null` -> `true` - - * Changed property `phaseSet` (string): - - Nullable changed: `null` -> `true` - - * Changed property `genotypeMetadata` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `dataType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldAbbreviation` (string): - - Nullable changed: `null` -> `true` + * Changed property `data` (array) - * Changed property `fieldName` (string): - - Nullable changed: `null` -> `true` + Changed items (array): - * Changed property `fieldValue` (string): - - Nullable changed: `null` -> `true` + Deleted properties: `genotype`, `genotype_likelihood`, `variantName` ##### `POST` /search/callsets @@ -1685,24 +1127,13 @@ Changed response : **200** Deleted properties: `variantSetDbIds` - * Changed property `sampleDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /search/callsets/{searchResultsDbId} @@ -1727,24 +1158,13 @@ Changed response : **200** Deleted properties: `variantSetDbIds` - * Changed property `sampleDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `POST` /search/observations @@ -1868,13 +1288,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /search/references/{searchResultsDbId} @@ -1910,13 +1325,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `POST` /search/variants @@ -1959,40 +1369,17 @@ Changed response : **200** Changed items (array): - New properties: `analysis`, `variantSetName` - - Deleted properties: `alternateBases`, `alternate_bases` - - * Changed property `referenceDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbId` (string): - - Nullable changed: `true` -> `null` + New properties: `analysis` - * Changed property `variantSetDbId` (array -> string): - - Type changed: `array` -> `string` + Deleted properties: `alternateBases`, `alternate_bases`, `variantSetDbIds` * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /search/variants/{searchResultsDbId} @@ -2017,40 +1404,17 @@ Changed response : **200** Changed items (array): - New properties: `analysis`, `variantSetName` - - Deleted properties: `alternateBases`, `alternate_bases` - - * Changed property `referenceDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbId` (string): - - Nullable changed: `true` -> `null` + New properties: `analysis` - * Changed property `variantSetDbId` (array -> string): - - Type changed: `array` -> `string` + Deleted properties: `alternateBases`, `alternate_bases`, `variantSetDbIds` * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `POST` /search/variantsets @@ -2078,10 +1442,7 @@ Changed response : **200** Deleted properties: `availableFormats` * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` + - Nullable changed: `false` -> `true` * Changed property `analysis` (array) @@ -2097,13 +1458,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `metadataFields` (array) @@ -2144,10 +1500,7 @@ Changed response : **200** Deleted properties: `availableFormats` * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` + - Nullable changed: `false` -> `true` * Changed property `analysis` (array) @@ -2163,13 +1516,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `metadataFields` (array) @@ -2197,47 +1545,18 @@ Changed response : **200** New properties: `transactions` - * Changed property `locationDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `locationName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `programDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `programName` (string): - - Nullable changed: `true` -> `null` - * Changed property `contentMixture` (array) Changed items (array): New properties: `germplasmPUI`, `seedLotDbId`, `seedLotName` - * Changed property `crossDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `PUT` /seedlots/{seedLotDbId} @@ -2248,47 +1567,18 @@ Changed response : **200** New properties: `transactions` - * Changed property `locationDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `locationName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `programDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `programName` (string): - - Nullable changed: `true` -> `null` - * Changed property `contentMixture` (array) Changed items (array): New properties: `germplasmPUI`, `seedLotDbId`, `seedLotName` - * Changed property `crossDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `POST` /studies @@ -2303,18 +1593,9 @@ Changed response : **200** Deleted properties: `contacts`, `observationVariableDbIds` - * Changed property `locationDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `locationName` (string): - - Nullable changed: `true` -> `null` - * Changed property `studyDescription` (string): - Nullable changed: `null` -> `true` - * Changed property `studyName` (string): - - Nullable changed: `true` -> `null` - * Changed property `environmentParameters` (array) Changed items (array): @@ -2333,13 +1614,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `growthFacility` (object): - Nullable changed: `true` -> `null` @@ -2366,18 +1642,9 @@ Changed response : **200** Deleted properties: `contacts`, `observationVariableDbIds` - * Changed property `locationDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `locationName` (string): - - Nullable changed: `true` -> `null` - * Changed property `studyDescription` (string): - Nullable changed: `null` -> `true` - * Changed property `studyName` (string): - - Nullable changed: `true` -> `null` - * Changed property `environmentParameters` (array) Changed items (array): @@ -2396,13 +1663,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `growthFacility` (object): - Nullable changed: `true` -> `null` @@ -2418,6 +1680,15 @@ Changed response : **200** New required properties: - `lastUpdateDbId` +##### `GET` /trials + + +###### Parameters: + +Deleted: `sortBy` in `query` + +Deleted: `sortOrder` in `query` + ##### `POST` /trials @@ -2429,12 +1700,6 @@ Changed response : **200** New properties: `studyDbIds` - * Changed property `programDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `programName` (string): - - Nullable changed: `true` -> `null` - * Changed property `datasetAuthorships` (array) Changed items (array): @@ -2445,13 +1710,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `publications` (array) @@ -2468,12 +1728,6 @@ Changed response : **200** New properties: `studyDbIds` - * Changed property `programDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `programName` (string): - - Nullable changed: `true` -> `null` - * Changed property `datasetAuthorships` (array) Changed items (array): @@ -2484,13 +1738,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `publications` (array) @@ -2501,10 +1750,6 @@ Changed response : **200** ##### `GET` /variants -###### Parameters: - -Added: `externalReferenceID` in `query` - ###### Return Type: Changed response : **200** @@ -2517,40 +1762,17 @@ Changed response : **200** Changed items (array): - New properties: `analysis`, `variantSetName` - - Deleted properties: `alternateBases`, `alternate_bases` - - * Changed property `referenceDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbId` (string): - - Nullable changed: `true` -> `null` + New properties: `analysis` - * Changed property `variantSetDbId` (array -> string): - - Type changed: `array` -> `string` + Deleted properties: `alternateBases`, `alternate_bases`, `variantSetDbIds` * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /variants/{variantDbId} @@ -2563,40 +1785,17 @@ Changed response : **200** * Changed property `result` (object) - New properties: `analysis`, `variantSetName` - - Deleted properties: `alternateBases`, `alternate_bases` - - * Changed property `referenceDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbId` (string): - - Nullable changed: `true` -> `null` + New properties: `analysis` - * Changed property `variantSetDbId` (array -> string): - - Type changed: `array` -> `string` + Deleted properties: `alternateBases`, `alternate_bases`, `variantSetDbIds` * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /variants/{variantDbId}/calls @@ -2617,29 +1816,6 @@ Changed response : **200** Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - * Changed property `genotypeValue` (string): - - Nullable changed: `null` -> `true` - - * Changed property `phaseSet` (string): - - Nullable changed: `null` -> `true` - - * Changed property `genotypeMetadata` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `dataType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldAbbreviation` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldName` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldValue` (string): - - Nullable changed: `null` -> `true` - ##### `GET` /variantsets @@ -2664,10 +1840,7 @@ Changed response : **200** Deleted properties: `availableFormats` * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` + - Nullable changed: `false` -> `true` * Changed property `analysis` (array) @@ -2683,13 +1856,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `metadataFields` (array) @@ -2722,10 +1890,7 @@ Changed response : **200** Deleted properties: `availableFormats` * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` + - Nullable changed: `false` -> `true` * Changed property `analysis` (array) @@ -2741,13 +1906,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `metadataFields` (array) @@ -2773,38 +1933,15 @@ Changed response : **200** * Changed content type : `application/json` - * Changed property `result` (object) - - Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` - - * Changed property `data` (array) - - Changed items (array): - - Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - - * Changed property `genotypeValue` (string): - - Nullable changed: `null` -> `true` - - * Changed property `phaseSet` (string): - - Nullable changed: `null` -> `true` - - * Changed property `genotypeMetadata` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): + * Changed property `result` (object) - * Changed property `dataType` (string): - - Nullable changed: `null` -> `true` + Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` - * Changed property `fieldAbbreviation` (string): - - Nullable changed: `null` -> `true` + * Changed property `data` (array) - * Changed property `fieldName` (string): - - Nullable changed: `null` -> `true` + Changed items (array): - * Changed property `fieldValue` (string): - - Nullable changed: `null` -> `true` + Deleted properties: `genotype`, `genotype_likelihood`, `variantName` ##### `GET` /variantsets/{variantSetDbId}/callsets @@ -2825,24 +1962,13 @@ Changed response : **200** Deleted properties: `variantSetDbIds` - * Changed property `sampleDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `GET` /variantsets/{variantSetDbId}/variants @@ -2859,40 +1985,17 @@ Changed response : **200** Changed items (array): - New properties: `analysis`, `variantSetName` - - Deleted properties: `alternateBases`, `alternate_bases` - - * Changed property `referenceDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbId` (string): - - Nullable changed: `true` -> `null` + New properties: `analysis` - * Changed property `variantSetDbId` (array -> string): - - Type changed: `array` -> `string` + Deleted properties: `alternateBases`, `alternate_bases`, `variantSetDbIds` * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed ##### `POST` /attributes @@ -2923,13 +2026,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `ontologyReference` (object): - Nullable changed: `true` -> `null` @@ -2973,13 +2071,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `ontologyReference` (object): - Nullable changed: `true` -> `null` @@ -3012,21 +2105,13 @@ Changed response : **200** * Changed property `mimeType` (string): - Pattern changed: `image/.*` -> `null` - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `imageLocation` (object): - Nullable changed: `true` -> `null` @@ -3051,21 +2136,13 @@ Changed response : **200** * Changed property `mimeType` (string): - Pattern changed: `image/.*` -> `null` - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array): - Nullable changed: `null` -> `true` Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `imageLocation` (object): - Nullable changed: `true` -> `null` @@ -3089,17 +2166,15 @@ Changed response : **200** Deleted properties: `parentLocationDbId`, `parentLocationName` + * Changed property `locationName` (string): + - Nullable changed: `null` -> `true` + * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `coordinates` (object): - Nullable changed: `true` -> `null` @@ -3121,17 +2196,15 @@ Changed response : **200** Deleted properties: `parentLocationDbId`, `parentLocationName` + * Changed property `locationName` (string): + - Nullable changed: `null` -> `true` + * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `coordinates` (object): - Nullable changed: `true` -> `null` @@ -3162,58 +2235,75 @@ Deleted response : **404** Deleted properties: `season` - * Changed property `germplasmDbId` (string): - - Nullable changed: `true` -> `null` + * Changed property `externalReferences` (array) - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` + Changed items (array): - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` + * Changed property `referenceID` (string): + - Deprecated status changed - * Changed property `observationUnitName` (string): + * Changed property `geoCoordinates` (object): - Nullable changed: `true` -> `null` - * Changed property `observationVariableDbId` (string): - - Nullable changed: `true` -> `null` + * Changed property `type` (string): + - Default changed: `Feature` -> `none` - * Changed property `observationVariableName` (string): - - Nullable changed: `true` -> `null` + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` +###### Return Type: + +Deleted response : **404** + +##### `POST` /observationunits + + +###### Request: + +* Changed content type : `application/json` + + Changed items (array): + + New properties: `germplasmPUI`, `studyPUI`, `trialPUI` * Changed property `externalReferences` (array) Changed items (array): - Deleted properties: `referenceID` + * Changed property `referenceID` (string): + - Deprecated status changed - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` + * Changed property `treatments` (array) - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + Changed items (array): - * Changed property `geoCoordinates` (object): + New properties: `observationUnitDbId`, `observationUnitName`, `observationUnitPUI` + + * Changed property `observationUnitPosition` (object): - Nullable changed: `true` -> `null` - * Changed property `type` (string): - - Default changed: `Feature` -> `none` + New properties: `observationUnitDbId`, `observationUnitName`, `observationUnitPUI` - * Changed property `geometry` (object -> null): - - Type changed: `object` -> `null` + * Changed property `geoCoordinates` (object -> array): + - Type changed: `object` -> `array` -###### Return Type: + * Changed property `positionCoordinateXType` (string): + - Nullable changed: `true` -> `null` -Deleted response : **404** + * Changed property `positionCoordinateYType` (string): + - Nullable changed: `true` -> `null` -##### `GET` /pedigree + * Changed property `observationLevelRelationships` (array) + Changed items (array): -###### Parameters: + New properties: `observationUnitName`, `observationUnitPUI` + + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` + +##### `GET` /pedigree -Added: `externalReferenceID` in `query` ###### Return Type: @@ -3254,13 +2344,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `parents` (array) @@ -3275,6 +2360,9 @@ Changed response : **200** * Changed property `germplasmName` (string): - Nullable changed: `true` -> `null` + * Changed property `parentType` (string): + - Removed enum values: [CLONAL] + ##### `POST` /pedigree @@ -3309,13 +2397,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `parents` (array) @@ -3330,6 +2413,9 @@ Changed response : **200** * Changed property `germplasmName` (string): - Nullable changed: `true` -> `null` + * Changed property `parentType` (string): + - Removed enum values: [CLONAL] + ###### Return Type: Deleted response : **404** @@ -3369,13 +2455,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `parents` (array) @@ -3390,6 +2471,9 @@ Changed response : **200** * Changed property `germplasmName` (string): - Nullable changed: `true` -> `null` + * Changed property `parentType` (string): + - Removed enum values: [CLONAL] + ##### `POST` /search/images @@ -3544,13 +2628,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `parents` (array) @@ -3565,6 +2644,9 @@ Changed response : **200** * Changed property `germplasmName` (string): - Nullable changed: `true` -> `null` + * Changed property `parentType` (string): + - Removed enum values: [CLONAL] + ##### `GET` /search/pedigree/{searchResultsDbId} @@ -3609,13 +2691,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `parents` (array) @@ -3630,6 +2707,9 @@ Changed response : **200** * Changed property `germplasmName` (string): - Nullable changed: `true` -> `null` + * Changed property `parentType` (string): + - Removed enum values: [CLONAL] + ##### `POST` /variables @@ -3659,13 +2739,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `ontologyReference` (object): - Nullable changed: `true` -> `null` @@ -3709,13 +2784,8 @@ Changed response : **200** Changed items (array): - Deleted properties: `referenceID` - - * Changed property `referenceId` (string): - - Nullable changed: `null` -> `true` - - * Changed property `referenceSource` (string): - - Nullable changed: `null` -> `true` + * Changed property `referenceID` (string): + - Deprecated status changed * Changed property `ontologyReference` (object): - Nullable changed: `true` -> `null` @@ -3732,3 +2802,115 @@ Changed response : **200** * Changed property `type` (string): - Nullable changed: `null` -> `true` +##### `POST` /germplasm + + +###### Request: + +* Changed content type : `application/json` + + Changed items (array): + + New properties: `sampleDbIds` + + * Changed property `donors` (array) + + Changed items (array): + + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + + * Changed property `externalReferences` (array) + + Changed items (array): + + * Changed property `referenceID` (string): + - Deprecated status changed + + * Changed property `storageTypes` (array) + + Changed items (array): + + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + + * Changed property `synonyms` (array) + + Changed items (array): + + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + + * Changed property `taxonIds` (array) + + Changed items (array): + + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + + * Changed property `germplasmOrigin` (array) + + Changed items (array): + + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + + * Changed property `coordinates` (object): + - Nullable changed: `true` -> `null` + + * Changed property `type` (string): + - Default changed: `Feature` -> `none` + + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` + +##### `PUT` /germplasm/{germplasmDbId} + + +###### Request: + +* Changed content type : `application/json` + + New properties: `sampleDbIds` + + * Changed property `donors` (array) + + Changed items (array): + + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + + * Changed property `externalReferences` (array) + + Changed items (array): + + * Changed property `referenceID` (string): + - Deprecated status changed + + * Changed property `storageTypes` (array) + + Changed items (array): + + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + + * Changed property `synonyms` (array) + + Changed items (array): + + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + + * Changed property `taxonIds` (array) + + Changed items (array): + + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + + * Changed property `germplasmOrigin` (array) + + Changed items (array): + + New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + + * Changed property `coordinates` (object): + - Nullable changed: `true` -> `null` + + * Changed property `type` (string): + - Default changed: `Feature` -> `none` + + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` + From d3b14a0462d6d44ccd311138952bcd8e75dc05f0 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 15 May 2026 21:41:48 +1200 Subject: [PATCH 42/62] change non-nullable for external refs, fixed other nullables --- .../BrAPI-Schema/BrAPI-Common/Variable.json | 5 +- .../BrAPI-Schema/BrAPI-Core/ListType.json | 3 +- .../BrAPI-Schema/BrAPI-Core/Study.json | 5 +- .../BrAPI-Schema/BrAPI-Genotyping/Call.json | 48 +++++++++++++++++++ .../BrAPI-Genotyping/CallSet.json | 5 +- .../BrAPI-Genotyping/Reference.json | 14 ++++-- .../BrAPI-Schema/BrAPI-Genotyping/Sample.json | 5 +- .../BrAPI-Genotyping/Variant.json | 5 +- .../BrAPI-Genotyping/VariantSet.json | 5 +- .../BrAPI-Schema/BrAPI-Germplasm/Cross.json | 5 +- .../BrAPI-Germplasm/PedigreeNode.json | 5 +- .../BrAPI-Schema/BrAPI-Phenotyping/Image.json | 5 +- .../BrAPI-Schema/Requests/ListRequest.json | 9 +--- .../Requests/LocationRequest.json | 25 +++++----- .../Requests/ObservationRequest.json | 14 +++--- .../Requests/ObservationUnitRequest.json | 12 ++--- .../Requests/PedigreeNodeRequest.json | 26 +++++----- .../Requests/ReferenceRequest.json | 10 ++-- .../BrAPI-Schema/Requests/StudyRequest.json | 6 +-- .../BrAPI-Schema/Requests/VarientRequest.json | 12 ++--- 20 files changed, 126 insertions(+), 98 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json index 59e0a822..d75f7524 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json @@ -81,7 +81,10 @@ "ontologyReference": { "description": "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", "relationshipType": "one-to-one", - "$ref": "../BrAPI-Phenotyping/OntologyReference.json#/$defs/OntologyReference" + "anyOf": [ + {"$ref": "../BrAPI-Phenotyping/OntologyReference.json#/$defs/OntologyReference"}, + {"type": "null"} + ] }, "scale": { "description": "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\".", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/ListType.json b/Specification/BrAPI-Schema/BrAPI-Core/ListType.json index a65944ff..bc697828 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/ListType.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/ListType.json @@ -14,7 +14,8 @@ "observationVariables", "samples" ], - "type": "string" + "type": "string", + "nullable": true } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Core/ListType.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index 92e4e735..1c8c75bf 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -209,10 +209,7 @@ }, "studyDescription": { "description": "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study", - "type": [ - "null", - "string" - ] + "type": "string" }, "studyName": { "description": "The human readable name for a study\n\nMIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json index ebd56cec..0aec7a90 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json @@ -34,6 +34,21 @@ "description": "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string.", "type": "string" }, + "genotype": { + "$ref": "../BrAPI-Genotyping/Call.json#/$defs/ListValue" + }, + "genotype_likelihood": { + "deprecated": true, + "description": "**Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491 \n
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec.", + "items": { + "format": "double", + "type": "number" + }, + "type": "array", + "example": [ + 1 + ] + }, "variant": { "$ref": "Variant.json#/$defs/Variant", "description": "The ID of the variant this call belongs to.", @@ -98,6 +113,39 @@ "brapi-metadata": { "primaryModel": false } + }, + "ListValue": { + "deprecated": true, + "type": "object", + "description": "**Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`. Github issue number #491 \n
`ListValue` is a wrapper around a repeated field of values.\n
The JSON representation for `ListValue` is JSON array.", + "properties": { + "values": { + "type": "array", + "deprecated": true, + "description": "**Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`. Github issue number #491 \n
Repeated field of dynamically typed values.", + "items": { + "oneOf": [ + { + "description": "Represents a boolean value.", + "format": "boolean", + "type": "boolean" + }, + { + "description": "Represents a double value.", + "format": "double", + "type": "number" + }, + { + "description": "Represents a string value.", + "type": "string" + } + ] + }, + "example": [ + "AA" + ] + } + } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json index ca811dc4..6d8299f1 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json @@ -62,10 +62,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "sample": { "anyOf": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json index 74f78810..88d3ba05 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json @@ -27,10 +27,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "isDerived": { "description": "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", @@ -62,7 +59,14 @@ "type": "string" }, "referenceSet": { - "$ref": "ReferenceSet.json#/$defs/ReferenceSet", + "anyOf": [ + { + "$ref": "ReferenceSet.json#/$defs/ReferenceSet" + }, + { + "type": "null" + } + ], "description": "The unique identifier for a `ReferenceSet`", "referencedAttribute": "references", "relationshipType": "many-to-one" diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json index e1474253..3270ac9c 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json @@ -38,10 +38,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "germplasm": { "description": "The ID which uniquely identifies a `Germplasm`", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json index 9a681b97..abd58af8 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json @@ -102,10 +102,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "filtersApplied": { "description": "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value.", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json index b2987c88..2aa3efe2 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json @@ -90,10 +90,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "metadataFields": { "description": "The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard ", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json index 4544ce5b..53db816f 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json @@ -57,10 +57,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "parent1": { "$ref": "CrossParent.json#/$defs/CrossParent", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json index c20173d4..3b54ef90 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json @@ -41,10 +41,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "familyCode": { "description": "The code representing the family of this germplasm", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json index 613a1642..f735551e 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json @@ -39,10 +39,7 @@ "description": "ExternalReferences" }, "title": "ExternalReferences", - "type": [ - "null", - "array" - ] + "type": "array" }, "imageContent": { "description": "The content of the image", diff --git a/Specification/BrAPI-Schema/Requests/ListRequest.json b/Specification/BrAPI-Schema/Requests/ListRequest.json index 37c8c3bf..ff26a1c1 100644 --- a/Specification/BrAPI-Schema/Requests/ListRequest.json +++ b/Specification/BrAPI-Schema/Requests/ListRequest.json @@ -89,14 +89,7 @@ ] }, "listType": { - "anyOf": [ - { - "$ref": "../BrAPI-Core/ListType.json#/$defs/ListType" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Core/ListType.json#/$defs/ListType" } } } diff --git a/Specification/BrAPI-Schema/Requests/LocationRequest.json b/Specification/BrAPI-Schema/Requests/LocationRequest.json index 43931d73..ac007b4c 100644 --- a/Specification/BrAPI-Schema/Requests/LocationRequest.json +++ b/Specification/BrAPI-Schema/Requests/LocationRequest.json @@ -16,7 +16,7 @@ "properties": { "abbreviations": { "description": "A list of shortened human readable names for a set of Locations", - "type": "array", + "type": ["array", "null"], "items": { "type": "string" }, @@ -27,17 +27,17 @@ }, "altitudeMin": { "description": "The minimum altitude to search for", - "type": "number", + "type": ["number", "null"], "example": 20 }, "altitudeMax": { "description": "The maximum altitude to search for", - "type": "number", + "type": ["number", "null"], "example": 200 }, "countryCodes": { "description": "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec", - "type": "array", + "type": ["array", "null"], "items": { "type": "string" }, @@ -48,7 +48,7 @@ }, "countryNames": { "description": "The full name of the country to search for", - "type": "array", + "type": ["array", "null"], "items": { "type": "string" }, @@ -58,11 +58,14 @@ ] }, "coordinates": { - "$ref": "Schemas/GeoJSONSearchArea.json#/$defs/GeoJSONSearchArea" + "anyOf": [ + {"$ref": "Schemas/GeoJSONSearchArea.json#/$defs/GeoJSONSearchArea"}, + {"type": "null"} + ] }, "instituteAddresses": { "description": "The street address of the institute to search for", - "type": "array", + "type": ["array", "null"], "items": { "type": "string" }, @@ -73,7 +76,7 @@ }, "instituteNames": { "description": "The name of the institute to search for", - "type": "array", + "type": ["array", "null"], "items": { "type": "string" }, @@ -84,7 +87,7 @@ }, "locationTypes": { "description": "The type of location this represents (ex. Breeding Location, Storage Location, etc)", - "type": "array", + "type": ["array", "null"], "items": { "type": "string" }, @@ -95,7 +98,7 @@ }, "parentLocationDbIds": { "description": "The unique identifier for a Location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", - "type": "array", + "type": ["array", "null"], "items": { "type": "string" }, @@ -106,7 +109,7 @@ }, "parentLocationNames": { "description": "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", - "type": "array", + "type": ["array", "null"], "items": { "type": "string" }, diff --git a/Specification/BrAPI-Schema/Requests/ObservationRequest.json b/Specification/BrAPI-Schema/Requests/ObservationRequest.json index 76bd4f28..17a1ddb3 100644 --- a/Specification/BrAPI-Schema/Requests/ObservationRequest.json +++ b/Specification/BrAPI-Schema/Requests/ObservationRequest.json @@ -31,7 +31,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "6a4a59d8", "3ff067e0" @@ -42,7 +42,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "76f559b5", "066bc5d3" @@ -50,7 +50,7 @@ }, "observationLevels": { "description": "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", - "type": "array", + "type": ["array", "null"], "items": { "$ref": "../BrAPI-Phenotyping/ObservationUnitLevel.json#/$defs/ObservationUnitLevel" }, @@ -71,7 +71,7 @@ }, "observationLevelRelationships": { "description": "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", - "type": "array", + "type": ["array", "null"], "items": { "$ref": "../BrAPI-Phenotyping/ObservationUnitLevelRelationship.json#/$defs/ObservationUnitLevelRelationship" }, @@ -134,19 +134,19 @@ "observationTimeStampRangeEnd": { "description": "Timestamp range end", "format": "date-time", - "type": "string" + "type": ["string", "null"] }, "observationTimeStampRangeStart": { "description": "Timestamp range start", "format": "date-time", - "type": "string" + "type": ["string", "null"] }, "seasonDbIds": { "description": "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "Spring 2018", "Season A" diff --git a/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json b/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json index 7b11365b..7775df5d 100644 --- a/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json +++ b/Specification/BrAPI-Schema/Requests/ObservationUnitRequest.json @@ -31,7 +31,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "66bab7e3", "0e5e7f99" @@ -42,7 +42,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "FieldA_PlotB", "SpecialPlantName" @@ -50,7 +50,7 @@ }, "observationLevels": { "description": "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", - "type": "array", + "type": ["array", "null"], "items": { "$ref": "../BrAPI-Phenotyping/ObservationUnitLevel.json#/$defs/ObservationUnitLevel" }, @@ -71,7 +71,7 @@ }, "observationLevelRelationships": { "description": "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", - "type": "array", + "type": ["array", "null"], "items": { "$ref": "../BrAPI-Phenotyping/ObservationUnitLevelRelationship.json#/$defs/ObservationUnitLevelRelationship" }, @@ -133,7 +133,7 @@ }, "includeObservations": { "description": "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", - "type": "boolean", + "type": ["boolean", "null"], "example": false }, "seasonDbIds": { @@ -141,7 +141,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "Spring 2018", "Season A" diff --git a/Specification/BrAPI-Schema/Requests/PedigreeNodeRequest.json b/Specification/BrAPI-Schema/Requests/PedigreeNodeRequest.json index 6b2854b7..e871142f 100644 --- a/Specification/BrAPI-Schema/Requests/PedigreeNodeRequest.json +++ b/Specification/BrAPI-Schema/Requests/PedigreeNodeRequest.json @@ -25,7 +25,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "http://pui.per/accession/A0000003", "http://pui.per/accession/A0000477" @@ -36,7 +36,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "A0000003", "A0000477" @@ -47,7 +47,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "RDP1", "MDP1" @@ -58,7 +58,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "f0000203", "fa009965" @@ -69,7 +69,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "PER001", "NOR001" @@ -80,7 +80,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "Aspergillus fructus", "Zea mays" @@ -91,7 +91,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "Aspergillus", "Zea" @@ -102,7 +102,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "fructus", "mays" @@ -113,7 +113,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "variety_1", "2c38f9b6" @@ -121,22 +121,22 @@ }, "includeParents": { "description": "If this parameter is true, include the array of parents in the response", - "type": "boolean", + "type": ["boolean", "null"], "example": true }, "includeSiblings": { "description": "If this parameter is true, include the array of siblings in the response", - "type": "boolean", + "type": ["boolean", "null"], "example": true }, "includeProgeny": { "description": "If this parameter is true, include the array of progeny in the response", - "type": "boolean", + "type": ["boolean", "null"], "example": true }, "includeFullTree": { "description": "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", - "type": "boolean", + "type": ["boolean", "null"], "example": true }, "pedigreeDepth": { diff --git a/Specification/BrAPI-Schema/Requests/ReferenceRequest.json b/Specification/BrAPI-Schema/Requests/ReferenceRequest.json index bd4f522f..adf1bae5 100644 --- a/Specification/BrAPI-Schema/Requests/ReferenceRequest.json +++ b/Specification/BrAPI-Schema/Requests/ReferenceRequest.json @@ -21,7 +21,7 @@ "type": "object", "properties": { "accessions": { - "type": "array", + "type": ["array", "null"], "description": "If specified, return the references for which the `accession` matches this string (case-sensitive, exact match).", "items": { "type": "string" @@ -32,7 +32,7 @@ ] }, "md5checksums": { - "type": "array", + "type": ["array", "null"], "description": "If specified, return the references for which the `md5checksum` matches this string (case-sensitive, exact match).", "items": { "type": "string" @@ -42,7 +42,7 @@ ] }, "referenceDbIds": { - "type": "array", + "type": ["array", "null"], "description": "A list of IDs which uniquely identify `References` within the given database server", "items": { "type": "string" @@ -53,7 +53,7 @@ ] }, "referenceSetDbIds": { - "type": "array", + "type": ["array", "null"], "description": "A list of IDs which uniquely identify `ReferenceSets` within the given database server", "items": { "type": "string" @@ -66,7 +66,7 @@ "isDerived": { "description": "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", "format": "boolean", - "type": "boolean" + "type": ["boolean", "null"] }, "minLength": { "description": "The minimum length of this `References` sequence.", diff --git a/Specification/BrAPI-Schema/Requests/StudyRequest.json b/Specification/BrAPI-Schema/Requests/StudyRequest.json index e87f9134..c034abaa 100644 --- a/Specification/BrAPI-Schema/Requests/StudyRequest.json +++ b/Specification/BrAPI-Schema/Requests/StudyRequest.json @@ -86,16 +86,16 @@ "studyType", "studyName", "studyLocation", - "programName" + "programName", + "germplasmDbId", + "observationVariableDbId" ], "type": ["null", "string"] }, "sortOrder": { "description": "Sort order direction. Ascending/Descending.", "enum": [ - "asc", "ASC", - "desc", "DESC" ], "type": ["null", "string"] diff --git a/Specification/BrAPI-Schema/Requests/VarientRequest.json b/Specification/BrAPI-Schema/Requests/VarientRequest.json index a337bbb1..46da2f1d 100644 --- a/Specification/BrAPI-Schema/Requests/VarientRequest.json +++ b/Specification/BrAPI-Schema/Requests/VarientRequest.json @@ -23,7 +23,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "4639fe3e", "b60d900b" @@ -37,7 +37,7 @@ "referenceDbId": { "deprecated": true, "description": "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", - "type": "string", + "type": ["string", "null"], "example": "120a2d5c" }, "referenceDbIds": { @@ -45,7 +45,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "89ab4d17", "74d3b63d" @@ -56,7 +56,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "d3b63d4d", "3b63d74b" @@ -72,7 +72,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "3b63d889", "ab4d174d" @@ -83,7 +83,7 @@ "items": { "type": "string" }, - "type": "array", + "type": ["array", "null"], "example": [ "ba63d810", "434d1760" From fb5a90a91325abce62bf060821884d45c52d4101 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Sun, 17 May 2026 20:20:47 +1200 Subject: [PATCH 43/62] fixed various --- .../Programs/Programs_GET_POST.yaml | 4 +- Specification/BrAPI-Core/Programs/README.md | 2 +- .../Schemas/ProgramSearchRequest.yaml | 6 +- ...ch_Observations_SearchResultsDbId_GET.yaml | 1 - .../BrAPI-Schema/BrAPI-Common/GeoJSON.json | 1 + .../BrAPI-Common/GeoJSONGeometry.json | 1 + .../BrAPI-Schema/BrAPI-Common/Variable.json | 5 +- .../BrAPI-Schema/BrAPI-Core/Location.json | 9 +-- .../BrAPI-Schema/BrAPI-Core/Program.json | 5 +- .../BrAPI-Schema/BrAPI-Core/Study.json | 16 ++--- .../BrAPI-Schema/BrAPI-Genotyping/Call.json | 1 + .../BrAPI-Genotyping/CallSet.json | 5 +- .../BrAPI-Genotyping/Reference.json | 26 +++++++- .../BrAPI-Schema/BrAPI-Genotyping/Sample.json | 2 +- .../BrAPI-Genotyping/Variant.json | 35 +++++++---- .../BrAPI-Genotyping/VariantSet.json | 4 +- .../BrAPI-Schema/BrAPI-Germplasm/Cross.json | 9 +++ .../BrAPI-Germplasm/CrossParent.json | 1 + .../BrAPI-Germplasm/Germplasm.json | 9 +-- .../BrAPI-Schema/BrAPI-Phenotyping/Event.json | 49 ++++++++++----- .../BrAPI-Phenotyping/ObservationUnit.json | 11 +--- .../BrAPI-Phenotyping/OntologyReference.json | 11 +--- .../Requests/AlleleMatrixRequest.json | 18 +++++- .../BrAPI-Schema/Requests/CallRequest.json | 4 ++ .../Requests/LocationRequest.json | 5 +- .../Responses/CallListResponse.json | 62 +++++++++++++++++++ 26 files changed, 208 insertions(+), 94 deletions(-) create mode 100644 Specification/BrAPI-Schema/Responses/CallListResponse.json diff --git a/Specification/BrAPI-Core/Programs/Programs_GET_POST.yaml b/Specification/BrAPI-Core/Programs/Programs_GET_POST.yaml index 5ef0aea4..f1844449 100644 --- a/Specification/BrAPI-Core/Programs/Programs_GET_POST.yaml +++ b/Specification/BrAPI-Core/Programs/Programs_GET_POST.yaml @@ -17,14 +17,14 @@ paths: - name: programType description: |- The type of program entity this object represents -
'STANARD' represents a standard, permenant breeding program +
'STANDARD' represents a standard, permenant breeding program
'PROJECT' represents a short term project, usually with a set time limit based on funding in: query required: false schema: type: string enum: - - STANARD + - STANDARD - PROJECT - $ref: '#/components/parameters/commonCropName' - $ref: '#/components/parameters/programDbId' diff --git a/Specification/BrAPI-Core/Programs/README.md b/Specification/BrAPI-Core/Programs/README.md index 684b2c78..4dd7a6fe 100644 --- a/Specification/BrAPI-Core/Programs/README.md +++ b/Specification/BrAPI-Core/Programs/README.md @@ -627,7 +627,7 @@ Review the 'STANARD' represents a standard, permenant breeding program +
'STANDARD' represents a standard, permenant breeding program
'PROJECT' represents a short term project, usually with a set time limit based on funding items: type: string enum: - - STANARD + - STANDARD - PROJECT type: array nullable: true - example: ['STANARD', 'PROJECT'] + example: ['STANDARD', 'PROJECT'] diff --git a/Specification/BrAPI-Phenotyping/Observations/Search_Observations_SearchResultsDbId_GET.yaml b/Specification/BrAPI-Phenotyping/Observations/Search_Observations_SearchResultsDbId_GET.yaml index a2d348a9..d763a2f9 100644 --- a/Specification/BrAPI-Phenotyping/Observations/Search_Observations_SearchResultsDbId_GET.yaml +++ b/Specification/BrAPI-Phenotyping/Observations/Search_Observations_SearchResultsDbId_GET.yaml @@ -14,7 +14,6 @@ paths: Use this endpoint to retrieve the results of the search.
Review the Search Services documentation for additional implementation details. parameters: - - $ref: '#/components/parameters/acceptHeader' - $ref: '#/components/parameters/authorizationHeader' - $ref: '#/components/parameters/searchResultsDbId' - $ref: '#/components/parameters/page' diff --git a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json index 64387253..fd533295 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json @@ -3,6 +3,7 @@ "GeoJSON": { "title": "GeoJSON", "type": "object", + "nullable" : true, "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", "properties": { "geometry": { diff --git a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json index 0993e0eb..6261c3d9 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json @@ -1,6 +1,7 @@ { "$defs": { "GeoJSONGeometry": { + "nullable": true, "oneOf": [ { "description": "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json index d75f7524..59e0a822 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json @@ -81,10 +81,7 @@ "ontologyReference": { "description": "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", "relationshipType": "one-to-one", - "anyOf": [ - {"$ref": "../BrAPI-Phenotyping/OntologyReference.json#/$defs/OntologyReference"}, - {"type": "null"} - ] + "$ref": "../BrAPI-Phenotyping/OntologyReference.json#/$defs/OntologyReference" }, "scale": { "description": "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\".", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Location.json b/Specification/BrAPI-Schema/BrAPI-Core/Location.json index ab5f1cb8..5764d055 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Location.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Location.json @@ -31,14 +31,7 @@ "coordinates": { "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", "relationshipType": "one-to-one", - "anyOf": [ - { - "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON" }, "countryCode": { "description": "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec\n
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.'", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Program.json b/Specification/BrAPI-Schema/BrAPI-Core/Program.json index 130c4604..f7990981 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Program.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Program.json @@ -84,10 +84,7 @@ "PROJECT", null ], - "type": [ - "null", - "string" - ] + "type": "string" }, "trials": { "title": "Trials", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index 1c8c75bf..e7b716d2 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -358,10 +358,6 @@ "description": "Human-readable value of the environment parameter (defined above) constant within the experiment", "type": "string" }, - "environmentParametersDbId": { - "description": "Human-readable value of the environment parameter (defined above) constant within the experiment", - "type": "string" - }, "parameterName": { "description": "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. ", "type": "string" @@ -420,6 +416,7 @@ } }, "ExperimentalDesign": { + "nullable": true, "properties": { "PUI": { "description": "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology.", @@ -450,13 +447,11 @@ } }, "GrowthFacility": { + "nullable": true, "properties": { "PUI": { "description": "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology.", - "type": [ - "null", - "string" - ] + "type": "string" }, "description": { "description": "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out.", @@ -480,11 +475,8 @@ } }, "LastUpdate": { + "nullable": true, "properties": { - "lastUpdateDbId": { - "description": "The ID which uniquely identifies a LastUpdate within the given database server", - "type": "string" - }, "timestamp": { "description": "The timestamp of the update.", "format": "date-time", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json index 0aec7a90..2eef2136 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json @@ -35,6 +35,7 @@ "type": "string" }, "genotype": { + "deprecated": true, "$ref": "../BrAPI-Genotyping/Call.json#/$defs/ListValue" }, "genotype_likelihood": { diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json index 6d8299f1..87be31cb 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/CallSet.json @@ -105,7 +105,10 @@ }, "referencedAttribute": "callSets", "relationshipType": "many-to-many", - "type": "array" + "type": [ + "null", + "array" + ] } }, "required": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json index 88d3ba05..e7d5f146 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json @@ -93,7 +93,7 @@ "relationshipType": "one-to-many", "referencedAttribute": "reference", "items": { - "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", + "$ref": "Reference.json#/$defs/SourceGermplasm", "description": "SourceGermplasm" }, "title": "SourceGermplasm", @@ -174,6 +174,30 @@ "brapi-metadata": { "primaryModel": false } + }, + "SourceGermplasm": { + "properties": { + "germplasmDbId": { + "description": "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.", + "type": "string" + }, + "germplasmName": { + "description": "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space.", + "type": "string" + }, + "reference": { + "description": "The Reference associated with this Source Germplasm", + "$ref": "Reference.json#/$defs/Reference", + "relationshipType": "many-to-one", + "referencedAttribute": "sourceGermplasm" + } + }, + "title": "SourceGermplasm", + "description": "A reference to a Germplasm", + "type": "object", + "brapi-metadata": { + "primaryModel": false + } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json index 3270ac9c..cad6ed7f 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Sample.json @@ -120,7 +120,7 @@ "string" ] }, - "sampleGroupId": { + "sampleGroupDbId": { "description": "The ID which uniquely identifies a group of `Samples`", "type": [ "null", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json index abd58af8..9d095cf4 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Variant.json @@ -2,6 +2,29 @@ "$defs": { "Variant": { "properties": { + "alternate_bases": { + "deprecated": true, + "description": "**Deprecated in v2.1** Please use `alternateBases`. Github issue number #549\n
The bases that appear instead of the reference bases. Multiple alternate alleles are possible.", + "items": { + "type": "string" + }, + "type": [ + "null", + "array" + ], + "examples": ["T", "TAC"] + }, + "alternateBases": { + "description": "The bases that appear instead of the reference bases. Multiple alternate alleles are possible.", + "items": { + "type": "string" + }, + "type": [ + "null", + "array" + ], + "examples": ["T", "TAC"] + }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", @@ -49,16 +72,6 @@ "array" ] }, - "analysis": { - "description": "Set of Analysis descriptors for this VariantSet", - "items": { - "type": "string" - }, - "type": [ - "null", - "array" - ] - }, "ciend": { "description": "Similar to \"cipos\", but for the variant's end position (which is derived from start + svlen).", "items": { @@ -200,7 +213,7 @@ "array" ] }, - "variantSet": { + "variantSets": { "items": { "$ref": "VariantSet.json#/$defs/VariantSet" }, diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json index 2aa3efe2..2c27e47d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json @@ -151,8 +151,8 @@ "variants": { "title": "variants", "description": "variants", - "referencedAttribute": "variantSet", - "relationshipType": "one-to-many", + "referencedAttribute": "variantSets", + "relationshipType": "many-to-many", "items": { "$ref": "Variant.json#/$defs/Variant", "description": "Variant" diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json index 53db816f..e1b5e705 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json @@ -80,6 +80,15 @@ } ] }, + "pollinationTimeStamp": { + "description": "**Deprecated in v2.1** Please use `pollinationEvents`. Github issue number #265\n
The timestamp when the pollination took place", + "deprecated": true, + "type": [ + "null", + "string" + ], + "format": "date-time" + }, "pollinationEvents": { "description": "The list of pollination events that occurred for this cross.", "relationshipType": "one-to-many", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json index fc638818..04993067 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json @@ -1,6 +1,7 @@ { "$defs": { "CrossParent": { + "nullable" : true, "properties": { "germplasm": { "description": "the germplasm of the cross parent", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index 8e690ca5..eb0acd44 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -889,14 +889,7 @@ }, "coordinates": { "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", - "anyOf": [ - { - "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON" }, "germplasm": { "description": "associated germplasm", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json index 44fbf5a7..f04064cb 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json @@ -7,16 +7,22 @@ "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", "relationshipType": "one-to-one" }, + "date": { + "description": "**Deprecated in v2.1** Please use `eventDateRange.discreteDates`. Github issue number #440\n
A list of dates when the event occurred\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", + "deprecated": true, + "items": { + "type": "string", + "format": "date-time" + }, + "type": [ + "null", + "array" + ], + "examples" : ["2018-10-08T18:15:11Z", "2018-11-09T18:16:12Z"] + }, "eventDateRange": { "description": "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)", - "anyOf": [ - { - "$ref": "../BrAPI-Phenotyping/Event.json#/$defs/EventDateRange" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Phenotyping/Event.json#/$defs/EventDateRange" }, "eventDbId": { "description": "Internal database identifier", @@ -61,10 +67,20 @@ }, "referencedAttribute": "events", "relationshipType": "many-to-many", - "type": "array" + "type": [ + "null", + "array" + ] }, "study": { - "$ref": "../BrAPI-Core/Study.json#/$defs/Study", + "anyOf": [ + { + "$ref": "../BrAPI-Core/Study.json#/$defs/Study" + }, + { + "type": "null" + } + ], "description": "The study in which the event occurred", "referencedAttribute": "events", "relationshipType": "many-to-one" @@ -82,6 +98,7 @@ } }, "EventDateRange": { + "nullable": true, "properties": { "discreteDates": { "description": "A list of dates when the event occurred\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", @@ -171,15 +188,19 @@ "key": { "deprecated": true, "description": "**Deprecated in v2.1** Please use `name`. Github issue number #440 \n
Specifies the relationship between the event and the given property. E.g. fertilizer, operator", - "type": "string", - "nullable": true, + "type": [ + "null", + "string" + ], "example": "operator" }, "rdfValue": { "deprecated": true, "description": "**Deprecated in v2.1** Please use `code`. Github issue number #440 \n Date: Tue, 19 May 2026 19:46:25 +1200 Subject: [PATCH 44/62] fixed various --- Specification/BrAPI-Core/Programs/README.md | 4 +-- .../Studies/Schemas/StudySearchRequest.yaml | 2 ++ .../BrAPI-Core/Studies/Studies_GET_POST.yaml | 2 ++ .../Schemas/AlleleMatrixParameters.yaml | 4 +-- .../VariantSets/VariantSets_GET.yaml | 1 + .../Crosses/Schemas/CrossParent.yaml | 1 + .../BrAPI-Schema/BrAPI-Core/ListType.json | 3 +- .../BrAPI-Genotyping/VariantSet.json | 18 +++--------- .../BrAPI-Germplasm/ParentType.json | 3 +- .../BrAPI-Germplasm/PedigreeNode.json | 29 ++++++++++++------- .../Requests/AlleleMatrixRequest.json | 20 ++++--------- .../BrAPI-Schema/Requests/StudyRequest.json | 4 ++- Specification/Generated/brapi_openapi.json | 10 +++---- .../Generated/brapi_openapi_comparison.md | 2 +- generator/build.gradle | 2 +- 15 files changed, 51 insertions(+), 54 deletions(-) diff --git a/Specification/BrAPI-Core/Programs/README.md b/Specification/BrAPI-Core/Programs/README.md index 4dd7a6fe..b429df62 100644 --- a/Specification/BrAPI-Core/Programs/README.md +++ b/Specification/BrAPI-Core/Programs/README.md @@ -38,7 +38,7 @@ Get a filtered list of breeding Programs. This list can be filtered by common cr + Parameters + abbreviation (Optional, ) ... A shortened version of the human readable name for a Program - + programType (Optional, ) ... The type of program entity this object represents
'STANARD' represents a standard, permenant breeding program
'PROJECT' represents a short term project, usually with a set time limit based on funding + + programType (Optional, ) ... The type of program entity this object represents
'STANDARD' represents a standard, permenant breeding program
'PROJECT' represents a short term project, usually with a set time limit based on funding + commonCropName (Optional, ) ... The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.Use this parameter to only return results associated with the given crop. Use `GET /commoncropnames` to find the list of available crops on a server. + programDbId (Optional, ) ... Use this parameter to only return results associated with the given `Program` unique identifier.
Use `GET /programs` to find the list of available `Programs` on a server. + programName (Optional, ) ... Use this parameter to only return results associated with the given `Program` by its human readable name.
Use `GET /programs` to find the list of available `Programs` on a server. @@ -548,7 +548,7 @@ Review the pageSizeintegerThe size of the pages to be returned. Default is `1000`. programDbIdsarray[string]A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. Use this parameter to only return results associated with the given programs. Use `GET /programs` to find the list of available programs on a server. programNamesarray[string]Use this parameter to only return results associated with the given program names. Program names are not required to be unique. Use `GET /programs` to find the list of available programs on a server. -programTypesarray[string]The type of program entity this object represents
'STANARD' represents a standard, permenant breeding program
'PROJECT' represents a short term project, usually with a set time limit based on funding +programTypesarray[string]The type of program entity this object represents
'STANDARD' represents a standard, permenant breeding program
'PROJECT' represents a short term project, usually with a set time limit based on funding diff --git a/Specification/BrAPI-Core/Studies/Schemas/StudySearchRequest.yaml b/Specification/BrAPI-Core/Studies/Schemas/StudySearchRequest.yaml index 99364617..8d7effd5 100644 --- a/Specification/BrAPI-Core/Studies/Schemas/StudySearchRequest.yaml +++ b/Specification/BrAPI-Core/Studies/Schemas/StudySearchRequest.yaml @@ -49,7 +49,9 @@ components: sortOrder: description: Order results should be sorted. ex. "ASC" or "DESC" enum: + - asc - ASC + - desc - DESC type: string nullable: true diff --git a/Specification/BrAPI-Core/Studies/Studies_GET_POST.yaml b/Specification/BrAPI-Core/Studies/Studies_GET_POST.yaml index d1d828e5..f50d7ecb 100644 --- a/Specification/BrAPI-Core/Studies/Studies_GET_POST.yaml +++ b/Specification/BrAPI-Core/Studies/Studies_GET_POST.yaml @@ -68,6 +68,8 @@ paths: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId type: string - description: Sort order direction. Ascending/Descending. in: query diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixParameters.yaml b/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixParameters.yaml index 8ee5b8a1..10b624af 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixParameters.yaml +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixParameters.yaml @@ -26,7 +26,7 @@ components: dataMatrixNames: name: dataMatrixNames description: |- - "dataMatrixNames" is a comma seperated list of names (ie 'Genotype, Read Depth' etc). This list controls which data matrices are returned in the response. + "dataMatrixNames" is a comma separated list of names (ie 'Genotype, Read Depth' etc). This list controls which data matrices are returned in the response.
This maps to a FORMAT field in the VCF file standard. in: query required: false @@ -35,7 +35,7 @@ components: dataMatrixAbbreviations: name: dataMatrixAbbreviations description: |- - "dataMatrixAbbreviations" is a comma seperated list of abbreviations (ie 'GT, RD' etc). This list controls which data matrices are returned in the response. + "dataMatrixAbbreviations" is a comma separated list of abbreviations (ie 'GT, RD' etc). This list controls which data matrices are returned in the response.
This maps to a FORMAT field in the VCF file standard. in: query required: false diff --git a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_GET.yaml b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_GET.yaml index c3dca6e1..59f33cb4 100644 --- a/Specification/BrAPI-Genotyping/VariantSets/VariantSets_GET.yaml +++ b/Specification/BrAPI-Genotyping/VariantSets/VariantSets_GET.yaml @@ -37,6 +37,7 @@ paths: - $ref: '#/components/parameters/studyDbId' - $ref: '#/components/parameters/studyName' - $ref: '#/components/parameters/externalReferenceId' + - $ref: '#/components/parameters/externalReferenceID' - $ref: '#/components/parameters/externalReferenceSource' - $ref: '#/components/parameters/page' - $ref: '#/components/parameters/pageSize' diff --git a/Specification/BrAPI-Germplasm/Crosses/Schemas/CrossParent.yaml b/Specification/BrAPI-Germplasm/Crosses/Schemas/CrossParent.yaml index ab72ec21..e088ce9f 100644 --- a/Specification/BrAPI-Germplasm/Crosses/Schemas/CrossParent.yaml +++ b/Specification/BrAPI-Germplasm/Crosses/Schemas/CrossParent.yaml @@ -35,5 +35,6 @@ components: - FEMALE - SELF - POPULATION + - CLONAL type: string example: MALE \ No newline at end of file diff --git a/Specification/BrAPI-Schema/BrAPI-Core/ListType.json b/Specification/BrAPI-Schema/BrAPI-Core/ListType.json index bc697828..a65944ff 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/ListType.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/ListType.json @@ -14,8 +14,7 @@ "observationVariables", "samples" ], - "type": "string", - "nullable": true + "type": "string" } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Core/ListType.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json index 2c27e47d..91a1095c 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json @@ -336,27 +336,17 @@ "string", "integer", "float", - "boolean", - null + "boolean" ], - "type": [ - "null", - "string" - ] + "type": "string" }, "fieldAbbreviation": { "description": "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"", - "type": [ - "null", - "string" - ] + "type": "string" }, "fieldName": { "description": "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"", - "type": [ - "null", - "string" - ] + "type": "string" }, "variantSet": { "description": "Formats associated with a variant set", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/ParentType.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/ParentType.json index e3e0a490..4651dca7 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/ParentType.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/ParentType.json @@ -6,7 +6,8 @@ "MALE", "FEMALE", "SELF", - "POPULATION" + "POPULATION", + "CLONAL" ], "type": "string" } diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json index 3b54ef90..250c92a1 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json @@ -8,13 +8,27 @@ "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo" }, "breedingMethod": { - "$ref": "BreedingMethod.json#/$defs/BreedingMethod", + "anyOf": [ + { + "$ref": "BreedingMethod.json#/$defs/BreedingMethod" + }, + { + "type": "null" + } + ], "description": "The unique identifier for the breeding method used to create this germplasm", "referencedAttribute": "pedigreeNodes", "relationshipType": "many-to-one" }, "crossingProject": { - "$ref": "CrossingProject.json#/$defs/CrossingProject", + "anyOf": [ + { + "$ref": "CrossingProject.json#/$defs/CrossingProject" + }, + { + "type": "null" + } + ], "description": "The crossing project used to generate this germplasm", "referencedAttribute": "pedigreeNodes", "relationshipType": "many-to-one" @@ -69,13 +83,6 @@ "array" ] }, - "pedigreeNodeDbId": { - "description": "The ID which uniquely identifies a pedigree node", - "type": [ - "null", - "string" - ] - }, "pedigreeString": { "description": "The string representation of the pedigree for this germplasm in PURDY notation", "type": [ @@ -123,7 +130,7 @@ }, "GermplasmParent": { "properties": { - "parentGermplasm": { + "germplasm": { "$ref": "Germplasm.json#/$defs/Germplasm", "description": "The parent germplasm", "referencedAttribute": "progenyPedigreeNodes", @@ -141,7 +148,7 @@ } }, "required": [ - "parentGermplasm", + "germplasm", "parentType" ], "title": "GermplasmParent", diff --git a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json index d17c9665..d0080959 100644 --- a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json +++ b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json @@ -67,25 +67,17 @@ "type": ["null", "integer"] }, "dataMatrixNames": { - "description": "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", - "type": ["null", "array"], - "items": { - "type": "string" - }, + "description": "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "type": ["null", "string"], "example": [ - "Genotype", - "Read Depth" + "Genotype,Read Depth" ] }, "dataMatrixAbbreviations": { - "description": "`dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", - "type": ["null", "array"], - "items": { - "type": "string" - }, + "description": "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "type": ["null", "string"], "example": [ - "GT", - "RD" + "GT,RD" ] }, "positionRanges": { diff --git a/Specification/BrAPI-Schema/Requests/StudyRequest.json b/Specification/BrAPI-Schema/Requests/StudyRequest.json index c034abaa..fbf16f09 100644 --- a/Specification/BrAPI-Schema/Requests/StudyRequest.json +++ b/Specification/BrAPI-Schema/Requests/StudyRequest.json @@ -96,7 +96,9 @@ "description": "Sort order direction. Ascending/Descending.", "enum": [ "ASC", - "DESC" + "DESC", + "asc", + "desc" ], "type": ["null", "string"] } diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index 0a52c98f..591a7ef3 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -11261,13 +11261,13 @@ }, "style" : "form" }, { - "description" : "The type of program entity this object represents\n
'STANARD' represents a standard, permenant breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permenant breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", "explode" : true, "in" : "query", "name" : "programType", "required" : false, "schema" : { - "enum" : [ "STANARD", "PROJECT" ], + "enum" : [ "STANDARD", "PROJECT" ], "type" : "string" }, "style" : "form" @@ -33137,10 +33137,10 @@ "type" : "array" }, "programTypes" : { - "description" : "The type of program entity this object represents\n
'STANARD' represents a standard, permenant breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", - "example" : [ "STANARD", "PROJECT" ], + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permenant breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "example" : [ "STANDARD", "PROJECT" ], "items" : { - "enum" : [ "STANARD", "PROJECT" ], + "enum" : [ "STANDARD", "PROJECT" ], "type" : "string" }, "nullable" : true, diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index 37f2977e..827a3253 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -914,7 +914,7 @@ Changed response : **200** Changed: `programType` in `query`: - Added enum values: [STANDARD] - - Removed enum values: [STANARD] + - Removed enum values: [STANDARD] ##### `POST` /programs diff --git a/generator/build.gradle b/generator/build.gradle index b326a4e0..ae6eacd7 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.65.0' + brapiSchemaToolsVersion = '0.68.0' } repositories { From a011f9ee72ac6b654ef1ca5559b1511e2317f05c Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 19 May 2026 19:57:16 +1200 Subject: [PATCH 45/62] removed OWL generation --- Specification/Generated/brapi_generated.ttl | 6676 ------------------- generator/build.gradle | 2 +- 2 files changed, 1 insertion(+), 6677 deletions(-) delete mode 100644 Specification/Generated/brapi_generated.ttl diff --git a/Specification/Generated/brapi_generated.ttl b/Specification/Generated/brapi_generated.ttl deleted file mode 100644 index 21f6decd..00000000 --- a/Specification/Generated/brapi_generated.ttl +++ /dev/null @@ -1,6676 +0,0 @@ -PREFIX owl: -PREFIX rdf: -PREFIX rdfs: -PREFIX xsd: - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; - rdfs:domain ; - rdfs:label "language"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Specifies a FASTA format file/string."@en; - rdfs:domain ; - rdfs:label "sourceURI"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes."@en; - rdfs:label "GermplasmChild"@en . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name of the taxonomy provider"@en; - rdfs:domain ; - rdfs:label "sourceName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Describes the approximate slope (height/distance) of a Location."@en; - rdfs:domain ; - rdfs:label "slope"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; - rdfs:domain ; - rdfs:label "levelOrder"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Unique DbId for the Seed Lot Transaction"@en; - rdfs:domain ; - rdfs:label "transactionDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "a custom attributes associated with a cross"@en; - rdfs:domain ; - rdfs:label "cross"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; - rdfs:domain ; - rdfs:label "scale"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "Metadata describing the acceptable values for this Scale"@en; - rdfs:label "ValidValues"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Other trait names"@en; - rdfs:domain ; - rdfs:label "synonyms"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name of the program"@en; - rdfs:domain ; - rdfs:label "programName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "donors associated with a germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; - rdfs:domain ; - rdfs:label "defaultValue"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "map"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observationUnits"@en; - rdfs:domain ; - rdfs:label "observationUnits"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; - rdfs:domain ; - rdfs:label "analysis"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated seedLot"@en; - rdfs:domain ; - rdfs:label "seedLot"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique DbId of the breeding program this Seed Lot belongs to"@en; - rdfs:domain ; - rdfs:label "program"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The shortened code name of an event parameter\n
ICASA \"Code_Display\""@en; - rdfs:domain ; - rdfs:label "code"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)"@en; - rdfs:domain ; - rdfs:label "locationType"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source"@en; - rdfs:domain ; - rdfs:label "seedSourceDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "If the event parameter 'unit' field is 'code', then use 'valueDescription' to add a human readable description to the value."@en; - rdfs:domain ; - rdfs:label "valueDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable description of a trial\n\nMIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail."@en; - rdfs:domain ; - rdfs:label "trialDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology."@en; - rdfs:domain ; - rdfs:label "PUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Experimental design associated with a study"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the human readable name for a cross"@en; - rdfs:domain ; - rdfs:label "crossName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) 10) Seed collection 11) Short term 12) Medium term 13) Long term 20) Field collection 30) In vitro collection 40) Cryo-preserved collection 50) DNA collection 99) Other (elaborate in REMARKS field)"@en; - rdfs:domain ; - rdfs:label "storageTypeCodes"@en; - rdfs:range . - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A sub-string of the bases that make up this reference. Bases are represented as IUPAC-IUB codes; this string matches the regular expression `[ACGTMRWSYKVHDBN]*`."@en; - rdfs:domain ; - rdfs:label "sequence"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)"@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Zero or more filters that failed for this variant. VCF column 7 \"FILTER\" shared across all alleles in the same VCF record."@en; - rdfs:domain ; - rdfs:label "filtersFailed"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "Links to various ontology documentation"@en; - rdfs:label "DocumentationLink"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The child germplasm"@en; - rdfs:domain ; - rdfs:label "childGermplasm"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name or identifier of the entity which took the `Sample` from the field"@en; - rdfs:domain ; - rdfs:label "takenBy"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; - rdfs:domain ; - rdfs:label "method"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A Permanent Unique Identifier for an observation unit\n\nMIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible."@en; - rdfs:domain ; - rdfs:label "observationUnitPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended."@en; - rdfs:label "Publication"@en . - - - rdf:type owl:Class; - rdfs:comment "The type of documentation, which can be OBO Foundry, an RDF term or a webpage."@en; - rdfs:label "DocumentationLinkType"@en . - - - rdf:type owl:Class; - rdfs:comment "A Season defines a period in time. A Season is made of two parts; (1) the primary year and (2) a term which defines a segment of the year. This term could be a traditional season, like \"Spring\" or \"Summer\", or this term could be a month, like \"May\" or \"June\", or this could be an arbitrary season name which is meaningful to the breeding Program like \"PlantingTime_3\" or \"Season E\"."@en; - rdfs:label "Season"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The version of the update."@en; - rdfs:domain ; - rdfs:label "version"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A general description of this Seed Lot Transaction"@en; - rdfs:domain ; - rdfs:label "transactionDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\"."@en; - rdfs:domain ; - rdfs:label "instituteCode"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "links to various ontology documentation"@en; - rdfs:domain ; - rdfs:label "documentationLinks"@en; - rdfs:range . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name of the `Sample`"@en; - rdfs:domain ; - rdfs:label "sampleName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Permanent Unique Identifier of an Attribute, usually in the form of a URI"@en; - rdfs:domain ; - rdfs:label "attributePUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "URI pointing to an ontology class for the unit"@en; - rdfs:domain ; - rdfs:label "unitPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The total number of elements that are available on the server and match the requested query parameters."@en; - rdfs:domain ; - rdfs:label "totalCount"@en; - rdfs:range xsd:integer . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable description of the analysis"@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "pedigreeNodes"@en; - rdfs:domain ; - rdfs:label "pedigreeNodes"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (COLLDATE) 17. Collecting date of the sample [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero]."@en; - rdfs:domain ; - rdfs:label "collectingDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Geometry associated with an image"@en; - rdfs:domain ; - rdfs:label "germplasmOrigin"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The code representing the family of this germplasm"@en; - rdfs:domain ; - rdfs:label "familyCode"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The linkage groups present in a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "linkageGroups"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of germplasm references that are direct children of this germplasm. These represent edges in the tree, connecting to other nodes.\n
The given germplasm could have a large number of progeny, across a number of different breeding methods. The 'parentType' shows \n the type of parent this germplasm is to each of the child germplasm references.\n
If the parameter 'includeProgeny' is set to false, then this array should be empty, null, or not present in the response."@en; - rdfs:domain ; - rdfs:label "progeny"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated ontology reference"@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; - rdfs:label "GermplasmOrigin"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "alleleMatrices"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The full name of the country where a Location is located\n
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code."@en; - rdfs:domain ; - rdfs:label "countryName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a representation for missing data."@en; - rdfs:domain ; - rdfs:label "unknownString"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a CallSet within the given database server"@en; - rdfs:domain ; - rdfs:label "callSetDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable description of an image."@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; - rdfs:label "BiologicalStatusOfAccessionCode"@en . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A program identifier to search for"@en; - rdfs:domain ; - rdfs:label "program"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of positional coordinate used for the Y coordinate of the position."@en; - rdfs:domain ; - rdfs:label "positionCoordinateYType"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study"@en; - rdfs:domain ; - rdfs:label "studyDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the value of a cross attribute"@en; - rdfs:domain ; - rdfs:label "crossAttributeValue"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the unique identifier for a program"@en; - rdfs:domain ; - rdfs:label "program"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; - rdfs:domain ; - rdfs:label "growthStage"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows."@en; - rdfs:domain ; - rdfs:label "dataMatrices"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (ACCENAME) 11. A collection of either a registered names or other designations given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase."@en; - rdfs:domain ; - rdfs:label "accessionNames"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Information about the collection of a germplasm"@en; - rdfs:domain ; - rdfs:label "collectingInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\". "@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\")."@en; - rdfs:domain ; - rdfs:label "subtaxon"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The contacts email address\n\nMIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person."@en; - rdfs:domain ; - rdfs:label "email"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The full name of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; - rdfs:domain ; - rdfs:label "instituteName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** "@en; - rdfs:domain ; - rdfs:label "observationLevelRelationships"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample"@en; - rdfs:label "CallSet"@en . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Formats associated with a variant set"@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "attributeValues"@en; - rdfs:domain ; - rdfs:label "attributeValues"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The timestamp for the last update to this Seed Lot (including transactions)"@en; - rdfs:domain ; - rdfs:label "lastUpdated"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The array of DbIds of the BrAPI objects contained in a List"@en; - rdfs:domain ; - rdfs:label "data"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "The record of an event where material was moved in or out of a particular SeedLot"@en; - rdfs:label "SeedLotTransaction"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Trait status (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; - rdfs:domain ; - rdfs:label "status"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID of the call set this variant call belongs to.\n\nIf this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same."@en; - rdfs:domain ; - rdfs:label "callSet"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The Ontology for this reference"@en; - rdfs:domain ; - rdfs:label "ontology"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "All known corresponding Germplasm"@en; - rdfs:domain ; - rdfs:label "sourceGermplasm"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observationUnits"@en; - rdfs:domain ; - rdfs:label "observationUnits"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier."@en; - rdfs:label "AlleleMatrix"@en . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "crosses"@en; - rdfs:domain ; - rdfs:label "crosses"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. \n
'dataFormat' defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)\n
'fileFormat' defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; - rdfs:domain ; - rdfs:label "availableFormats"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding "@en; - rdfs:domain ; - rdfs:label "programType"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Environment parameters associated with a study"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The start position at which this variant occurs (0-based). This corresponds to the first base of the string \nof reference bases. Genomic positions are non-negative integers less than reference length. Variants spanning \nthe join of circular genomes are represented as two variants one on each side of the join (position 0)."@en; - rdfs:domain ; - rdfs:label "start"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`."@en; - rdfs:domain ; - rdfs:label "sourceAccessions"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The beginning of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event."@en; - rdfs:domain ; - rdfs:label "startDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Data matrices associated with an alleleMatrix"@en; - rdfs:domain ; - rdfs:label "alleleMatrix"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the type of cross"@en; - rdfs:domain ; - rdfs:label "crossType"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "variants"@en; - rdfs:domain ; - rdfs:label "variants"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the type of cross"@en; - rdfs:domain ; - rdfs:label "crossType"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The an observation unit\n
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. \n
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response."@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a trait"@en; - rdfs:domain ; - rdfs:label "traitDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The complete history of transactions for this seed lot. This includes seed increases, seed usage (planting), and trading with other breeding programs."@en; - rdfs:domain ; - rdfs:label "transactions"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The techniques and protocol used to produce a Cross or Germplasm"@en; - rdfs:label "BreedingMethod"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated pedigreeNode"@en; - rdfs:domain ; - rdfs:label "pedigreeNode"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit."@en; - rdfs:label "Observation"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; - rdfs:domain ; - rdfs:label "contextOfUse"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (DECLATITUDE) 15.1 Latitude expressed in decimal degrees. Positive values are North of the Equator; negative values are South of the Equator (e.g. -44.6975)."@en; - rdfs:domain ; - rdfs:label "latitudeDecimal"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name for a crossing project"@en; - rdfs:domain ; - rdfs:label "crossingProjectName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The reference bases for this variant. They start at the given start position."@en; - rdfs:domain ; - rdfs:label "referenceBases"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The literal string \"Point\""@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name of a ReferenceSet"@en; - rdfs:domain ; - rdfs:label "referenceSetName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated valid values"@en; - rdfs:domain ; - rdfs:label "validValues"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "An identifier for the source system or database of this reference"@en; - rdfs:domain ; - rdfs:label "referenceSource"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes."@en; - rdfs:label "GermplasmParent"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The publication reference."@en; - rdfs:domain ; - rdfs:label "publicationReference"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Uniquely Identifiable name of a `LinkageGroup`
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable."@en; - rdfs:domain ; - rdfs:label "linkageGroupName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "references"@en; - rdfs:domain ; - rdfs:label "references"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of `Sample` taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; - rdfs:domain ; - rdfs:label "sampleType"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "All positional and layout information related to this Observation Unit"@en; - rdfs:label "ObservationUnitPosition"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)"@en; - rdfs:domain ; - rdfs:label "expandHomozygotes"@en; - rdfs:range xsd:boolean . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties."@en; - rdfs:domain ; - rdfs:label "germplasmPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format"@en; - rdfs:domain ; - rdfs:label "plateFormat"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The value recorded for a particular Trait/Attribute and a particular Germplasm. Similar to an Observation value, but more concrete, applying to the whole Germplasm instead of a single ObservationUnit."@en; - rdfs:label "GermplasmAttributeValue"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)"@en; - rdfs:label "DataFormat"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; - rdfs:domain ; - rdfs:label "levelOrder"@en; - rdfs:range xsd:integer . - - - rdf:type owl:Class; - rdfs:comment "A `Call` represents the determination of genotype with respect to a particular `Variant`. \n\nIt may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345."@en; - rdfs:label "Call"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The copyright information of this image. Example 'Copyright 2018 Bob Robertson'"@en; - rdfs:domain ; - rdfs:label "copyright"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero]."@en; - rdfs:domain ; - rdfs:label "acquisitionDate"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:Class; - rdfs:comment "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable."@en; - rdfs:label "Reference"@en . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\""@en; - rdfs:label "EntryType"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; - rdfs:domain ; - rdfs:label "submissionTimestamp"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology database unique identifier"@en; - rdfs:domain ; - rdfs:label "ontologyDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A string representation of the `Reference` base alleles."@en; - rdfs:label "ReferenceBases"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of institution submitting the variable"@en; - rdfs:domain ; - rdfs:label "institution"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name of an image. Might be the same as 'imageFileName', but could be different."@en; - rdfs:domain ; - rdfs:label "imageName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A shortened version of the human readable name for a Location"@en; - rdfs:domain ; - rdfs:label "abbreviation"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The description of where a List originated from"@en; - rdfs:domain ; - rdfs:label "listSource"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name of the institute that maintains the material"@en; - rdfs:domain ; - rdfs:label "instituteName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (LONGITUDE) 15.4 Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West) (e.g. 0762510W). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 076"@en; - rdfs:domain ; - rdfs:label "longitudeDegrees"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "License and citation information for the data in this trial"@en; - rdfs:label "DatasetAuthorships"@en . - - - rdf:type owl:Class; - rdfs:comment "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy."@en; - rdfs:label "Germplasm"@en . - - - rdf:type owl:Class; - rdfs:comment "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy."@en; - rdfs:label "GermplasmMCPD"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Persons first name"@en; - rdfs:domain ; - rdfs:label "firstName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "markerPositions"@en; - rdfs:domain ; - rdfs:label "markerPositions"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard."@en; - rdfs:domain ; - rdfs:label "donorInstituteCode"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")"@en; - rdfs:domain ; - rdfs:label "mlsStatus"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A representation of a particular Germplasm within a pedigree tree, and all the links to its parents, siblings, and children. From a list of PedigreeNode objects, a client application should have all the information it needs to draw a pedigree tree visualization, or calculate genetic distances."@en; - rdfs:label "PedigreeNode"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology licence"@en; - rdfs:domain ; - rdfs:label "licence"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Y position coordinate for an observation unit. Different systems may use different coordinate systems."@en; - rdfs:domain ; - rdfs:label "positionCoordinateY"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name or identifier of the entity which collected the observation"@en; - rdfs:domain ; - rdfs:label "collector"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name or id of the user who uploaded the observation to the database system"@en; - rdfs:domain ; - rdfs:label "uploadedBy"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a `Reference`"@en; - rdfs:domain ; - rdfs:label "referenceDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a ReferenceSet"@en; - rdfs:domain ; - rdfs:label "referenceSet"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Genotype metadata associated with a call"@en; - rdfs:domain ; - rdfs:label "call"@en; - rdfs:range . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

"@en , "The type of field represented in this data matrix. This is intended to help parse the data out of JSON."@en , "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON."@en; - rdfs:label "DataType"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; - rdfs:domain ; - rdfs:label "germplasmOrigin"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Supplemental text description for 'biologicalStatusOfAccessionCode'"@en; - rdfs:domain ; - rdfs:label "biologicalStatusOfAccessionDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "Pagination info for the matrix"@en; - rdfs:label "Pagination"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'"@en; - rdfs:domain ; - rdfs:label "seasonDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Permanent Unique Identifier of a Observation Variable, usually in the form of a URI"@en; - rdfs:domain ; - rdfs:label "observationVariablePUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the germplasm of the cross parent"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "email address for this person"@en; - rdfs:domain ; - rdfs:label "emailAddress"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; - rdfs:domain ; - rdfs:label "contextOfUse"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated event"@en; - rdfs:domain ; - rdfs:label "event"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a LastUpdate within the given database server"@en; - rdfs:domain ; - rdfs:label "lastUpdateDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "seedLots"@en; - rdfs:domain ; - rdfs:label "seedLots"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated observation Unit"@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a separator for phased allele calls."@en; - rdfs:domain ; - rdfs:label "sepPhased"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Permanent Unique Identifier of a Trait, usually in the form of a URI"@en; - rdfs:domain ; - rdfs:label "traitPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Unique DbId for the Seed Lot"@en; - rdfs:domain ; - rdfs:label "seedLotDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; - rdfs:label "FileFormat"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository."@en; - rdfs:domain ; - rdfs:label "submissionDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\""@en; - rdfs:domain ; - rdfs:label "entryType"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Length of the - if labeled as such in variant_type - structural variation. Based on the use in VCF v4.2"@en; - rdfs:domain ; - rdfs:label "svlen"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; - rdfs:domain ; - rdfs:label "submissionTimestamp"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Pagination for the matrix"@en; - rdfs:domain ; - rdfs:label "pagination"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (COLLMISSID) 4.2 Identifier of the collecting mission used by the Collecting Institute (4 or 4.1) (e.g. \"CIATFOR_052\", \"CN_426\")."@en; - rdfs:domain ; - rdfs:label "collectingMissionIdentifier"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "variantSets"@en; - rdfs:domain ; - rdfs:label "variantSets"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable description of this attribute"@en; - rdfs:domain ; - rdfs:label "attributeDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date the study ends\n\nMIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended"@en; - rdfs:domain ; - rdfs:label "endDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "calls"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The identifier and metadata needed to reference an external controlled vocabulary"@en; - rdfs:label "Ontology"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species.\n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended."@en; - rdfs:domain ; - rdfs:label "taxonIds"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The germplasm using in this content mixture"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The X position coordinate for an observation unit. Different systems may use different coordinate systems."@en; - rdfs:domain ; - rdfs:label "positionCoordinateX"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system."@en; - rdfs:domain ; - rdfs:label "userID"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The remaining information is about the source of the sequences Public id of this reference set, such as `GRCH_37`."@en; - rdfs:domain ; - rdfs:label "assemblyPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used."@en; - rdfs:label "Analysis"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The complete, absolute URI path to the image file. Images might be stored on a different host or path than the BrAPI web server."@en; - rdfs:domain ; - rdfs:label "imageURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Environmental parameters that were kept constant throughout the study and did not change between observation units.\n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)."@en; - rdfs:domain ; - rdfs:label "environmentParameters"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A unique combination of Trait, Method, and Scale to define a clear context for an Observation."@en; - rdfs:label "Variable"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc."@en; - rdfs:domain ; - rdfs:label "parentType"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; - rdfs:domain ; - rdfs:label "levelName"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:label "AdditionalInfo"@en . - - - rdf:type owl:Class; - rdfs:comment "A geographic Location on earth. This is usually used to describe the general area where an experiment took place. For example, a natural site, an experimental field, a greenhouse, a phenotyping facility, etc."@en; - rdfs:label "Location"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string representation of the pedigree for this germplasm in PURDY notation"@en; - rdfs:domain ; - rdfs:label "pedigreeString"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of units being transferred between SeedLots. Could be a count (seeds, bulbs, etc) or a weight (kg of seed)."@en; - rdfs:domain ; - rdfs:label "amount"@en; - rdfs:range xsd:double . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the unique identifier for a crossing project"@en; - rdfs:domain ; - rdfs:label "crossingProject"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The related observation unit identifier, if relevant."@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL."@en; - rdfs:domain ; - rdfs:label "descriptiveOntologyTerms"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "The identifiers and metadata associated with a physical piece of biological material collected from the field for external analysis. A Sample can take many forms (leaf clipping, seed, DNA, etc) and might be used for a variety of analysis procedures (spectra, genotyping, etc)."@en; - rdfs:label "Sample"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop associated with this study"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The DOI or other permanent identifier for a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "mapPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc"@en; - rdfs:domain ; - rdfs:label "mimeType"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; - rdfs:domain ; - rdfs:label "trait"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "calls"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below."@en; - rdfs:domain ; - rdfs:label "germplasmDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. "@en; - rdfs:domain ; - rdfs:label "parentType"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies an observation variable"@en; - rdfs:domain ; - rdfs:label "observationVariable"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "siblingPedigreeNodes"@en; - rdfs:domain ; - rdfs:label "siblingPedigreeNodes"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit"@en; - rdfs:label "GermplasmAttribute"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observations"@en; - rdfs:domain ; - rdfs:label "observations"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies this attribute within the given database server"@en; - rdfs:domain ; - rdfs:label "attributeDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Minimum value for numerical, date, and time scales. Typically used for data capture control and QC."@en; - rdfs:domain ; - rdfs:label "minimumValue"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "events"@en; - rdfs:domain ; - rdfs:label "events"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A supplemental text description of the storage type"@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observationUnits"@en; - rdfs:domain ; - rdfs:label "observationUnits"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Similar to \"cipos\", but for the variant's end position (which is derived from start + svlen)."@en; - rdfs:domain ; - rdfs:label "ciend"@en; - rdfs:range xsd:integer . - - - rdf:type owl:ObjectProperty; - rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:domain ; - rdfs:label "coordinates"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable unique identifier\n\nMIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation."@en; - rdfs:domain ; - rdfs:label "observationVariableDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for the breeding method used to create this germplasm"@en; - rdfs:domain ; - rdfs:label "breedingMethod"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:domain ; - rdfs:label "coordinates"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated observation Unit"@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; - rdfs:domain ; - rdfs:label "scale"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observationUnits"@en; - rdfs:domain ; - rdfs:label "observationUnits"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a Location"@en; - rdfs:domain ; - rdfs:label "locationDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "physical address of this person"@en; - rdfs:domain ; - rdfs:label "mailingAddress"@en; - rdfs:range xsd:string . - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name of a trial\n\nMIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation."@en; - rdfs:domain ; - rdfs:label "trialName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string."@en; - rdfs:domain ; - rdfs:label "phaseSet"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard "@en; - rdfs:label "MetadataField"@en . - - - rdf:type owl:Class; - rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; - rdfs:label "Method"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name for an observation unit"@en; - rdfs:domain ; - rdfs:label "observationUnitName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "crosses"@en; - rdfs:domain ; - rdfs:label "crosses"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a separator for unphased allele calls."@en; - rdfs:domain ; - rdfs:label "sepUnphased"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the description for a crossing project"@en; - rdfs:domain ; - rdfs:label "crossingProjectDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The time stamp for when this seed lot was created"@en; - rdfs:domain ; - rdfs:label "createdDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Column identifier for this `Sample` location in the `Plate`"@en; - rdfs:domain ; - rdfs:label "column"@en; - rdfs:range xsd:integer . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Program` within the given database server"@en; - rdfs:domain ; - rdfs:label "program"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A descriptive classification for this synonym"@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date this trial ends"@en; - rdfs:domain ; - rdfs:label "endDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology copyright"@en; - rdfs:domain ; - rdfs:label "copyright"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The IDs of the variantSets this callSet has calls in."@en; - rdfs:domain ; - rdfs:label "variantSets"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Analysis associated with a variant set"@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID of the reference set that describes the sequences used by the variants in this set."@en; - rdfs:domain ; - rdfs:label "referenceSet"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The single value of this event parameter. This single value is accurate for all the dates in the date range. If 'value' is populated then 'valuesByDate' should NOT be populated."@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Information about an accession donor"@en; - rdfs:domain ; - rdfs:label "donorInfo"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:Class; - rdfs:label "ObservationVariable"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "donors associated with a germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted."@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; - rdfs:domain ; - rdfs:label "language"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "progenyPedigreeNodes"@en; - rdfs:domain ; - rdfs:label "progenyPedigreeNodes"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of elements in a List"@en; - rdfs:domain ; - rdfs:label "listSize"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "True if all filters for this variant passed. VCF column 7 \"FILTER\" value PASS."@en; - rdfs:domain ; - rdfs:label "filtersPassed"@en; - rdfs:range xsd:boolean . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "**Deprecated in v2.1** Please use `code`. Github issue number #440 \n; - rdfs:label "rdfValue"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A unique identifier physically attached to the `Sample`"@en; - rdfs:domain ; - rdfs:label "sampleBarcode"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:Class; - rdfs:comment "Identifier assigned to an accession by the material donor."@en; - rdfs:label "Donor"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The external reference ID. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "referenceId"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; - rdfs:label "SampleType"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a Reference"@en; - rdfs:domain ; - rdfs:label "reference"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')."@en; - rdfs:domain ; - rdfs:label "status"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date and time a `Sample` was collected from the field\n
MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested"@en; - rdfs:domain ; - rdfs:label "sampleTimestamp"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observations"@en; - rdfs:domain ; - rdfs:label "observations"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name associated with a `Variant`"@en; - rdfs:domain ; - rdfs:label "variantNames"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "parentPedigreeNodes"@en; - rdfs:domain ; - rdfs:label "parentPedigreeNodes"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space."@en; - rdfs:domain ; - rdfs:label "instituteAddress"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a trial"@en; - rdfs:domain ; - rdfs:label "trial"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a separator for phased allele calls."@en; - rdfs:domain ; - rdfs:label "sepPhased"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name of a List"@en; - rdfs:domain ; - rdfs:label "listName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended."@en; - rdfs:domain ; - rdfs:label "license"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of unique identifiers for the Variants contained in the matrix response. This array should match the ordering for rows in the matrix."@en; - rdfs:domain ; - rdfs:label "variants"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "bases"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology version (no specific format)"@en; - rdfs:domain ; - rdfs:label "version"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" "@en; - rdfs:domain ; - rdfs:label "species"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "Genotype Metadata are additional layers of metadata associated with each genotype."@en; - rdfs:label "GenotypeMetadata"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Uniquely Identifiable name of a `LinkageGroup`\n
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable."@en; - rdfs:domain ; - rdfs:label "linkageGroupName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Description the storage location"@en; - rdfs:domain ; - rdfs:label "storageLocation"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Information describing the grant or funding source for this program"@en; - rdfs:domain ; - rdfs:label "fundingInformation"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date and time when this observation was made"@en; - rdfs:domain ; - rdfs:label "observationTimeStamp"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "The type of objects that are referenced in a List"@en; - rdfs:label "ListType"@en . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Permanent Unique Identifier of an Attribute, usually in the form of a URI"@en; - rdfs:domain ; - rdfs:label "attributePUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "studies"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec\n
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.'"@en; - rdfs:domain ; - rdfs:label "countryCode"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The mulit-crop passport descriptors (MCPD) for this germplasm"@en; - rdfs:domain ; - rdfs:label "mcpd"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observations"@en; - rdfs:domain ; - rdfs:label "observations"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; - rdfs:domain ; - rdfs:label "status"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Specific epithet portion of the scientific name in lowercase letters.\n\nMCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" \n\nMIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature."@en; - rdfs:domain ; - rdfs:label "species"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described."@en; - rdfs:domain ; - rdfs:label "publicReleaseDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of scientist submitting the variable."@en; - rdfs:domain ; - rdfs:label "scientist"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Information about the location where the sample was collected"@en; - rdfs:domain ; - rdfs:label "collectingSite"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The identifier for the Seed Lot being transferred out of"@en; - rdfs:domain ; - rdfs:label "fromSeedLot"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "callSets"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Numerical or categorical value\n\nMIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment."@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human-readable value of the environment parameter (defined above) constant within the experiment"@en; - rdfs:domain ; - rdfs:label "environmentParametersDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. "@en; - rdfs:domain ; - rdfs:label "alternateIDs"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "General category for the attribute. very similar to Trait class."@en; - rdfs:domain ; - rdfs:label "attributeCategory"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for the originating Seed Lot"@en; - rdfs:domain ; - rdfs:label "seedLot"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention."@en; - rdfs:domain ; - rdfs:label "alternativeAbbreviations"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Permanent Unique Identifier of a Scale, usually in the form of a URI"@en; - rdfs:domain ; - rdfs:label "scalePUI"@en; - rdfs:range xsd:string . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The mixture of germplasm present in the seed lot.\n
\nIf this seed lot only contains a single germplasm, the response should contain the name \nand DbId of that germplasm with a mixturePercentage value of 100\n
\nIf the seed lot contains a mixture of different germplasm, the response should contain \nthe name and DbId every germplasm present. The mixturePercentage field should contain \nthe ratio of each germplasm in the total mixture. All of the mixturePercentage values \nin this array should sum to equal 100."@en; - rdfs:domain ; - rdfs:label "contentMixture"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The identifier (name, ID, URI) of a particular taxonomy within the source provider"@en; - rdfs:domain ; - rdfs:label "taxonId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the maximum number of elements per page in this dimension of the matrix"@en; - rdfs:domain ; - rdfs:label "pageSize"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "An array of linear rings"@en; - rdfs:domain ; - rdfs:label "coordinates"@en; - rdfs:range xsd:double . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies the program"@en; - rdfs:domain ; - rdfs:label "programDbId"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)"@en; - rdfs:domain ; - rdfs:label "expandHomozygotes"@en; - rdfs:range xsd:boolean . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for the breeding method used to create this germplasm"@en; - rdfs:domain ; - rdfs:label "breedingMethod"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON."@en; - rdfs:domain ; - rdfs:label "dataType"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there are not any additional results."@en; - rdfs:domain ; - rdfs:label "nextPageToken"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\""@en; - rdfs:domain ; - rdfs:label "entity"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; - rdfs:domain ; - rdfs:label "scale"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "crossingProjects"@en; - rdfs:domain ; - rdfs:label "crossingProjects"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the unique identifier for a cross"@en; - rdfs:domain ; - rdfs:label "crossDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow."@en; - rdfs:domain ; - rdfs:label "provenance"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'."@en; - rdfs:label "CrossType"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "True if the pollination was successful"@en; - rdfs:domain ; - rdfs:label "pollinationSuccessful"@en; - rdfs:range xsd:boolean . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name for this analysis"@en; - rdfs:domain ; - rdfs:label "analysisName"@en; - rdfs:range xsd:string . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:label "GeoJSONPolygon"@en . - - - rdf:type owl:Class; - rdfs:comment "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:label "GeoJSONPoint"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the human readable name of a cross attribute"@en; - rdfs:domain ; - rdfs:label "crossAttributeName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required."@en; - rdfs:domain ; - rdfs:label "genus"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Persons last name"@en; - rdfs:domain ; - rdfs:label "lastName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Geometry associated with an image"@en; - rdfs:domain ; - rdfs:label "image"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Short description of the facility in which the study was carried out."@en; - rdfs:domain ; - rdfs:label "growthFacility"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the human readable name for a planned cross"@en; - rdfs:domain ; - rdfs:label "plannedCrossName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop which this program is for"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A shortened version of the human readable name for a Breeding Method"@en; - rdfs:domain ; - rdfs:label "abbreviation"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; - rdfs:domain ; - rdfs:label "trait"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field."@en; - rdfs:label "PlannedCross"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies this attribute within the given database server"@en; - rdfs:domain ; - rdfs:label "attribute"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "calls"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; - rdfs:domain ; - rdfs:label "submissionTimestamp"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:domain ; - rdfs:label "imageLocation"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (GEOREFMETH) 15.7 The georeferencing method used (GPS, determined from map, gazetteer, or estimated using software). Leave the value empty if georeferencing method is not known."@en; - rdfs:domain ; - rdfs:label "georeferencingMethod"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the requested page number (zero indexed)"@en; - rdfs:domain ; - rdfs:label "page"@en; - rdfs:range xsd:integer . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The common name of the `Crop`"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A classification to describe the type of trait and the context it should be considered in.\n
examples- \"morphological\", \"phenological\", \"agronomical\", \"physiological\", \"abiotic stress\", \"biotic stress\", \"biochemical\", \"quality traits\", \"fertility\", etc."@en; - rdfs:domain ; - rdfs:label "traitClass"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a ontology reference"@en; - rdfs:domain ; - rdfs:label "ontologyReferenceDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a pedigree node"@en; - rdfs:domain ; - rdfs:label "pedigreeNodeDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "The GenomeMap represents the metadata associated with a reference map of a particular species genome. A GenomeMap can either represent a physical map or genetic map."@en; - rdfs:label "GenomeMap"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "markerPositions"@en; - rdfs:domain ; - rdfs:label "markerPositions"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; - rdfs:domain ; - rdfs:label "scale"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The permanent unique identifier of the publication."@en; - rdfs:domain ; - rdfs:label "publicationPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. "@en; - rdfs:domain ; - rdfs:label "modality"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter."@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The time stamp for when the transaction occurred"@en; - rdfs:domain ; - rdfs:label "transactionTimestamp"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A flag to indicate the type of objects that are referenced in a List"@en; - rdfs:domain ; - rdfs:label "listType"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`."@en; - rdfs:domain ; - rdfs:label "sourceAccessions"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Plate` of `Sample`"@en; - rdfs:domain ; - rdfs:label "plate"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The Cross associated with this Pollination Event"@en; - rdfs:domain ; - rdfs:label "cross"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A Pollination Event that was used or attempted for a Cross."@en; - rdfs:label "PollinationEvent"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated \nby `start + referenceBases.length`."@en; - rdfs:domain ; - rdfs:label "end"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "phone number of this person"@en; - rdfs:domain ; - rdfs:label "phoneNumber"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The usage license associated with the study data"@en; - rdfs:domain ; - rdfs:label "license"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "variants"@en; - rdfs:domain ; - rdfs:label "variants"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; - rdfs:domain ; - rdfs:label "method"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "An identifier for the source of the biological material\n
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: \"mother_accession X father_accession\", or, if father is unknown, as \"mother_accession X UNKNOWN\". For in situ material, the region of provenance may be used when an accession is not available."@en; - rdfs:domain ; - rdfs:label "seedSource"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "studies"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program."@en; - rdfs:label "Person"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name for a VariantSet"@en; - rdfs:domain ; - rdfs:label "variantSetName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; - rdfs:domain ; - rdfs:label "growthStage"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "trials"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The code for the institute that maintains the material. \n\nMCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\"."@en; - rdfs:domain ; - rdfs:label "instituteCode"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the `getReferenceBases()` method to obtain sequence bases for a `Reference` instead of attempting to retrieve this URI."@en; - rdfs:domain ; - rdfs:label "sourceURI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Optional free text description of this reference set."@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observationUnits"@en; - rdfs:domain ; - rdfs:label "observationUnits"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies an observation unit"@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name for this attribute"@en; - rdfs:domain ; - rdfs:label "attributeName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The \"variant_type\" is used to denote e.g. structural variants.\nExamples:\n DUP : duplication of sequence following \"start\"\n DEL : deletion of sequence following \"start\""@en; - rdfs:domain ; - rdfs:label "variantType"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "The date and time when this study was last modified"@en; - rdfs:label "LastUpdate"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "plates"@en; - rdfs:domain ; - rdfs:label "plates"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name for a study\n\nMIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study"@en; - rdfs:domain ; - rdfs:label "studyName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of the affected observation units. If this parameter is not given, it is understood that the event affected all units in the study"@en; - rdfs:domain ; - rdfs:label "observationUnits"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case."@en; - rdfs:domain ; - rdfs:label "callSets"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A general description of this Seed Lot"@en; - rdfs:domain ; - rdfs:label "seedLotDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of institutes that were involved with breeding a material/germplasm\n
MCPD (v2.1) (BREDCODE) 18. FAO WIEWS code of the institute that has bred the material. If the holding institute has bred the material, the breeding institute code (BREDCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard.\n
MCPD (v2.1) (BREDNAME) 18.1 Name of the institute (or person) that bred the material. This descriptor should be used only if BREDCODE can not be filled because the FAO WIEWS code for this institute is not available."@en; - rdfs:domain ; - rdfs:label "breedingInstitutes"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The primary objective of the program"@en; - rdfs:domain ; - rdfs:label "objective"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard "@en; - rdfs:domain ; - rdfs:label "metadataFields"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:ObjectProperty; - rdfs:comment "List of donor institutes"@en; - rdfs:domain ; - rdfs:label "donors"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; - rdfs:domain ; - rdfs:label "sampleType"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)"@en; - rdfs:domain ; - rdfs:label "topography"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A description of the things being transferred between SeedLots in a transaction (seeds, bulbs, kg, etc)"@en; - rdfs:domain ; - rdfs:label "units"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The timestamp of the update."@en; - rdfs:domain ; - rdfs:label "timestamp"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word \"GT\" is reserved for the allele matrix. Examples of other metadata matrices include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard."@en; - rdfs:domain ; - rdfs:label "dataMatrixAbbreviation"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:label "GeoJSON"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "plates"@en; - rdfs:domain ; - rdfs:label "plates"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A reference set may be derived from a source if it contains additional sequences, or some of the sequences within it are derived (see the definition of `isDerived` in `Reference`)."@en; - rdfs:domain ; - rdfs:label "isDerived"@en; - rdfs:range xsd:boolean . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Description of a `Sample`\n
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing."@en; - rdfs:domain ; - rdfs:label "sampleDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "alleleMatrices"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a crossing project"@en; - rdfs:domain ; - rdfs:label "crossingProjectDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a ReferenceSet"@en; - rdfs:domain ; - rdfs:label "referenceSetDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Pagination associated with an alleleMatrix"@en; - rdfs:domain ; - rdfs:label "alleleMatrix"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Description of the accessibility of the location (ex. Public, Private)"@en; - rdfs:domain ; - rdfs:label "siteStatus"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID of the variant this call belongs to."@en; - rdfs:domain ; - rdfs:label "variant"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "An array of values corresponding to each timestamp in the 'discreteDates' array of this event. The 'valuesByDate' array should exactly match the size of the 'discreteDates' array. If 'valuesByDate' is populated then 'value' should NOT be populated."@en; - rdfs:domain ; - rdfs:label "valuesByDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases."@en; - rdfs:domain ; - rdfs:label "isDerived"@en; - rdfs:range xsd:boolean . - - - rdf:type owl:Class; - rdfs:comment "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species. \n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended."@en; - rdfs:label "TaxonId"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The literal string \"Feature\""@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of unique identifiers for the VariantSets contained in the matrix response. A VariantSet is a data set originating from a sequencing event. Often, users will only be interested in data from a single VariantSet, but in some cases a user might be interested in a matrix with data from multiple VariantSets."@en; - rdfs:domain ; - rdfs:label "variantSets"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed."@en; - rdfs:domain ; - rdfs:label "geometry"@en; - rdfs:range , . - - - rdf:type owl:Class; - rdfs:comment "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')."@en; - rdfs:label "PlannedCrossStatus"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation"@en; - rdfs:domain ; - rdfs:label "methodName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature."@en; - rdfs:domain ; - rdfs:label "genus"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of institution submitting the variable"@en; - rdfs:domain ; - rdfs:label "institution"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; - rdfs:domain ; - rdfs:label "submissionTimestamp"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human-readable value of the environment parameter (defined above) constant within the experiment"@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "All positional and layout information related to this Observation Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) \nor level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. \nLevels of observation must be consistent with those listed in the Study section."@en; - rdfs:domain ; - rdfs:label "observationUnitPosition"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "seedLots"@en; - rdfs:domain ; - rdfs:label "seedLots"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "lists"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Trial` within the given database server"@en; - rdfs:domain ; - rdfs:label "trial"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; - rdfs:domain ; - rdfs:label "observationLevel"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of tissue sampled. ex. 'Leaf', 'Root', etc.\n
MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology)."@en; - rdfs:domain ; - rdfs:label "tissueType"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name."@en; - rdfs:domain ; - rdfs:label "speciesAuthority"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier of an image"@en; - rdfs:domain ; - rdfs:label "imageDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "human readable description of the breeding method"@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "eventType"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The authority organization responsible for tracking and maintaining the species name \n\nMCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name."@en; - rdfs:domain ; - rdfs:label "speciesAuthority"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; - rdfs:domain ; - rdfs:label "biologicalStatusOfAccessionCode"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a group of `Samples`"@en; - rdfs:domain ; - rdfs:label "sampleGroupId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated pedigreeNode"@en; - rdfs:domain ; - rdfs:label "pedigreeNode"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:label "OntologyReference"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; - rdfs:domain ; - rdfs:label "language"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The MD5 checksum uniquely representing this `Reference` as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM)."@en; - rdfs:domain ; - rdfs:label "md5checksum"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows."@en; - rdfs:domain ; - rdfs:label "dataMatrix"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable"@en; - rdfs:domain ; - rdfs:label "scaleName"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study."@en; - rdfs:label "List"@en . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The timestamp when the pollination took place"@en; - rdfs:domain ; - rdfs:label "pollinationTimeStamp"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for this pollination event"@en; - rdfs:domain ; - rdfs:label "pollinationNumber"@en; - rdfs:range xsd:string . - - rdf:type owl:Ontology . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The time at which this record was created, in ISO 8601 format."@en; - rdfs:domain ; - rdfs:label "created"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The `GenomeMap` to which this `LinkageGroup` belongs "@en; - rdfs:domain ; - rdfs:label "genomeMap"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "If the Scale is a categorical type, these objects define the valid options"@en; - rdfs:label "ValidValuesCategory"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'."@en; - rdfs:domain ; - rdfs:label "pedigree"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a `ReferenceSet`"@en; - rdfs:domain ; - rdfs:label "referenceSet"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero]."@en; - rdfs:domain ; - rdfs:label "acquisitionDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of institution submitting the variable"@en; - rdfs:domain ; - rdfs:label "institution"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "List of links to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; - rdfs:domain ; - rdfs:label "dataLinks"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a germplasm within the given database server"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; - rdfs:domain ; - rdfs:label "method"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level."@en; - rdfs:domain ; - rdfs:label "subtaxonAuthority"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (COLLSITE) 14. Location information below the country level that describes where the accession was collected, preferable in English. This might include the distance in kilometres and direction from the nearest town, village or map grid reference point, (e.g. 7 km south of Townsville)."@en; - rdfs:domain ; - rdfs:label "locationDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "studies"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The dimension of the matrix being paginated"@en; - rdfs:label "Dimension"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the human readable identifier for this breeding method"@en; - rdfs:domain ; - rdfs:label "breedingMethodName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology version (no specific format)"@en; - rdfs:domain ; - rdfs:label "version"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Set of custom attributes associated with a cross"@en; - rdfs:domain ; - rdfs:label "crossAttributes"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of study being performed. ex. \"Yield Trial\", etc"@en; - rdfs:domain ; - rdfs:label "studyType"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:domain ; - rdfs:label "validValues"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc"@en; - rdfs:domain ; - rdfs:label "scientificType"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The list of pollination events that occurred for this cross."@en; - rdfs:domain ; - rdfs:label "pollinationEvents"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The description of a trait"@en; - rdfs:domain ; - rdfs:label "traitDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Genotype Metadata are additional layers of metadata associated with each genotype."@en; - rdfs:domain ; - rdfs:label "genotypeMetadata"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; - rdfs:domain ; - rdfs:label "biologicalStatusOfAccessionCode"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The value of this attribute for a given germplasm"@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; - rdfs:label "StorageTypeCode"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology's list of authors (no specific format)"@en; - rdfs:domain ; - rdfs:label "authors"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:domain ; - rdfs:label "safetyDuplicateInstitutes"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Institutes which collected the sample"@en; - rdfs:domain ; - rdfs:label "collectingInstitutes"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date this call set was created"@en; - rdfs:domain ; - rdfs:label "created"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Other variable names"@en; - rdfs:domain ; - rdfs:label "synonyms"@en; - rdfs:range xsd:string . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of positional coordinate used for the X coordinate of the position."@en; - rdfs:domain ; - rdfs:label "positionCoordinateXType"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis."@en; - rdfs:label "Plate"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The 4 digit year of the season."@en; - rdfs:domain ; - rdfs:label "year"@en; - rdfs:range xsd:integer . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; - rdfs:domain ; - rdfs:label "levelName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown."@en; - rdfs:domain ; - rdfs:label "coordinateUncertainty"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Order-independent MD5 checksum which identifies this `ReferenceSet`.\n\nTo compute this checksum, make a list of `Reference.md5checksum` for all\n`Reference` s in this set. Then sort that list, and take the MD5 hash of\nall the strings concatenated together. Express the hash as a lower-case\nhexadecimal string."@en; - rdfs:domain ; - rdfs:label "md5checksum"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of analysis."@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies."@en; - rdfs:label "Study"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "URL describing the location of this data file to view or download\n\nMIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission."@en; - rdfs:domain ; - rdfs:label "url"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Alternative name or ID used to reference this germplasm"@en; - rdfs:domain ; - rdfs:label "synonym"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Species associated with a referenceSet"@en; - rdfs:domain ; - rdfs:label "referenceSet"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of scientist submitting the variable."@en; - rdfs:domain ; - rdfs:label "scientist"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Trial` within the given database server"@en; - rdfs:domain ; - rdfs:label "trial"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The value of this genotype call"@en; - rdfs:domain ; - rdfs:label "genotypeValue"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "callSets"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated scale"@en; - rdfs:domain ; - rdfs:label "scale"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Siblings share at least one parent with the given germplasm. \n
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response."@en; - rdfs:domain ; - rdfs:label "siblings"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100."@en; - rdfs:label "ContentMixture"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (DECLONGITUDE) 15.3 Longitude expressed in decimal degrees. Positive values are East of the Greenwich Meridian; negative values are West of the Greenwich Meridian (e.g. +120.9123)."@en; - rdfs:domain ; - rdfs:label "longitudeDecimal"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable identifier for a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "mapName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a location, associated with this study"@en; - rdfs:domain ; - rdfs:label "location"@en; - rdfs:range . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The end of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event."@en; - rdfs:domain ; - rdfs:label "endDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "The identifying information gor the parent material of a cross."@en; - rdfs:label "CrossParent"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name for a `Plate`"@en; - rdfs:domain ; - rdfs:label "plateName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the unique identifier for a crossing project"@en; - rdfs:domain ; - rdfs:label "crossingProject"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the Observation Unit of the cross parent"@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a trial"@en; - rdfs:domain ; - rdfs:label "trial"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a List Owner. (usually a user or person)"@en; - rdfs:domain ; - rdfs:label "listOwnerPerson"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; - rdfs:domain ; - rdfs:label "language"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. "@en; - rdfs:label "ParentType"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The current balance of the amount of material in a SeedLot. Could be a count (seeds, bulbs, etc) or a weight (kg of seed)."@en; - rdfs:domain ; - rdfs:label "amount"@en; - rdfs:range xsd:double . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "MCPD (v2.1) (MLSSTAT) 27. The status of an accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture. Leave the value empty if the status is not known 0 No (not included) 1 Yes (included) 99 Other (elaborate in REMARKS field, e.g. \"under development\")"@en; - rdfs:label "MlsStatus"@en . - - - rdf:type owl:Class; - rdfs:label "Attribute"@en . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the second parent used in the cross"@en; - rdfs:domain ; - rdfs:label "parent2"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; - rdfs:domain ; - rdfs:label "dataFormat"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space."@en; - rdfs:domain ; - rdfs:label "instituteName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The list of Observation Variables being used in this study. \n\nThis list is intended to be the wishlist of variables to collect in this study. It may or may not match the set of variables used in the collected observation records. "@en; - rdfs:domain ; - rdfs:label "observationVariables"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Other variable names"@en; - rdfs:domain ; - rdfs:label "synonyms"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:NamedIndividual , . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "Information about the collection of a germplasm"@en; - rdfs:label "CollectingInfo"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "List of contact entities associated with this trial"@en; - rdfs:domain ; - rdfs:label "contacts"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "For numerical, number of decimal places to be reported"@en; - rdfs:domain ; - rdfs:label "decimalPlaces"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\""@en; - rdfs:domain ; - rdfs:label "fieldName"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)"@en; - rdfs:label "AcquisitionSourceCode"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'."@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A shortened version of the human readable name for a Program"@en; - rdfs:domain ; - rdfs:label "abbreviation"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers\" variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note: Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\"."@en; - rdfs:domain ; - rdfs:label "countryOfOrigin"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)"@en; - rdfs:domain ; - rdfs:label "coordinateDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The percentage of the given germplasm in the seed lot mixture."@en; - rdfs:domain ; - rdfs:label "mixturePercentage"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; - rdfs:domain ; - rdfs:label "levelName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a trial\n\nMIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution."@en; - rdfs:domain ; - rdfs:label "trialDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID of the dataset this variant set belongs to."@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A two dimensional array that holds allele data or associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows."@en; - rdfs:label "DataMatrix"@en . - - - rdf:type owl:NamedIndividual , . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:ObjectProperty; - rdfs:comment "plannedCrosses"@en; - rdfs:domain ; - rdfs:label "plannedCrosses"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The value of the data collected as an observation"@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Other variable names"@en; - rdfs:domain ; - rdfs:label "synonyms"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name of a List Owner. (usually a user or person)"@en; - rdfs:domain ; - rdfs:label "listOwnerName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "General category for the attribute. very similar to Trait class."@en; - rdfs:domain ; - rdfs:label "attributeCategory"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "attributeValues"@en; - rdfs:domain ; - rdfs:label "attributeValues"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies an observation unit\n\nMIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. "@en; - rdfs:domain ; - rdfs:label "observationUnitDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Germplasm associated with a reference"@en; - rdfs:domain ; - rdfs:label "referenceSet"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "variants"@en; - rdfs:domain ; - rdfs:label "variants"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "List of seasons over which this study was performed."@en; - rdfs:domain ; - rdfs:label "seasons"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing."@en; - rdfs:label "Trial"@en . - - - rdf:type owl:Class; - rdfs:comment "The metadata for an image file that is connected to some phenotypic observation data."@en; - rdfs:label "Image"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of CallSets included in this VariantSet"@en; - rdfs:domain ; - rdfs:label "callSetCount"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Unit of the value for this parameter"@en; - rdfs:domain ; - rdfs:label "unit"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A persons contact information"@en; - rdfs:label "Contact"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of Variants included in this VariantSet"@en; - rdfs:domain ; - rdfs:label "variantCount"@en; - rdfs:range xsd:integer . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; - rdfs:domain ; - rdfs:label "method"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the first parent used in the cross"@en; - rdfs:domain ; - rdfs:label "parent1"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The actual value for a category"@en; - rdfs:domain ; - rdfs:label "value"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A SeedLot, also known as an InventoryLot, is a collection of starting material (seeds, bulbs, root-stock, etc) for a particular Germplasm. The amount of material available for each Germplasm can be increased by seed production and decreased by planting or trading with another breeding Program."@en; - rdfs:label "SeedLot"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'."@en; - rdfs:domain ; - rdfs:label "ancestralData"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)"@en; - rdfs:domain ; - rdfs:label "dataFormat"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The year the parents were originally crossed"@en; - rdfs:domain ; - rdfs:label "crossingYear"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies this attribute value within the given database server"@en; - rdfs:domain ; - rdfs:label "attributeValueDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of documentation, which can be OBO Foundry, an RDF term or a webpage."@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended."@en; - rdfs:domain ; - rdfs:label "publications"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The MIME type of the file (ie text/csv, application/excel, application/zip).\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; - rdfs:domain ; - rdfs:label "fileFormat"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; - rdfs:label "ObservationUnitLevel"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\""@en; - rdfs:domain ; - rdfs:label "attribute"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The Cross that was used in the planning of this one."@en; - rdfs:domain ; - rdfs:label "plannedCross"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Additional comments about a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "comments"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MIAPPE V1.1 (DM-25) Observation unit description - General description of the observation units in the study."@en; - rdfs:domain ; - rdfs:label "observationUnitsDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a program"@en; - rdfs:domain ; - rdfs:label "program"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date this `GenomeMap` was published"@en; - rdfs:domain ; - rdfs:label "publishedDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of linkage groups present in a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "linkageGroupCount"@en; - rdfs:range xsd:integer . - - - rdf:type owl:NamedIndividual , . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The child locations that belong to this Location. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; - rdfs:domain ; - rdfs:label "childLocations"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

"@en; - rdfs:label "TraitDataType"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An ontology term describing an attribute."@en; - rdfs:domain ; - rdfs:label "species"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A unique identifier physically attached to a `Plate`"@en; - rdfs:domain ; - rdfs:label "plateBarcode"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a List"@en; - rdfs:domain ; - rdfs:label "listDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** "@en; - rdfs:label "ObservationUnitLevelRelationship"@en . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Variant` within the given database server\n
A `Variant` can also represent a Marker "@en; - rdfs:domain ; - rdfs:label "variant"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; - rdfs:domain ; - rdfs:label "donorAccessionNumber"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Full scientific binomial format name. This includes Genus, Species, and Sub-species"@en; - rdfs:domain ; - rdfs:label "scientificName"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor."@en; - rdfs:label "ObservationTreatment"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A single position"@en; - rdfs:domain ; - rdfs:label "coordinates"@en; - rdfs:range xsd:double . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date this study started\n\nMIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started"@en; - rdfs:domain ; - rdfs:label "startDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (COORDDATUM) 15.6 The geodetic datum or spatial reference system upon which the coordinates given in decimal latitude and decimal longitude are based (e.g. WGS84). The GPS uses the WGS84 datum."@en; - rdfs:domain ; - rdfs:label "spatialReferenceSystem"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The literal string \"Polygon\""@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other."@en; - rdfs:label "AvailableFormat"@en . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; - rdfs:domain ; - rdfs:label "defaultValue"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The full name of this contact person\n\nMIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications)"@en; - rdfs:domain ; - rdfs:label "name"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; - rdfs:domain ; - rdfs:label "donorAccessionNumber"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study."@en; - rdfs:domain ; - rdfs:label "culturalPractices"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "plates"@en; - rdfs:domain ; - rdfs:label "plates"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated event"@en; - rdfs:domain ; - rdfs:label "event"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; - rdfs:label "Trait"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (LATITUDE) 15.2 Degrees (2 digits) minutes (2 digits), and seconds (2 digits) followed by N (North) or S (South) (e.g. 103020S). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required (e.g. 10"@en; - rdfs:domain ; - rdfs:label "latitudeDegrees"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A flag to indicate if a Trial is currently active and ongoing"@en; - rdfs:domain ; - rdfs:label "active"@en; - rdfs:range xsd:boolean . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor."@en; - rdfs:domain ; - rdfs:label "factor"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (COLLNUMB) 3. Original identifier assigned by the collector(s) of the sample, normally composed of the name or initials of the collector(s) followed by a number (e.g. \"ab109909\"). This identifier is essential for identifying duplicates held in different collections."@en; - rdfs:domain ; - rdfs:label "collectingNumber"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a separator for unphased allele calls."@en; - rdfs:domain ; - rdfs:label "sepUnphased"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard."@en; - rdfs:domain ; - rdfs:label "fieldAbbreviation"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The identifying information for the entity acting as an accession donor\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.\n
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available."@en; - rdfs:domain ; - rdfs:label "donorInstitute"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A `ReferenceSet` is a set of `Reference` s which typically comprise a reference assembly, such as `GRCH_38`. A `ReferenceSet` defines a common coordinate space for comparing reference-aligned experimental data."@en; - rdfs:label "ReferenceSet"@en . - - - rdf:type owl:Class; - rdfs:comment "An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. \n
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other"@en; - rdfs:label "Event"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard."@en; - rdfs:domain ; - rdfs:label "fieldName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a `Variant`"@en; - rdfs:domain ; - rdfs:label "variantDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The cross for the germplasm using in this content mixture"@en; - rdfs:domain ; - rdfs:label "cross"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A flag to indicate if a Study is currently active and ongoing"@en; - rdfs:domain ; - rdfs:label "active"@en; - rdfs:range xsd:boolean . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A permanent unique identifier associated with this study data. For example, a URI or DOI"@en; - rdfs:domain ; - rdfs:label "studyPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A detailed, human-readable description of this event\n
MIAPPE V1.1 (DM-67) Event description - Description of the event, including details such as amount applied and possibly duration of the event. "@en; - rdfs:domain ; - rdfs:label "eventDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of all the potential parents in the crossing block, available in the crossing project\n
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object."@en; - rdfs:domain ; - rdfs:label "potentialParents"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name which identifies a germplasm within the given database server"@en; - rdfs:domain ; - rdfs:label "callSetName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; - rdfs:domain ; - rdfs:label "defaultValue"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; - rdfs:label "Scale"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:ObjectProperty; - rdfs:comment "events"@en; - rdfs:domain ; - rdfs:label "events"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The crossing project used to generate this germplasm"@en; - rdfs:domain ; - rdfs:label "crossingProject"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; - rdfs:domain ; - rdfs:label "fileFormat"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; - rdfs:domain ; - rdfs:label "levelOrder"@en; - rdfs:range xsd:integer . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "images"@en; - rdfs:domain ; - rdfs:label "images"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (ELEVATION) 16. Elevation of collecting site expressed in metres above sea level. Negative values are allowed."@en; - rdfs:domain ; - rdfs:label "elevation"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Unique identifier for this analysis description"@en; - rdfs:domain ; - rdfs:label "analysisDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown."@en; - rdfs:domain ; - rdfs:label "coordinateUncertainty"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The date and time when this study was last modified"@en; - rdfs:domain ; - rdfs:label "lastUpdate"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The units used to describe the data in a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "unit"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)"@en; - rdfs:domain ; - rdfs:label "methodClass"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)"@en; - rdfs:domain ; - rdfs:label "eventDateRange"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The full name of an event parameter\n
ICASA \"Variable_Name\""@en; - rdfs:domain ; - rdfs:label "name"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of observation Ids this image is associated with, if applicable."@en; - rdfs:domain ; - rdfs:label "observations"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the second parent used in the cross"@en; - rdfs:domain ; - rdfs:label "parent2"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of markers present in a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "markerCount"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the unique identifier for a planned cross"@en; - rdfs:domain ; - rdfs:label "plannedCrossDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A short human readable code for a study"@en; - rdfs:domain ; - rdfs:label "studyCode"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Describes the level of protection/exposure for things like sun light and wind at a particular Location"@en; - rdfs:domain ; - rdfs:label "exposure"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "Alternative names or IDs used to reference this germplasm"@en; - rdfs:label "Synonym"@en . - - - rdf:type owl:Class; - rdfs:comment "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology"@en; - rdfs:label "ExperimentalDesign"@en . - - - rdf:type owl:Class; - rdfs:comment "Information about an accession donor"@en; - rdfs:label "DonorInfo"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; - rdfs:domain ; - rdfs:label "status"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "PUI (DOI mostly) of the accession in the donor system."@en; - rdfs:domain ; - rdfs:label "donorAccessionPui"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Formats associated with a variant set"@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Germplasm associated with a reference"@en; - rdfs:domain ; - rdfs:label "reference"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "Short description of the facility in which the study was carried out."@en; - rdfs:label "GrowthFacility"@en . - - - rdf:type owl:Class; - rdfs:comment "A pointer to an ontology used by a genomic reference"@en; - rdfs:label "OntologyTerm"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The additional metadata value associated with this genotype call"@en; - rdfs:domain ; - rdfs:label "fieldValue"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The content of the image"@en; - rdfs:domain ; - rdfs:label "imageContent"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (COORDUNCERT) 15.5 Uncertainty associated with the coordinates in metres. Leave the value empty if the uncertainty is unknown."@en; - rdfs:domain ; - rdfs:label "coordinateUncertainty"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; - rdfs:domain ; - rdfs:label "analysis"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The number of markers associated with a `LinkageGroup`."@en; - rdfs:domain ; - rdfs:label "markerCount"@en; - rdfs:range xsd:integer . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a Location\n
The Parent Location defines the encompassing Location that a smaller Location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; - rdfs:domain ; - rdfs:label "parentLocation"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The time at which this variant was last updated."@en; - rdfs:domain ; - rdfs:label "updated"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation"@en; - rdfs:domain ; - rdfs:label "traitName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the unique identifier for a cross"@en; - rdfs:domain ; - rdfs:label "cross"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "variantSets"@en; - rdfs:domain ; - rdfs:label "variantSets"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MCPD (v2.1) (COLLSRC) 21. The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes (in bold-face) such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. \n\n10) Wild habitat \n11) Forest or woodland \n12) Shrubland \n13) Grassland \n14) Desert or tundra \n15) Aquatic habitat \n20) Farm or cultivated habitat \n21) Field \n22) Orchard \n23) Backyard, kitchen or home garden (urban, peri-urban or rural) \n24) Fallow land \n25) Pasture \n26) Farm store \n27) Threshing floor \n28) Park \n30) Market or shop \n40) Institute, Experimental station, Research organization, Genebank \n50) Seed company \n60) Weedy, disturbed or ruderal habitat \n61) Roadside \n62) Field margin \n99) Other (Elaborate in REMARKS field)"@en; - rdfs:domain ; - rdfs:label "acquisitionSourceCode"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Internal database identifier"@en; - rdfs:domain ; - rdfs:label "eventDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The time at which this record was last updated, in ISO 8601 format."@en; - rdfs:domain ; - rdfs:label "updated"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "alleleMatrices"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date and time the image was taken"@en; - rdfs:domain ; - rdfs:label "imageTimeStamp"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Growth facility associated with a study"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier of the program leader"@en; - rdfs:domain ; - rdfs:label "leadPerson"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A text label for a category"@en; - rdfs:domain ; - rdfs:label "label"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A permanent unique identifier for the `Sample` (DOI, URL, UUID, etc)\n
MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible. "@en; - rdfs:domain ; - rdfs:label "samplePUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The season for this Observation"@en; - rdfs:domain ; - rdfs:label "season"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The position of a marker or variant within a `LinkageGroup`"@en; - rdfs:domain ; - rdfs:label "position"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; - rdfs:domain ; - rdfs:label "growthStage"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. "@en; - rdfs:domain ; - rdfs:label "parameterName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The identifier for the Seed Lot being transferred into"@en; - rdfs:domain ; - rdfs:label "toSeedLot"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding "@en; - rdfs:label "ProgramType"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of institution submitting the variable"@en; - rdfs:domain ; - rdfs:label "institution"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI"@en; - rdfs:domain ; - rdfs:label "eventParameters"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; - rdfs:domain ; - rdfs:label "code"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "the first parent used in the cross"@en; - rdfs:domain ; - rdfs:label "parent1"@en; - rdfs:range . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL to the human readable documentation of an object"@en; - rdfs:domain ; - rdfs:label "documentationURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a VariantSet"@en; - rdfs:domain ; - rdfs:label "variantSetDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology"@en; - rdfs:domain ; - rdfs:label "experimentalDesign"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Maximum value for numerical, date, and time scales. Typically used for data capture control and QC."@en; - rdfs:domain ; - rdfs:label "maximumValue"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "images"@en; - rdfs:domain ; - rdfs:label "images"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "The type of positional coordinate. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; - rdfs:label "PositionCoordinateType"@en . - - - rdf:type owl:Class; - rdfs:comment "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)"@en; - rdfs:label "EventDateRange"@en . - - - rdf:type owl:Class; - rdfs:comment "A project structure where a list of PlannedCrosses is generated, the crossing events occur in the field, and the resulting actual Crosses can documented."@en; - rdfs:label "CrossingProject"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies an observation"@en; - rdfs:domain ; - rdfs:label "observationDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "List of possible values with optional labels"@en; - rdfs:domain ; - rdfs:label "categories"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:label "ExternalReference"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The time at which this call set was last updated"@en; - rdfs:domain ; - rdfs:label "updated"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observationUnits"@en; - rdfs:domain ; - rdfs:label "observationUnits"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies this attribute within the given database server"@en; - rdfs:domain ; - rdfs:label "attributeDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "License and citation information for the data in this trial"@en; - rdfs:domain ; - rdfs:label "datasetAuthorships"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group)."@en; - rdfs:domain ; - rdfs:label "subtaxa"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\")."@en; - rdfs:domain ; - rdfs:label "accessionNumber"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a study within the given database server\n\nMIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution."@en; - rdfs:domain ; - rdfs:label "studyDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology name"@en; - rdfs:domain ; - rdfs:label "ontologyName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a Location"@en; - rdfs:domain ; - rdfs:label "location"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The type of map this represents, usually \"Genetic\" or \"Physical\""@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format"@en; - rdfs:label "PlateFormat"@en . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon."@en; - rdfs:domain ; - rdfs:label "synonyms"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a `Sample`\n
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample."@en; - rdfs:domain ; - rdfs:label "sampleDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology term - the label of the ontology term the termId is pointing to."@en; - rdfs:domain ; - rdfs:label "term"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The DOI or other permanent unique identifier for this published dataset"@en; - rdfs:domain ; - rdfs:label "datasetPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; - rdfs:domain ; - rdfs:label "growthStage"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies an `ObservationUnit`"@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "A VariantSet is a collection of variants and variant calls intended to be analyzed together."@en; - rdfs:label "VariantSet"@en . - - - rdf:type owl:Class; - rdfs:comment "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present."@en; - rdfs:label "Cross"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Timestamp when the entity was last updated"@en; - rdfs:domain ; - rdfs:label "dateModified"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name used for display purposes"@en; - rdfs:domain ; - rdfs:label "defaultDisplayName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level."@en; - rdfs:domain ; - rdfs:label "subtaxaAuthority"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The version number for this data \n\nMIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data)."@en; - rdfs:domain ; - rdfs:label "version"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'"@en; - rdfs:label "CrossAttribute"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The human readable name of a `Reference` within a `ReferenceSet`."@en; - rdfs:domain ; - rdfs:label "referenceName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from."@en; - rdfs:domain ; - rdfs:label "sourceDivergence"@en; - rdfs:range xsd:double . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The height of the image in Pixels."@en; - rdfs:domain ; - rdfs:label "imageHeight"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The units or data type of the 'value'. \n
If the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'. \n
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. \n
If the value IS a number, then 'unit' should specify the units used eg. 'ml', 'cm', etc\n
ICASA \"Unit_or_type\""@en; - rdfs:domain ; - rdfs:label "units"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A permanent identifier for a trial. Could be DOI or other URI formatted identifier."@en; - rdfs:domain ; - rdfs:label "trialPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The general description of this data link\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Permanent Unique Identifier of a Method, usually in the form of a URI"@en; - rdfs:domain ; - rdfs:label "methodPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)"@en; - rdfs:domain ; - rdfs:label "units"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The study in which the event occurred"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of the season. ex. 'Spring', 'Q2', 'Season A', etc."@en; - rdfs:domain ; - rdfs:label "seasonName"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable description of Ontology"@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. "@en; - rdfs:domain ; - rdfs:label "levelCode"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "pedigreeNodes"@en; - rdfs:domain ; - rdfs:label "pedigreeNodes"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation."@en; - rdfs:domain ; - rdfs:label "termURI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\")."@en; - rdfs:domain ; - rdfs:label "accessionNumber"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."@en; - rdfs:domain ; - rdfs:label "orcid"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Method unique identifier"@en; - rdfs:domain ; - rdfs:label "methodDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The offset position (0-based) of the given sequence from the start of this `Reference`. This value will differ for each page in a request."@en; - rdfs:domain ; - rdfs:label "offset"@en; - rdfs:range xsd:integer . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observationUnits"@en; - rdfs:domain ; - rdfs:label "observationUnits"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Dataset authorships associated with a trial"@en; - rdfs:domain ; - rdfs:label "trial"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "**Deprecated in v2.1** Please use `name`. Github issue number #440 \n
Specifies the relationship between the event and the given property. E.g. fertilizer, operator"@en; - rdfs:domain ; - rdfs:label "key"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (REMARKS) 28. The remarks field is used to add notes or to elaborate on descriptors with value 99 or 999 (= Other). Prefix remarks with the field name they refer to and a colon (:) without space (e.g. COLLSRC:riverside). Distinct remarks referring to different fields are separated by semi-colons without space."@en; - rdfs:domain ; - rdfs:label "remarks"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A specific panel/collection/population name this germplasm belongs to."@en; - rdfs:domain ; - rdfs:label "collection"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; - rdfs:domain ; - rdfs:label "status"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "eventTypeDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:domain ; - rdfs:label "geoCoordinates"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name for this Seed Lot"@en; - rdfs:domain ; - rdfs:label "seedLotName"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; - rdfs:label "ObservationUnitHierarchyLevel"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation"@en; - rdfs:domain ; - rdfs:label "formula"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; - rdfs:domain ; - rdfs:label "ontologyReference"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Germplasm`"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop \n\nMCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\"."@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID."@en; - rdfs:domain ; - rdfs:label "scaleDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; - rdfs:domain ; - rdfs:label "contextOfUse"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a `Program` within the given database server"@en; - rdfs:domain ; - rdfs:label "program"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; - rdfs:domain ; - rdfs:label "geoCoordinates"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The maximum position of a marker within a `LinkageGroup`."@en; - rdfs:domain ; - rdfs:label "maxPosition"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name of the institution which this contact is part of\n\nMIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to"@en; - rdfs:domain ; - rdfs:label "instituteName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Describes the general type of environment of a Location. (ex. forest, field, nursery, etc)"@en; - rdfs:domain ; - rdfs:label "environmentType"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "associated germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "Information about the location where the sample was collected"@en; - rdfs:label "CollectingSite"@en . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out."@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space."@en; - rdfs:domain ; - rdfs:label "instituteCode"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "A link to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; - rdfs:label "DataLink"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A Trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the Entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" "@en; - rdfs:domain ; - rdfs:label "entityPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; - rdfs:domain ; - rdfs:label "observationLevels"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a VariantSet"@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The width of the image in Pixels."@en; - rdfs:domain ; - rdfs:label "imageWidth"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "This field can be used to describe the units used for this scale. This should be the abbreviated \nform of the units, intended to be displayed with every value using this scale. Usually this only \napplies when `dataType` is Numeric, but could also be included for other dataTypes when applicable."@en; - rdfs:domain ; - rdfs:label "units"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Unique ID for a person"@en; - rdfs:domain ; - rdfs:label "personDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "URI pointing to an ontology class for the parameter value"@en; - rdfs:domain ; - rdfs:label "valuePUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF."@en; - rdfs:label "Variant"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the unique identifier for this breeding method"@en; - rdfs:domain ; - rdfs:label "breedingMethodDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of storage this germplasm is kept in at a genebank."@en; - rdfs:domain ; - rdfs:label "storageTypes"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The description of the source where this material was originally collected (wild, nursery, etc)"@en; - rdfs:domain ; - rdfs:label "sourceCollection"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The URL or URI to the documentation"@en; - rdfs:domain ; - rdfs:label "URL"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space."@en; - rdfs:domain ; - rdfs:label "germplasmName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of field represented in this data matrix. This is intended to help parse the data out of JSON."@en; - rdfs:domain ; - rdfs:label "dataType"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. \n
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response."@en; - rdfs:domain ; - rdfs:label "parents"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; - rdfs:domain ; - rdfs:label "contextOfUse"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name for this attribute"@en; - rdfs:domain ; - rdfs:label "attributeName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The parent germplasm"@en; - rdfs:domain ; - rdfs:label "parentGermplasm"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. "@en; - rdfs:domain ; - rdfs:label "levelCode"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "Additional metadata to describe an event, based on the ICASA standard model. For example, 'Tillage Implement' (tiimp), 'Tillage Depth' (tidep), and 'Tillage Mix Effectiveness' (timix) might all be recorded parameters for a Tillage event."@en; - rdfs:label "EventParameter"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary."@en; - rdfs:domain ; - rdfs:label "germplasmPreprocessing"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "In the case of structural variants, start and end of the variant may not\nbe known with an exact base position. \"cipos\" provides an interval with\nhigh confidence for the start position. The interval is provided by 0 or\n2 signed integers which are added to the start position.\nBased on the use in VCF v4.2"@en; - rdfs:domain ; - rdfs:label "cipos"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies this contact\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."@en; - rdfs:domain ; - rdfs:label "contactDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable name (usually a short name)\n\nMIAPPE V1.1 (DM-84) Variable name - Name of the variable."@en; - rdfs:domain ; - rdfs:label "observationVariableName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The software run to generate this analysis."@en; - rdfs:domain ; - rdfs:label "software"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The type of storage this germplasm is kept in at a genebank."@en; - rdfs:label "StorageType"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A list of dates when the event occurred\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event."@en; - rdfs:domain ; - rdfs:label "discreteDates"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Last update associated with a study"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "programs"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\""@en; - rdfs:domain ; - rdfs:label "attributePUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Bibliographical reference describing the method.\n
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method."@en; - rdfs:domain ; - rdfs:label "bibliographicalReference"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)"@en; - rdfs:domain ; - rdfs:label "totalPages"@en; - rdfs:range xsd:integer . - - - rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Description of a List"@en; - rdfs:domain ; - rdfs:label "listDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Other variable names"@en; - rdfs:domain ; - rdfs:label "synonyms"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable name for a Location\n
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place."@en; - rdfs:domain ; - rdfs:label "locationName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; - rdfs:domain ; - rdfs:label "trait"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A URL which indicates the location of the file version of this VariantSet. Could be a static file URL or an API endpoint which generates the file."@en; - rdfs:domain ; - rdfs:label "fileURL"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The string used as a representation for missing data."@en; - rdfs:domain ; - rdfs:label "unknownString"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Common name for the crop associated with this trial"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of scientist submitting the variable."@en; - rdfs:domain ; - rdfs:label "scientist"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "samples"@en; - rdfs:domain ; - rdfs:label "samples"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The details of an Institute or other simular entity."@en; - rdfs:label "Institute"@en . - - - rdf:type owl:Class; - rdfs:comment "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap."@en; - rdfs:label "MarkerPosition"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "URI pointing to an ontology class for the parameter"@en; - rdfs:domain ; - rdfs:label "parameterPUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The unique identifier for a `GenomeMap`"@en; - rdfs:domain ; - rdfs:label "mapDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:Class; - rdfs:comment "a `LinkageGroup` is the generic term for a named section of a `GenomeMap`. A `LinkageGroup` can represent a Chromosome, Scaffold, or Linkage Group."@en; - rdfs:label "LinkageGroup"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date this trial started"@en; - rdfs:domain ; - rdfs:label "startDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A human readable description of this attribute"@en; - rdfs:domain ; - rdfs:label "attributeDescription"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Human readable name used for display purposes"@en; - rdfs:domain ; - rdfs:label "defaultDisplayName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; - rdfs:domain ; - rdfs:label "defaultValue"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; - rdfs:domain ; - rdfs:label "study"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The timestamp when this variant was created."@en; - rdfs:domain ; - rdfs:label "created"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The size of the image in Bytes."@en; - rdfs:domain ; - rdfs:label "imageFileSize"@en; - rdfs:range xsd:integer . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The length of this `Reference` sequence."@en; - rdfs:domain ; - rdfs:label "length"@en; - rdfs:range xsd:integer . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The ID which uniquely identifies a `Plate`"@en; - rdfs:domain ; - rdfs:label "plateDbId"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

"@en; - rdfs:domain ; - rdfs:label "dataType"@en; - rdfs:range . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:Class; - rdfs:comment "Environmental parameters that were kept constant throughout the study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)."@en; - rdfs:label "EnvironmentParameter"@en . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Name of scientist submitting the variable."@en; - rdfs:domain ; - rdfs:label "scientist"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Timestamp when the entity was first created"@en; - rdfs:domain ; - rdfs:label "dateCreated"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name of the image file. Might be the same as 'imageName', but could be different."@en; - rdfs:domain ; - rdfs:label "imageFileName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "**Deprecated in v2.1** Please use `referenceId`. Github issue number #460
The external reference ID. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "referenceID"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "List of contact entities associated with this study"@en; - rdfs:domain ; - rdfs:label "contacts"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "3-letter ISO 3166-1 code of the country in which the sample was originally collected \n\nMCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\"."@en; - rdfs:domain ; - rdfs:label "countryOfOriginCode"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An ontology term describing an attribute."@en; - rdfs:domain ; - rdfs:label "species"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "the common name of a crop (for multi-crop systems)"@en; - rdfs:domain ; - rdfs:label "commonCropName"@en; - rdfs:range xsd:string . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name of the field represented in this data matrix. The key word \"Genotype\" is reserved for the allele matrix. Examples of other metadata matrices include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard."@en; - rdfs:domain ; - rdfs:label "dataMatrixName"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Persons middle name"@en; - rdfs:domain ; - rdfs:label "middleName"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The Biosample entity the call set data was generated from."@en; - rdfs:domain ; - rdfs:label "sample"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Geometry associated with an image"@en; - rdfs:domain ; - rdfs:label "observationUnit"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; - rdfs:domain ; - rdfs:label "status"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "description of this person"@en; - rdfs:domain ; - rdfs:label "description"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "All known corresponding Germplasm"@en; - rdfs:domain ; - rdfs:label "sourceGermplasm"@en; - rdfs:range . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The date the value of this attribute was determined for a given germplasm"@en; - rdfs:domain ; - rdfs:label "determinedDate"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The dimension of the matrix being paginated"@en; - rdfs:domain ; - rdfs:label "dimension"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON."@en; - rdfs:domain ; - rdfs:label "dataType"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; - rdfs:domain ; - rdfs:label "instituteAddress"@en; - rdfs:range xsd:string . - - - rdf:type , , owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value."@en; - rdfs:domain ; - rdfs:label "filtersApplied"@en; - rdfs:range xsd:boolean . - - - rdf:type owl:Class; - rdfs:comment "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples."@en; - rdfs:label "ObservationUnit"@en . - - - rdf:type owl:Class; - rdfs:comment "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies."@en; - rdfs:label "Program"@en . - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Well identifier for this `Sample` location in the `Plate`. Usually a concatenation of Row and Column, or just a number if the `Samples` are not part of an ordered `Plate`."@en; - rdfs:domain ; - rdfs:label "well"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\""@en; - rdfs:domain ; - rdfs:label "fieldAbbreviation"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "A shortened version of the human readable name for a Trait"@en; - rdfs:domain ; - rdfs:label "mainAbbreviation"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology."@en; - rdfs:domain ; - rdfs:label "PUI"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observations"@en; - rdfs:domain ; - rdfs:label "observations"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; - rdfs:domain ; - rdfs:label "additionalInfo"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; - rdfs:domain ; - rdfs:label "trait"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The unique identifier for a Location"@en; - rdfs:domain ; - rdfs:label "location"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; - rdfs:domain ; - rdfs:label "externalReferences"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Geometry associated with an image"@en; - rdfs:domain ; - rdfs:label "observation"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Species associated with a reference"@en; - rdfs:domain ; - rdfs:label "reference"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The name of the external data link\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; - rdfs:domain ; - rdfs:label "name"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. "@en; - rdfs:domain ; - rdfs:label "parentType"@en; - rdfs:range . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "The Row identifier for this `Sample` location in the `Plate`"@en; - rdfs:domain ; - rdfs:label "row"@en; - rdfs:range xsd:string . - - - rdf:type owl:ObjectProperty; - rdfs:comment "List of treatments applied to an observation unit.\n\nMIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit."@en; - rdfs:domain ; - rdfs:label "treatments"@en; - rdfs:range . - - - rdf:type , owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment ""@en; - rdfs:domain ; - rdfs:label "callSets"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - rdfs:comment "Publications associated with a trial"@en; - rdfs:domain ; - rdfs:label "trial"@en; - rdfs:range . diff --git a/generator/build.gradle b/generator/build.gradle index ae6eacd7..f694fb39 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -112,7 +112,7 @@ tasks.register("generateAll") { dependsOn generateGraphQL dependsOn generateOpenAPI dependsOn generateOpenAPIJSON - dependsOn generateOWL + //dependsOn generateOWL } tasks.register("compareOpenAPI", JavaExec) { From e032b8cd977a1e36aa2dc47074998f04af21fd94 Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Tue, 19 May 2026 08:03:29 +0000 Subject: [PATCH 46/62] Generate specifications (manually triggered) --- Specification/Generated/BrAPI-Core.yaml | 1131 +++-- Specification/Generated/BrAPI-Genotyping.yaml | 1697 ++++--- Specification/Generated/BrAPI-Germplasm.yaml | 1220 +++-- .../Generated/BrAPI-Phenotyping.yaml | 1112 +++-- .../Generated/brapi_generated.graphqls | 337 +- Specification/Generated/brapi_generated.json | 4264 +++++++++++------ Specification/Generated/brapi_openapi.json | 40 +- .../Generated/brapi_openapi_comparison.md | 2649 +--------- 8 files changed, 6528 insertions(+), 5922 deletions(-) diff --git a/Specification/Generated/BrAPI-Core.yaml b/Specification/Generated/BrAPI-Core.yaml index f466fad5..9695bd1f 100644 --- a/Specification/Generated/BrAPI-Core.yaml +++ b/Specification/Generated/BrAPI-Core.yaml @@ -638,6 +638,8 @@ paths: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId - name: sortOrder in: query description: Sort order direction. Ascending/Descending. @@ -646,10 +648,10 @@ paths: type: string description: Sort order direction. Ascending/Descending. enum: - - asc - ASC - - desc - DESC + - asc + - desc - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" @@ -1479,6 +1481,10 @@ paths: responses: "200": $ref: "#/components/responses/ListListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1517,6 +1523,10 @@ paths: responses: "200": $ref: "#/components/responses/LocationListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1555,6 +1565,10 @@ paths: responses: "200": $ref: "#/components/responses/PersonListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1593,6 +1607,10 @@ paths: responses: "200": $ref: "#/components/responses/ProgramListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1631,6 +1649,10 @@ paths: responses: "200": $ref: "#/components/responses/StudyListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1669,6 +1691,10 @@ paths: responses: "200": $ref: "#/components/responses/TrialListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1812,21 +1838,41 @@ components: items: type: string dataMatrixAbbreviations: - type: array - description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ + type: string + description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ \ in the response." nullable: true - items: - type: string + example: "GT,RD" dataMatrixNames: - type: array - description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ - \ Depth' etc). This list controls which data matrices are returned in\ - \ the response." + type: string + description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ + \ 'Read Depth' etc). This list controls which data matrices are returned\ + \ in the response." + nullable: true + example: "Genotype,Read Depth" + dimensionCallSetPage: + type: integer + description: The requested page number for the CallSet dimension of the + matrix + format: int32 + nullable: true + dimensionCallSetPageSize: + type: integer + description: The requested page size for the CallSet dimension of the matrix + format: int32 + nullable: true + dimensionVariantPage: + type: integer + description: The requested page number for the Variant dimension of the + matrix + format: int32 + nullable: true + dimensionVariantPageSize: + type: integer + description: The requested page size for the Variant dimension of the matrix + format: int32 nullable: true - items: - type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single @@ -1895,6 +1941,7 @@ components: \ or not set (default), then the server should return all the matrix\n\ data as requested." example: true + default: false sampleDbIds: type: array description: A list of IDs which uniquely identify `Samples` within the @@ -1934,11 +1981,9 @@ components: Attribute: required: - attributeName - - methodDbId - - methodName - - scaleDbId - - scaleName - - traitName + - method + - scale + - trait type: object properties: additionalInfo: @@ -2006,20 +2051,12 @@ components: description: 2 letter ISO 639-1 code for the language of submission of the variable. nullable: true - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string + method: + $ref: "#/components/schemas/Method" ontologyReference: $ref: "#/components/schemas/OntologyReference" - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string + scale: + $ref: "#/components/schemas/Scale" scientist: type: string description: Name of scientist submitting the variable. @@ -2040,12 +2077,8 @@ components: nullable: true items: type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + trait: + $ref: "#/components/schemas/Trait" CallRequest: type: object properties: @@ -2062,6 +2095,12 @@ components: occurrence (false) nullable: true example: true + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. sepPhased: type: string description: The string used as a separator for phased allele calls. @@ -2454,17 +2493,10 @@ components: description: MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository. nullable: true - trialDbId: - type: string - trialName: - type: string - trialPUI: - type: string description: License and citation information for the data in this trial EnvironmentParameter: required: - description - - environmentParametersDbId - parameterName type: object properties: @@ -2472,10 +2504,6 @@ components: type: string description: Human-readable value of the environment parameter (defined above) constant within the experiment - environmentParametersDbId: - type: string - description: Human-readable value of the environment parameter (defined - above) constant within the experiment parameterName: type: string description: "Name of the environment parameter constant within the experiment\n\ @@ -2485,12 +2513,6 @@ components: type: string description: URI pointing to an ontology class for the parameter nullable: true - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string unit: type: string description: Unit of the value for this parameter @@ -2569,14 +2591,9 @@ components: \ several studies, the experimental design can be \"unknown\"/\"NA\",\ \ \"aggregated/reduced data\", or simply 'none'." nullable: true - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string description: The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology + nullable: true ExternalReference: type: object properties: @@ -2586,6 +2603,7 @@ components: \ number #460
The external reference ID. Could be a simple string\ \ or a URI." nullable: true + deprecated: true referenceId: type: string description: The external reference ID. Could be a simple string or a URI. @@ -2601,6 +2619,7 @@ components: \ Github issue number #460 \n
List of external reference IDs. Could\ \ be a simple strings or a URIs. (use with `externalReferenceSources`\ \ parameter)" + deprecated: true items: type: string externalReferenceIds: @@ -2697,6 +2716,7 @@ components: type: string description: The literal string "Feature" example: Feature + default: Feature description: |- One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. @@ -2704,10 +2724,12 @@ components: A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + nullable: true GeoJSONGeometry: + nullable: true oneOf: - required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2719,13 +2741,14 @@ components: type: type: string description: The literal string "Point" + default: Point description: |- Copied from RFC 7946 Section 3.1.1 A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. - required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2741,6 +2764,7 @@ components: type: type: string description: The literal string "Polygon" + default: Polygon description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ @@ -2748,7 +2772,7 @@ components: \ MAY be included as an optional third element." GeoJSONPoint: required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2760,6 +2784,7 @@ components: type: type: string description: The literal string "Point" + default: Point description: |- Copied from RFC 7946 Section 3.1.1 @@ -2767,7 +2792,7 @@ components: easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. GeoJSONPolygon: required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2783,6 +2808,7 @@ components: type: type: string description: The literal string "Polygon" + default: Polygon description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ @@ -2799,14 +2825,21 @@ components: type: string imageName: type: string + imagePUI: + type: string observationDbId: type: string + observationName: + type: string + observationPUI: + type: string observationUnit: $ref: "#/components/schemas/ObservationUnitPosition" type: type: string description: The literal string "Feature" example: Feature + default: Feature GermplasmAttributeRequest: type: object properties: @@ -2928,6 +2961,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -3270,7 +3304,6 @@ components: description: "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth\ \ facility in which the study was carried out, in the form of an accession\ \ number from the Crop Ontology." - nullable: true description: type: string description: MIAPPE V1.1 (DM-26) Description of growth facility - Short @@ -3278,6 +3311,7 @@ components: nullable: true description: Short description of the facility in which the study was carried out. + nullable: true ImageRequest: type: object properties: @@ -3389,20 +3423,8 @@ components: items: type: string LastUpdate: - required: - - lastUpdateDbId type: object properties: - lastUpdateDbId: - type: string - description: The ID which uniquely identifies a LastUpdate within the given - database server - studyDbId: - type: string - studyName: - type: string - studyPUI: - type: string timestamp: type: string description: The timestamp of the update. @@ -3413,6 +3435,7 @@ components: description: The version of the update. nullable: true description: The date and time when this study was last modified + nullable: true List: allOf: - $ref: "#/components/schemas/ListNewRequest" @@ -3470,6 +3493,8 @@ components: type: string description: Human readable name of a List Owner. (usually a user or person) nullable: true + listOwnerPersonDbId: + type: string listSize: type: integer description: The number of elements in a List @@ -3481,8 +3506,6 @@ components: nullable: true listType: $ref: "#/components/schemas/ListType" - personDbId: - type: string description: "A List represents a collection of other BrAPI data objects. Typically\ \ these are custom lists generated by a user to keep track of interesting\ \ data. For example, a user might build a List of Germplasm that they have\ @@ -3582,20 +3605,6 @@ components: ListSearchRequest: type: object properties: - dateCreatedRangeStart: - type: string - description: Define the beginning for an interval of time and only include - Lists that are created within this interval. - format: date-time - nullable: true - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string commonCropNames: type: array description: "The BrAPI Common Crop Name is the simple, generalized, widely\ @@ -3607,37 +3616,51 @@ components: \ of available crops on a server." items: type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - dateModifiedRangeEnd: + dateCreatedRangeEnd: type: string description: Define the end for an interval of time and only include Lists - that are modified within this interval. + that are created within this interval. format: date-time nullable: true - listSources: - type: array - description: "An array of terms identifying lists from different sources\ - \ (ie 'USER', 'SYSTEM', etc)" + dateCreatedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are created within this interval. + format: date-time nullable: true - items: - type: string - listType: - $ref: "#/components/schemas/ListType" - dateCreatedRangeEnd: + dateModifiedRangeEnd: type: string description: Define the end for an interval of time and only include Lists - that are created within this interval. + that are modified within this interval. format: date-time nullable: true + dateModifiedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are modified within this interval. + format: date-time + nullable: true + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string listDbIds: type: array description: An array of primary database identifiers to identify a set @@ -3651,6 +3674,13 @@ components: nullable: true items: type: string + listOwnerNames: + type: array + description: An array of names for the people or entities who are responsible + for a set of Lists + nullable: true + items: + type: string listOwnerPersonDbIds: type: array description: An array of primary database identifiers to identify people @@ -3658,19 +3688,44 @@ components: nullable: true items: type: string - dateModifiedRangeStart: - type: string - description: Define the beginning for an interval of time and only include - Lists that are modified within this interval. - format: date-time - nullable: true - listOwnerNames: + listSources: type: array - description: An array of names for the people or entities who are responsible - for a set of Lists + description: "An array of terms identifying lists from different sources\ + \ (ie 'USER', 'SYSTEM', etc)" nullable: true items: type: string + listType: + $ref: "#/components/schemas/ListType" + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string description: "A List represents a collection of other BrAPI data objects. Typically\ \ these are custom lists generated by a user to keep track of interesting\ \ data. For example, a user might build a List of Germplasm that they have\ @@ -3781,17 +3836,25 @@ components: The full name of the institute at a particular Location
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. nullable: true - locationDbId: - type: string - nullable: true locationName: type: string - nullable: true + description: |- + A human readable name for a Location +
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place. locationType: type: string description: "A short description of a type of Location (ex. Field Station,\ \ Breeding Location, Storage Location, etc)" nullable: true + parentLocationDbId: + type: string + nullable: true + parentLocationName: + type: string + nullable: true + parentLocationPUI: + type: string + nullable: true siteStatus: type: string description: "Description of the accessibility of the location (ex. Public,\ @@ -3828,15 +3891,18 @@ components: abbreviations: type: array description: A list of shortened human readable names for a set of Locations + nullable: true items: type: string altitudeMax: type: number description: The maximum altitude to search for + nullable: true example: 200 altitudeMin: type: number description: The minimum altitude to search for + nullable: true example: 20 commonCropNames: type: array @@ -3855,21 +3921,25 @@ components: type: array description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ \ spec" + nullable: true items: type: string countryNames: type: array description: The full name of the country to search for + nullable: true items: type: string instituteAddresses: type: array description: The street address of the institute to search for + nullable: true items: type: string instituteNames: type: array description: The name of the institute to search for + nullable: true items: type: string locationDbIds: @@ -3886,6 +3956,7 @@ components: type: array description: "The type of location this represents (ex. Breeding Location,\ \ Storage Location, etc)" + nullable: true items: type: string parentLocationDbIds: @@ -3894,6 +3965,7 @@ components: \ defines the encompassing location that this location belongs to. \n\ For example, an Institution might have multiple Field Stations inside\ \ it and each Field Station might have multiple Fields." + nullable: true items: type: string parentLocationNames: @@ -3902,6 +3974,7 @@ components: \ defines the encompassing location that this location belongs to. \n\ For example, an Institution might have multiple Field Stations inside\ \ it and each Field Station might have multiple Fields." + nullable: true items: type: string programDbIds: @@ -3925,35 +3998,22 @@ components: LocationSearchRequest: type: object properties: - locationDbIds: + abbreviations: type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - countryNames: - type: array - description: The full name of the country to search for - items: - type: string - coordinates: - $ref: "#/components/schemas/GeoJSONSearchArea" - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: A list of shortened human readable names for a set of Locations + nullable: true items: type: string altitudeMax: type: number description: The maximum altitude to search for + nullable: true example: 200 + altitudeMin: + type: number + description: The minimum altitude to search for + nullable: true + example: 20 commonCropNames: type: array description: "The BrAPI Common Crop Name is the simple, generalized, widely\ @@ -3965,61 +4025,116 @@ components: \ of available crops on a server." items: type: string - programDbIds: + coordinates: + $ref: "#/components/schemas/GeoJSONSearchArea" + countryCodes: type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." + description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ + \ spec" + nullable: true + items: + type: string + countryNames: + type: array + description: The full name of the country to search for + nullable: true + items: + type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + instituteAddresses: + type: array + description: The street address of the institute to search for + nullable: true items: type: string instituteNames: type: array description: The name of the institute to search for + nullable: true items: type: string - countryCodes: + locationDbIds: type: array - description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ - \ spec" + description: The location ids to search for items: type: string - parentLocationNames: + locationNames: type: array - description: "A human readable name for a location\n
The Parent Location\ - \ defines the encompassing location that this location belongs to. \n\ - For example, an Institution might have multiple Field Stations inside\ - \ it and each Field Station might have multiple Fields." + description: A human readable names to search for items: type: string locationTypes: type: array description: "The type of location this represents (ex. Breeding Location,\ \ Storage Location, etc)" + nullable: true items: type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 parentLocationDbIds: type: array description: "The unique identifier for a Location\n
The Parent Location\ \ defines the encompassing location that this location belongs to. \n\ For example, an Institution might have multiple Field Stations inside\ \ it and each Field Station might have multiple Fields." + nullable: true items: type: string - instituteAddresses: + parentLocationNames: type: array - description: The street address of the institute to search for + description: "A human readable name for a location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + nullable: true items: type: string - altitudeMin: - type: number - description: The minimum altitude to search for - example: 20 - abbreviations: + programDbIds: type: array - description: A list of shortened human readable names for a set of Locations + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string description: "A geographic Location on earth. This is usually used to describe\ @@ -4149,29 +4264,35 @@ components: observationDbIds: type: array description: The unique id of an Observation + nullable: true items: type: string observationLevelRelationships: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevelRelationship" observationLevels: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevel" observationTimeStampRangeEnd: type: string description: Timestamp range end format: date-time + nullable: true observationTimeStampRangeStart: type: string description: Timestamp range start format: date-time + nullable: true observationUnitDbIds: type: array description: The unique id of an Observation Unit + nullable: true items: type: string observationUnitLevelCodes: @@ -4284,6 +4405,7 @@ components: type: array description: "The year or Phenotyping campaign of a multi-annual study (trees,\ \ grape, ...)" + nullable: true items: type: string studyDbIds: @@ -4372,6 +4494,7 @@ components: \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ \ your own risk. It may return large, unpaginated lists of observation\ \ data. Only set this value to True if you are sure you need to." + nullable: true example: false locationDbIds: type: array @@ -4386,16 +4509,19 @@ components: observationLevelRelationships: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevelRelationship" observationLevels: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevel" observationUnitDbIds: type: array description: The unique id of an observation unit + nullable: true items: type: string observationUnitLevelCodes: @@ -4473,6 +4599,7 @@ components: observationUnitNames: type: array description: The human readable identifier for an Observation Unit + nullable: true items: type: string observationVariableDbIds: @@ -4513,6 +4640,7 @@ components: type: array description: "The year or Phenotyping campaign of a multi-annual study (trees,\ \ grape, ...)" + nullable: true items: type: string studyDbIds: @@ -4652,6 +4780,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -4790,18 +4919,21 @@ components: A collection of unique identifiers for materials or germplasm within a genebank MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true items: type: string binomialNames: type: array description: List of the full binomial name (scientific name) to identify a germplasm + nullable: true items: type: string collections: type: array description: A specific panel/collection/population name this germplasm belongs to. + nullable: true items: type: string commonCropNames: @@ -4819,11 +4951,13 @@ components: type: array description: A familyCode representing the family this germplasm belongs to. + nullable: true items: type: string genus: type: array description: List of Genus names to identify germplasm + nullable: true items: type: string germplasmDbIds: @@ -4842,27 +4976,32 @@ components: germplasmPUIs: type: array description: List of Permanent Unique Identifiers to identify germplasm + nullable: true items: type: string includeFullTree: type: boolean description: "If this parameter is true, recursively include ALL of the\ \ nodes available in this pedigree tree" + nullable: true example: true includeParents: type: boolean description: "If this parameter is true, include the array of parents in\ \ the response" + nullable: true example: true includeProgeny: type: boolean description: "If this parameter is true, include the array of progeny in\ \ the response" + nullable: true example: true includeSiblings: type: boolean description: "If this parameter is true, include the array of siblings in\ \ the response" + nullable: true example: true instituteCodes: type: array @@ -4874,6 +5013,7 @@ components: \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ \ rules (v)\"." + nullable: true items: type: string pedigreeDepth: @@ -4909,6 +5049,7 @@ components: species: type: array description: List of Species names to identify germplasm + nullable: true items: type: string studyDbIds: @@ -4924,6 +5065,7 @@ components: synonyms: type: array description: List of alternative names or IDs used to reference this germplasm + nullable: true items: type: string trialDbIds: @@ -5082,10 +5224,15 @@ components: PersonSearchRequest: type: object properties: - middleNames: + commonCropNames: type: array - description: Persons middle name - nullable: true + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." items: type: string emailAddresses: @@ -5094,46 +5241,25 @@ components: nullable: true items: type: string - userIDs: - type: array - description: A systems user ID associated with this person. Different from - personDbId because you could have a person who is not a user of the system. - nullable: true - items: - type: string - personDbIds: - type: array - description: Unique ID for this person - nullable: true - items: - type: string - programNames: + externalReferenceIDs: type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: type: string - commonCropNames: + externalReferenceIds: type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) items: type: string - programDbIds: + externalReferenceSources: type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) items: type: string firstNames: @@ -5154,12 +5280,60 @@ components: nullable: true items: type: string + middleNames: + type: array + description: Persons middle name + nullable: true + items: + type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + personDbIds: + type: array + description: Unique ID for this person + nullable: true + items: + type: string phoneNumbers: type: array description: phone number of this person nullable: true items: type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + userIDs: + type: array + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + nullable: true + items: + type: string description: "A generic object used to maintain the metadata needed to describe\ \ a human. The Person might be a software user, a field technician, or a primary\ \ contact for a Program." @@ -5380,13 +5554,16 @@ components: description: Information describing the grant or funding source for this program nullable: true - objective: + leadPersonDbId: type: string - description: The primary objective of the program nullable: true - personDbId: + leadPersonName: type: string nullable: true + objective: + type: string + description: The primary objective of the program + nullable: true programName: type: string description: Human readable name of the program @@ -5396,7 +5573,6 @@ components: \ represents a standard, permanent breeding program\n
'PROJECT' represents\ \ a short term project, usually with a set time limit based on funding\ \ " - nullable: true enum: - STANDARD - PROJECT @@ -5499,20 +5675,12 @@ components: ProgramSearchRequest: type: object properties: - leadPersonNames: + abbreviations: type: array - description: The names of the program leader to search for + description: A list of shortened human readable names for a set of Programs nullable: true items: type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string commonCropNames: type: array description: "The BrAPI Common Crop Name is the simple, generalized, widely\ @@ -5524,6 +5692,56 @@ components: \ of available crops on a server." items: type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + leadPersonDbIds: + type: array + description: The person DbIds of the program leader to search for + nullable: true + items: + type: string + leadPersonNames: + type: array + description: The names of the program leader to search for + nullable: true + items: + type: string + objectives: + type: array + description: A program objective to search for + nullable: true + items: + type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -5534,16 +5752,12 @@ components: \ on a server." items: type: string - objectives: - type: array - description: A program objective to search for - nullable: true - items: - type: string - leadPersonDbIds: + programNames: type: array - description: The person DbIds of the program leader to search for - nullable: true + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string programTypes: @@ -5561,12 +5775,6 @@ components: enum: - STANDARD - PROJECT - abbreviations: - type: array - description: A list of shortened human readable names for a set of Programs - nullable: true - items: - type: string description: A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can @@ -5590,12 +5798,6 @@ components: type: string description: The publication reference. nullable: true - trialDbId: - type: string - trialName: - type: string - trialPUI: - type: string description: MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended. @@ -5628,6 +5830,7 @@ components: type: array description: "If specified, return the references for which the `accession`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string commonCropNames: @@ -5662,6 +5865,7 @@ components: \ same official sequence share the same coordinates and annotations, and\ \ can be replaced with the official sequence for certain use cases." format: boolean + nullable: true maxLength: type: integer description: The minimum length of this `References` sequence. @@ -5671,6 +5875,7 @@ components: type: array description: "If specified, return the references for which the `md5checksum`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string minLength: @@ -5700,12 +5905,14 @@ components: type: array description: A list of IDs which uniquely identify `References` within the given database server + nullable: true items: type: string referenceSetDbIds: type: array description: A list of IDs which uniquely identify `ReferenceSets` within the given database server + nullable: true items: type: string studyDbIds: @@ -6094,14 +6301,16 @@ components: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId SortOrder: type: string description: Sort order direction. Ascending/Descending. enum: - - asc - ASC - - desc - DESC + - asc + - desc Study: allOf: - $ref: "#/components/schemas/StudyNewRequest" @@ -6134,6 +6343,12 @@ components: type: string description: Common name for the crop associated with this study nullable: true + contacts: + type: array + description: List of contact entities associated with this study + nullable: true + items: + $ref: "#/components/schemas/Contact" culturalPractices: type: string description: MIAPPE V1.1 (DM-28) Cultural practices - General description @@ -6211,6 +6426,14 @@ components: description: MIAPPE V1.1 (DM-25) Observation unit description - General description of the observation units in the study. nullable: true + observationVariableDbIds: + type: array + description: "The list of Observation Variables being used in this study.\ + \ \n\nThis list is intended to be the wishlist of variables to collect\ + \ in this study. It may or may not match the set of variables used in\ + \ the collected observation records. " + items: + type: string seasons: type: array description: List of seasons over which this study was performed. @@ -6235,7 +6458,6 @@ components: The description of this study MIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study - nullable: true studyName: type: string description: |- @@ -6256,8 +6478,6 @@ components: type: string trialName: type: string - trialPUI: - type: string description: A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from @@ -6371,15 +6591,17 @@ components: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId sortOrder: type: string description: Sort order direction. Ascending/Descending. nullable: true enum: - - asc - ASC - - desc - DESC + - asc + - desc studyCodes: type: array description: A short human readable code for a study @@ -6422,43 +6644,6 @@ components: StudySearchRequest: type: object properties: - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - seasonDbIds: - type: array - description: The ID which uniquely identifies a season - nullable: true - items: - type: string active: type: boolean description: A flag to indicate if a Study is currently active and ongoing @@ -6475,74 +6660,101 @@ components: \ of available crops on a server." items: type: string - programDbIds: + externalReferenceIDs: type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: type: string - studyCodes: + externalReferenceIds: type: array - description: A short human readable code for a study - nullable: true + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) items: type: string - studyPUIs: + externalReferenceSources: type: array - description: "Permanent unique identifier associated with study data. For\ - \ example, a URI or DOI" + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for nullable: true items: type: string - observationVariablePUIs: + germplasmNames: type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" + description: List of human readable names to identify germplasm to search + for + nullable: true items: type: string - trialDbIds: + locationDbIds: type: array - description: The ID which uniquely identifies a trial to search for + description: The location ids to search for items: type: string - studyDbIds: + locationNames: type: array - description: List of study identifiers to search for + description: A human readable names to search for items: type: string - trialNames: + observationVariableDbIds: type: array - description: The human readable name of a trial to search for + description: The DbIds of Variables to search for items: type: string observationVariableNames: type: array - description: The names of Variables to search for + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." items: type: string - studyNames: + programNames: type: array - description: List of study names to filter search results + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string - observationVariableDbIds: + seasonDbIds: type: array - description: The DbIds of Variables to search for + description: The ID which uniquely identifies a season + nullable: true items: type: string - sortOrder: - type: string - description: Sort order direction. Ascending/Descending. - nullable: true - enum: - - asc - - ASC - - desc - - DESC sortBy: type: string description: Name of the field to sort by. @@ -6557,12 +6769,56 @@ components: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + nullable: true + enum: + - ASC + - DESC + - asc + - desc + studyCodes: + type: array + description: A short human readable code for a study + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + studyPUIs: + type: array + description: "Permanent unique identifier associated with study data. For\ + \ example, a URI or DOI" + nullable: true + items: + type: string studyTypes: type: array description: "The type of study being performed. ex. \"Yield Trial\", etc" nullable: true items: type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string description: A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from @@ -6590,6 +6846,7 @@ components: \ a prior response to construct a query and move to the next or previous\ \ page respectively. " example: 33c27874 + deprecated: true TraitDataType: type: string description: |- @@ -6737,12 +6994,6 @@ components: type: string description: The date this trial started nullable: true - studyDbIds: - type: array - description: "" - nullable: true - items: - type: string trialDescription: type: string description: |- @@ -6880,35 +7131,6 @@ components: TrialSearchRequest: type: object properties: - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - searchDateRangeEnd: - type: string - description: "The end of the overlapping search date range. `searchDateRangeStart`\ - \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ - \ of the following cases are true\n\n- `searchDateRangeStart` is before\ - \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ - \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ - \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is before `trial.endDate`" - format: date - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string active: type: boolean description: A flag to indicate if a Trial is currently active and ongoing @@ -6924,47 +7146,82 @@ components: \ of available crops on a server." items: type: string - programDbIds: + contactDbIds: type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." + description: List of contact entities associated with this trial items: type: string - trialDbIds: + externalReferenceIDs: type: array - description: The ID which uniquely identifies a trial to search for + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: type: string - studyDbIds: + externalReferenceIds: type: array - description: List of study identifiers to search for + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) items: type: string - trialNames: + externalReferenceSources: type: array - description: The human readable name of a trial to search for + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) items: type: string - trialPUIs: + locationDbIds: type: array - description: A permanent identifier for a trial. Could be DOI or other URI - formatted identifier. + description: The location ids to search for items: type: string - studyNames: + locationNames: type: array - description: List of study names to filter search results + description: A human readable names to search for items: type: string - contactDbIds: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: type: array - description: List of contact entities associated with this trial + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string + searchDateRangeEnd: + type: string + description: "The end of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date searchDateRangeStart: type: string description: "The start of the overlapping search date range. `searchDateRangeStart`\ @@ -6976,17 +7233,41 @@ components: \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ \ is before `trial.endDate`" format: date + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + trialPUIs: + type: array + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + items: + type: string description: "A Trial represents a collection of Study objects, and the metadata\ \ associated with that collection. A Trial could represent a multi-location\ \ experiment, and could contain information related to publications and data\ \ licensing." Variable: required: - - methodDbId - - methodName - - scaleDbId - - scaleName - - traitName + - method + - scale + - trait type: object properties: additionalInfo: @@ -7033,20 +7314,12 @@ components: description: 2 letter ISO 639-1 code for the language of submission of the variable. nullable: true - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string + method: + $ref: "#/components/schemas/Method" ontologyReference: $ref: "#/components/schemas/OntologyReference" - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string + scale: + $ref: "#/components/schemas/Scale" scientist: type: string description: Name of scientist submitting the variable. @@ -7067,12 +7340,8 @@ components: nullable: true items: type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + trait: + $ref: "#/components/schemas/Trait" description: "A unique combination of Trait, Method, and Scale to define a clear\ \ context for an Observation." VariableBaseClassParameters: @@ -7157,6 +7426,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -7240,6 +7510,8 @@ components: \ number #474 \n
Only return variant calls which belong to call sets\ \ with these IDs. If unspecified, return all variants and no variant call\ \ objects." + nullable: true + deprecated: true items: type: string commonCropNames: @@ -7282,15 +7554,19 @@ components: description: |- **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472
Only return variants on this reference. + nullable: true example: 120a2d5c + deprecated: true referenceDbIds: type: array description: The unique identifier representing a genotype `Reference` + nullable: true items: type: string referenceSetDbIds: type: array description: The unique identifier representing a genotype `ReferenceSet` + nullable: true items: type: string start: @@ -7325,11 +7601,13 @@ components: variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` + nullable: true items: type: string VariantSetRequest: @@ -7847,6 +8125,59 @@ components: type: array items: $ref: "#/components/schemas/Study" + CallListResponse: + description: OK + content: + application/json: + schema: + title: CallListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + description: "The `data` array is part of the BrAPI standard List\ + \ Response JSON container. `data` will always contain the primary\ + \ list of objects being returned by a BrAPI endpoint. `data`\ + \ is also the only array impacted by the `metadata.pagination`\ + \ details. When the pagination parameters change, the `data`\ + \ array will reflect those changes in the JSON response." + items: + $ref: "#/components/schemas/Call" + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed + into a single occurrence (false) + nullable: true + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele + calls. + nullable: true + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele + calls. + nullable: true + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + nullable: true + example: "." LocationSingleResponse: description: OK content: diff --git a/Specification/Generated/BrAPI-Genotyping.yaml b/Specification/Generated/BrAPI-Genotyping.yaml index 93734846..fccd0df3 100644 --- a/Specification/Generated/BrAPI-Genotyping.yaml +++ b/Specification/Generated/BrAPI-Genotyping.yaml @@ -3,6 +3,153 @@ info: title: BrAPI-Genotyping version: "2.1" paths: + /allelematrix: + get: + tags: + - AlleleMatrix + summary: Get a filtered list of AlleleMatrix + description: Get a list of AlleleMatrix + parameters: + - name: preview + in: query + description: "Default Value = false\n
\nIf 'preview' is set to true, then\ + \ the server should only return the lists of 'callSetDbIds', \n'variantDbIds',\ + \ and 'variantSetDbIds'. The server should not return any matrix data. This\n\ + is intended to be a preview and give the client a sense of how large the\ + \ matrix returned will be\n
\nIf 'preview' is set to false or not set\ + \ (default), then the server should return all the matrix\ndata as requested." + required: false + schema: + type: boolean + - name: dimensionVariantPage + in: query + description: The requested page number for the Variant dimension of the matrix + required: false + schema: + type: integer + format: int32 + - name: dimensionVariantPageSize + in: query + description: The requested page size for the Variant dimension of the matrix + required: false + schema: + type: integer + format: int32 + - name: dimensionCallSetPage + in: query + description: The requested page number for the CallSet dimension of the matrix + required: false + schema: + type: integer + format: int32 + - name: dimensionCallSetPageSize + in: query + description: The requested page size for the CallSet dimension of the matrix + required: false + schema: + type: integer + format: int32 + - name: dataMatrixNames + in: query + description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ + \ 'Read Depth' etc). This list controls which data matrices are returned\ + \ in the response." + required: false + schema: + type: string + - name: dataMatrixAbbreviations + in: query + description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ + \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ + \ in the response." + required: false + schema: + type: string + - name: positionRange + in: query + description: "The postion range to search\n
\nUses the format \":-\"\ + \ where is the chromosome name, is \nthe starting position\ + \ of the range, and is the ending position of the range" + required: false + schema: + type: string + - name: germplasmName + in: query + description: A list of human readable `Germplasm` names + required: false + schema: + type: string + - name: germplasmPUI + in: query + description: A list of permanent unique identifiers associated with `Germplasm` + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: A list of IDs which uniquely identify `Germplasm` within the + given database server + required: false + schema: + type: string + - name: callSetDbId + in: query + description: A list of IDs which uniquely identify `CallSets` within the given + database server + required: false + schema: + type: string + - name: variantDbId + in: query + description: A list of IDs which uniquely identify `Variants` within the given + database server + required: false + schema: + type: string + - name: variantSetDbId + in: query + description: A list of IDs which uniquely identify `VariantSets` within the + given database server + required: false + schema: + type: string + - name: expandHomozygotes + in: query + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + required: false + schema: + type: boolean + - name: sepPhased + in: query + description: The string used as a separator for phased allele calls. + required: false + schema: + type: string + - name: sepUnphased + in: query + description: The string used as a separator for unphased allele calls. + required: false + schema: + type: string + - name: unknownString + in: query + description: The string used as a representation for missing data. + required: false + schema: + type: string + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/AlleleMatrixSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /calls: get: tags: @@ -56,6 +203,15 @@ paths: required: false schema: type: string + - name: pageToken + in: query + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + required: false + schema: + type: string - $ref: "#/components/parameters/pageToken" - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" @@ -683,13 +839,13 @@ paths: example: "{_1={additionalInfo={}, callSets=[{}], column=10,\ \ externalReferences=[{}], germplasm={}, observationUnit={}, plate={},\ \ program={}, row=00358167, sampleBarcode=6a6db74b, sampleDescription=3388964f,\ - \ sampleDbId=079d6d5e, sampleGroupId=70fcb311, sampleName=082a6b4c,\ + \ sampleDbId=079d6d5e, sampleGroupDbId=2455eef3, sampleName=082a6b4c,\ \ samplePUI=08863647, sampleTimestamp=2020-08-12T18:10:40.413Z, sampleType=0889ec7d,\ \ study={}, takenBy=599da043, tissueType=4d105e22, trial={}, well=06bc78f3},\ \ _2={additionalInfo={}, callSets=[{}], column=20, externalReferences=[{}],\ \ germplasm={}, observationUnit={}, plate={}, program={}, row=00358168,\ \ sampleBarcode=6a6db74c, sampleDescription=33889650, sampleDbId=079d6d5f,\ - \ sampleGroupId=70fcb312, sampleName=082a6b4d, samplePUI=08863648,\ + \ sampleGroupDbId=2455eef4, sampleName=082a6b4d, samplePUI=08863648,\ \ sampleTimestamp=2020-08-12T18:10:40.413Z, sampleType=0889ec7e, study={},\ \ takenBy=599da044, tissueType=4d105e23, trial={}, well=06bc78f4}}" responses: @@ -925,14 +1081,14 @@ paths: responses: "200": $ref: "#/components/responses/CallListResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" /maps/{mapDbId}: get: tags: @@ -977,14 +1133,14 @@ paths: responses: "200": $ref: "#/components/responses/LinkageGroupListResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" /plates/{plateDbId}: get: tags: @@ -1210,14 +1366,14 @@ paths: responses: "200": $ref: "#/components/responses/CallListResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" /variantsets/{variantSetDbId}: get: tags: @@ -1288,14 +1444,14 @@ paths: responses: "200": $ref: "#/components/responses/CallListResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" /variantsets/{variantSetDbId}/callsets: get: tags: @@ -1328,14 +1484,14 @@ paths: responses: "200": $ref: "#/components/responses/CallSetListResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" /variantsets/{variantSetDbId}/variants: get: tags: @@ -1362,14 +1518,14 @@ paths: responses: "200": $ref: "#/components/responses/VariantListResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" /search/allelematrix: post: tags: @@ -1392,7 +1548,7 @@ paths: $ref: "#/components/schemas/AlleleMatrixSearchRequest" responses: "200": - $ref: "#/components/responses/AlleleMatrixListResponse" + $ref: "#/components/responses/AlleleMatrixSingleResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" "400": @@ -1704,7 +1860,11 @@ paths: - $ref: "#/components/parameters/authorizationHeader" responses: "200": - $ref: "#/components/responses/AlleleMatrixListResponse" + $ref: "#/components/responses/AlleleMatrixSingleResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1743,6 +1903,10 @@ paths: responses: "200": $ref: "#/components/responses/CallListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1781,6 +1945,10 @@ paths: responses: "200": $ref: "#/components/responses/CallSetListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1820,6 +1988,10 @@ paths: responses: "200": $ref: "#/components/responses/MarkerPositionListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1858,6 +2030,10 @@ paths: responses: "200": $ref: "#/components/responses/PlateListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1896,6 +2072,10 @@ paths: responses: "200": $ref: "#/components/responses/ReferenceListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1934,6 +2114,10 @@ paths: responses: "200": $ref: "#/components/responses/ReferenceSetListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1972,6 +2156,10 @@ paths: responses: "200": $ref: "#/components/responses/SampleListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -2010,6 +2198,10 @@ paths: responses: "200": $ref: "#/components/responses/VariantListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -2048,6 +2240,10 @@ paths: responses: "200": $ref: "#/components/responses/VariantSetListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -2066,8 +2262,20 @@ components: \ by the BrAPI specification." nullable: true AlleleMatrix: + required: + - callSetDbIds + - variantSetDbIds type: object properties: + callSetDbIds: + type: array + description: "A list of unique identifiers for the CallSets contained in\ + \ the matrix response. This array should match the ordering for columns\ + \ in the matrix. A CallSet is a unique combination of a Sample and a sequencing\ + \ event. CallSets often have a 1-to-1 relationship with Samples, but this\ + \ is not always the case." + items: + type: string dataMatrices: type: array description: "The 'dataMatrices' are an array of matrix objects that hold\ @@ -2100,6 +2308,23 @@ components: type: string description: The string used as a representation for missing data. nullable: true + variantDbIds: + type: array + description: A list of unique identifiers for the Variants contained in + the matrix response. This array should match the ordering for rows in + the matrix. + nullable: true + items: + type: string + variantSetDbIds: + type: array + description: "A list of unique identifiers for the VariantSets contained\ + \ in the matrix response. A VariantSet is a data set originating from\ + \ a sequencing event. Often, users will only be interested in data from\ + \ a single VariantSet, but in some cases a user might be interested in\ + \ a matrix with data from multiple VariantSets." + items: + type: string description: "The AlleleMatrix object is used to describe a matrix of genotyping\ \ results. This 2d array of data reduces the overall size of the response\ \ for larger datasets, when compared to the Calls endpoints. This makes genotype\ @@ -2135,21 +2360,41 @@ components: items: type: string dataMatrixAbbreviations: - type: array - description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ + type: string + description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ \ in the response." nullable: true - items: - type: string + example: "GT,RD" dataMatrixNames: - type: array - description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ - \ Depth' etc). This list controls which data matrices are returned in\ - \ the response." + type: string + description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ + \ 'Read Depth' etc). This list controls which data matrices are returned\ + \ in the response." + nullable: true + example: "Genotype,Read Depth" + dimensionCallSetPage: + type: integer + description: The requested page number for the CallSet dimension of the + matrix + format: int32 + nullable: true + dimensionCallSetPageSize: + type: integer + description: The requested page size for the CallSet dimension of the matrix + format: int32 + nullable: true + dimensionVariantPage: + type: integer + description: The requested page number for the Variant dimension of the + matrix + format: int32 + nullable: true + dimensionVariantPageSize: + type: integer + description: The requested page size for the Variant dimension of the matrix + format: int32 nullable: true - items: - type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single @@ -2218,6 +2463,7 @@ components: \ or not set (default), then the server should return all the matrix\n\ data as requested." example: true + default: false sampleDbIds: type: array description: A list of IDs which uniquely identify `Samples` within the @@ -2257,6 +2503,54 @@ components: AlleleMatrixSearchRequest: type: object properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + dataMatrixAbbreviations: + type: string + description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ + \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ + \ in the response." + nullable: true + example: "GT,RD" + dataMatrixNames: + type: string + description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ + \ 'Read Depth' etc). This list controls which data matrices are returned\ + \ in the response." + nullable: true + example: "Genotype,Read Depth" + dimensionCallSetPage: + type: integer + description: The requested page number for the CallSet dimension of the + matrix + format: int32 + nullable: true + dimensionCallSetPageSize: + type: integer + description: The requested page size for the CallSet dimension of the matrix + format: int32 + nullable: true + dimensionVariantPage: + type: integer + description: The requested page number for the Variant dimension of the + matrix + format: int32 + nullable: true + dimensionVariantPageSize: + type: integer + description: The requested page size for the Variant dimension of the matrix + format: int32 + nullable: true + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + nullable: true + example: true germplasmDbIds: type: array description: A list of IDs which uniquely identify `Germplasm` within the @@ -2264,22 +2558,18 @@ components: nullable: true items: type: string - preview: - type: boolean - description: "Default Value = false\n
\nIf 'preview' is set to true,\ - \ then the server should only return the lists of 'callSetDbIds', \n'variantDbIds',\ - \ and 'variantSetDbIds'. The server should not return any matrix data.\ - \ This\nis intended to be a preview and give the client a sense of how\ - \ large the matrix returned will be\n
\nIf 'preview' is set to false\ - \ or not set (default), then the server should return all the matrix\n\ - data as requested." - example: true germplasmNames: type: array description: A list of human readable `Germplasm` names nullable: true items: type: string + germplasmPUIs: + type: array + description: A list of permanent unique identifiers associated with `Germplasm` + nullable: true + items: + type: string pagination: type: array description: Pagination for the matrix @@ -2305,17 +2595,6 @@ components: of the matrix format: int32 example: 500 - unknownString: - type: string - description: The string used as a representation for missing data. - nullable: true - example: "." - germplasmPUIs: - type: array - description: A list of permanent unique identifiers associated with `Germplasm` - nullable: true - items: - type: string positionRanges: type: array description: "The postion range to search\n
\nUses the format \":-\"\ @@ -2324,6 +2603,17 @@ components: nullable: true items: type: string + preview: + type: boolean + description: "Default Value = false\n
\nIf 'preview' is set to true,\ + \ then the server should only return the lists of 'callSetDbIds', \n'variantDbIds',\ + \ and 'variantSetDbIds'. The server should not return any matrix data.\ + \ This\nis intended to be a preview and give the client a sense of how\ + \ large the matrix returned will be\n
\nIf 'preview' is set to false\ + \ or not set (default), then the server should return all the matrix\n\ + data as requested." + example: true + default: false sampleDbIds: type: array description: A list of IDs which uniquely identify `Samples` within the @@ -2331,27 +2621,21 @@ components: nullable: true items: type: string - variantSetDbIds: - type: array - description: A list of IDs which uniquely identify `VariantSets` within - the given database server + sepPhased: + type: string + description: The string used as a separator for phased allele calls. nullable: true - items: - type: string - dataMatrixAbbreviations: - type: array - description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. nullable: true - items: - type: string - expandHomozygotes: - type: boolean - description: Should homozygotes be expanded (true) or collapsed into a single - occurrence (false) + example: / + unknownString: + type: string + description: The string used as a representation for missing data. nullable: true - example: true + example: "." variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` within the @@ -2359,30 +2643,13 @@ components: nullable: true items: type: string - callSetDbIds: - type: array - description: A list of IDs which uniquely identify `CallSets` within the - given database server - items: - type: string - dataMatrixNames: + variantSetDbIds: type: array - description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ - \ Depth' etc). This list controls which data matrices are returned in\ - \ the response." + description: A list of IDs which uniquely identify `VariantSets` within + the given database server nullable: true items: type: string - sepPhased: - type: string - description: The string used as a separator for phased allele calls. - nullable: true - example: '|' - sepUnphased: - type: string - description: The string used as a separator for unphased allele calls. - nullable: true - example: / description: "The AlleleMatrix object is used to describe a matrix of genotyping\ \ results. This 2d array of data reduces the overall size of the response\ \ for larger datasets, when compared to the Calls endpoints. This makes genotype\ @@ -2425,21 +2692,15 @@ components: \ format." format: date-time nullable: true - variantSetDbId: - type: string - variantSetName: - type: string description: "An analysis contains an interpretation of one or several experiments.\ \ (e.g. SNVs, copy number variations, methylation status) together with information\ \ about the methodology used." Attribute: required: - attributeName - - methodDbId - - methodName - - scaleDbId - - scaleName - - traitName + - method + - scale + - trait type: object properties: additionalInfo: @@ -2507,20 +2768,12 @@ components: description: 2 letter ISO 639-1 code for the language of submission of the variable. nullable: true - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string + method: + $ref: "#/components/schemas/Method" ontologyReference: $ref: "#/components/schemas/OntologyReference" - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string + scale: + $ref: "#/components/schemas/Scale" scientist: type: string description: Name of scientist submitting the variable. @@ -2541,12 +2794,8 @@ components: nullable: true items: type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + trait: + $ref: "#/components/schemas/Trait" AvailableFormat: type: object properties: @@ -2598,10 +2847,6 @@ components: type: string description: The string used as a representation for missing data. nullable: true - variantSetDbId: - type: string - variantSetName: - type: string description: Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other. @@ -2618,6 +2863,10 @@ components: type: string callSetName: type: string + genotype: + deprecated: true + allOf: + - $ref: "#/components/schemas/ListValue" genotypeMetadata: type: array description: Genotype Metadata are additional layers of metadata associated @@ -2627,6 +2876,18 @@ components: genotypeValue: type: string description: The value of this genotype call + genotype_likelihood: + type: array + description: "**Deprecated in v2.1** Please use `genotypeMetadata`. Github\ + \ issue number #491 \n
The genotype likelihood for this\ + \ variant call. Each array entry represents how likely a specific genotype\ + \ is for this call as log10(P(data | genotype)), analogous to the GL tag\ + \ in the VCF spec. The value ordering is defined by the GL tag in the\ + \ VCF spec." + deprecated: true + items: + type: number + format: double phaseSet: type: string description: "If this field is populated, this variant call's genotype ordering\ @@ -2634,6 +2895,8 @@ components: \ calls on the same contig which have the same phase set string." variantDbId: type: string + variantName: + type: string variantSetDbId: type: string variantSetName: @@ -2659,6 +2922,12 @@ components: occurrence (false) nullable: true example: true + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. sepPhased: type: string description: The string used as a separator for phased allele calls. @@ -2691,24 +2960,51 @@ components: CallSearchRequest: type: object properties: - variantSetDbIds: + callSetDbIds: type: array - description: A list of IDs which uniquely identify `VariantSets` within - the given database server + description: A list of IDs which uniquely identify `CallSets` within the + given database server nullable: true items: type: string - unknownString: - type: string - description: The string used as a representation for missing data. - nullable: true - example: "." expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single occurrence (false) nullable: true example: true + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + nullable: true + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + nullable: true + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + nullable: true + example: "." variantDbIds: type: array description: A list of IDs which uniquely identify `Variant` within the @@ -2716,23 +3012,13 @@ components: nullable: true items: type: string - callSetDbIds: + variantSetDbIds: type: array - description: A list of IDs which uniquely identify `CallSets` within the - given database server + description: A list of IDs which uniquely identify `VariantSets` within + the given database server nullable: true items: type: string - sepPhased: - type: string - description: The string used as a separator for phased allele calls. - nullable: true - example: '|' - sepUnphased: - type: string - description: The string used as a separator for unphased allele calls. - nullable: true - example: / description: "A `Call` represents the determination of genotype with respect\ \ to a particular `Variant`. \n\nIt may include associated information such\ \ as quality and phasing. For example, a call might assign a probability of\ @@ -2764,32 +3050,25 @@ components: description: An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - nullable: true items: $ref: "#/components/schemas/ExternalReference" sampleDbId: type: string nullable: true - sampleName: - type: string - nullable: true - samplePUI: - type: string - nullable: true studyDbId: type: string nullable: true - studyName: - type: string - nullable: true - studyPUI: - type: string - nullable: true updated: type: string description: The time at which this call set was last updated format: date-time nullable: true + variantSetDbIds: + type: array + description: The IDs of the variantSets this callSet has calls in. + nullable: true + items: + type: string description: A CallSet is a collection of Calls that were generated by the same analysis of the same Sample CallSetRequest: @@ -2893,27 +3172,19 @@ components: CallSetSearchRequest: type: object properties: - germplasmDbIds: + callSetDbIds: type: array - description: List of IDs which uniquely identify germplasm to search for + description: A list of IDs which uniquely identify `CallSets` within the + given database server nullable: true items: type: string - germplasmNames: + callSetNames: type: array - description: List of human readable names to identify germplasm to search - for + description: A list of human readable names associated with `CallSets` nullable: true items: type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string commonCropNames: type: array description: "The BrAPI Common Crop Name is the simple, generalized, widely\ @@ -2925,6 +3196,51 @@ components: \ of available crops on a server." items: type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -2935,9 +3251,12 @@ components: \ on a server." items: type: string - trialDbIds: + programNames: type: array - description: The ID which uniquely identifies a trial to search for + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string sampleDbIds: @@ -2947,27 +3266,15 @@ components: nullable: true items: type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - variantSetDbIds: + sampleNames: type: array - description: A list of IDs which uniquely identify `VariantSets` within - the given database server + description: A list of human readable names associated with `Samples` nullable: true items: type: string - callSetNames: + studyDbIds: type: array - description: A list of human readable names associated with `CallSets` - nullable: true + description: List of study identifiers to search for items: type: string studyNames: @@ -2975,16 +3282,20 @@ components: description: List of study names to filter search results items: type: string - sampleNames: + trialDbIds: type: array - description: A list of human readable names associated with `Samples` - nullable: true + description: The ID which uniquely identifies a trial to search for items: type: string - callSetDbIds: + trialNames: type: array - description: A list of IDs which uniquely identify `CallSets` within the - given database server + description: The human readable name of a trial to search for + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server nullable: true items: type: string @@ -3177,15 +3488,6 @@ components: description: "A two dimensional array that holds allele data or associated metadata.\ \ Each matrix should be the same size and orientation, aligned with the \"\ callSetDbIds\" as columns and the \"variantDbIds\" as rows." - DataType: - type: string - description: The type of field represented in this Genotype Field. This is intended - to help parse the data out of JSON. - enum: - - string - - integer - - float - - boolean Dimension: type: string description: The dimension of the matrix being paginated @@ -3237,6 +3539,7 @@ components: \ number #460
The external reference ID. Could be a simple string\ \ or a URI." nullable: true + deprecated: true referenceId: type: string description: The external reference ID. Could be a simple string or a URI. @@ -3252,6 +3555,7 @@ components: \ Github issue number #460 \n
List of external reference IDs. Could\ \ be a simple strings or a URIs. (use with `externalReferenceSources`\ \ parameter)" + deprecated: true items: type: string externalReferenceIds: @@ -3450,6 +3754,7 @@ components: type: string description: The literal string "Feature" example: Feature + default: Feature description: |- One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. @@ -3457,10 +3762,12 @@ components: A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + nullable: true GeoJSONGeometry: + nullable: true oneOf: - required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -3472,13 +3779,14 @@ components: type: type: string description: The literal string "Point" + default: Point description: |- Copied from RFC 7946 Section 3.1.1 A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. - required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -3494,6 +3802,7 @@ components: type: type: string description: The literal string "Polygon" + default: Polygon description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ @@ -3501,7 +3810,7 @@ components: \ MAY be included as an optional third element." GeoJSONPoint: required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -3513,6 +3822,7 @@ components: type: type: string description: The literal string "Point" + default: Point description: |- Copied from RFC 7946 Section 3.1.1 @@ -3520,7 +3830,7 @@ components: easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. GeoJSONPolygon: required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -3536,6 +3846,7 @@ components: type: type: string description: The literal string "Polygon" + default: Polygon description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ @@ -3552,14 +3863,21 @@ components: type: string imageName: type: string + imagePUI: + type: string observationDbId: type: string + observationName: + type: string + observationPUI: + type: string observationUnit: $ref: "#/components/schemas/ObservationUnitPosition" type: type: string description: The literal string "Feature" example: Feature + default: Feature GermplasmAttributeRequest: type: object properties: @@ -3681,6 +3999,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -4244,6 +4563,26 @@ components: Use `GET /programs` to find the list of available programs on a server. items: type: string + ListValue: + type: object + properties: + values: + type: array + description: "**Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`.\ + \ Github issue number #491 \n
Repeated field of dynamically\ + \ typed values." + deprecated: true + items: + oneOf: + - type: boolean + format: boolean + - type: number + format: double + - type: string + description: "**Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`.\ + \ Github issue number #491 \n
`ListValue` is a wrapper around\ + \ a repeated field of values.\n
The JSON representation for `ListValue`\ + \ is JSON array." LocationParameters: type: object properties: @@ -4263,15 +4602,18 @@ components: abbreviations: type: array description: A list of shortened human readable names for a set of Locations + nullable: true items: type: string altitudeMax: type: number description: The maximum altitude to search for + nullable: true example: 200 altitudeMin: type: number description: The minimum altitude to search for + nullable: true example: 20 commonCropNames: type: array @@ -4290,21 +4632,25 @@ components: type: array description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ \ spec" + nullable: true items: type: string countryNames: type: array description: The full name of the country to search for + nullable: true items: type: string instituteAddresses: type: array description: The street address of the institute to search for + nullable: true items: type: string instituteNames: type: array description: The name of the institute to search for + nullable: true items: type: string locationDbIds: @@ -4321,6 +4667,7 @@ components: type: array description: "The type of location this represents (ex. Breeding Location,\ \ Storage Location, etc)" + nullable: true items: type: string parentLocationDbIds: @@ -4329,6 +4676,7 @@ components: \ defines the encompassing location that this location belongs to. \n\ For example, an Institution might have multiple Field Stations inside\ \ it and each Field Station might have multiple Fields." + nullable: true items: type: string parentLocationNames: @@ -4337,6 +4685,7 @@ components: \ defines the encompassing location that this location belongs to. \n\ For example, an Institution might have multiple Field Stations inside\ \ it and each Field Station might have multiple Fields." + nullable: true items: type: string programDbIds: @@ -4382,6 +4731,9 @@ components: variantDbId: type: string nullable: true + variantName: + type: string + nullable: true description: A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap. @@ -4429,13 +4781,6 @@ components: nullable: true items: type: string - variantDbIds: - type: array - description: A list of IDs which uniquely identify `Variants` within the - given database server - nullable: true - items: - type: string mapDbIds: type: array description: A list of IDs which uniquely identify `GenomeMaps` within the @@ -4455,6 +4800,24 @@ components: format: int32 nullable: true example: 250 + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server + nullable: true + items: + type: string description: A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap. @@ -4465,7 +4828,6 @@ components: type: string description: The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON. - nullable: true enum: - string - integer @@ -4476,17 +4838,11 @@ components: description: "The abbreviated code of the field represented in this Genotype\ \ Field. These codes should match the VCF standard when possible. Examples\ \ include: \"GQ\", \"RD\", and \"HQ\"" - nullable: true fieldName: type: string description: "The name of the field represented in this Genotype Field.\ \ Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype\ \ Quality\"" - nullable: true - variantSetDbId: - type: string - variantSetName: - type: string description: "Indicates which types of genotyping data and metadata are available\ \ in the VariantSet. \n
When possible, these field names and abbreviations\ \ should follow the VCF standard " @@ -4579,29 +4935,35 @@ components: observationDbIds: type: array description: The unique id of an Observation + nullable: true items: type: string observationLevelRelationships: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevelRelationship" observationLevels: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevel" observationTimeStampRangeEnd: type: string description: Timestamp range end format: date-time + nullable: true observationTimeStampRangeStart: type: string description: Timestamp range start format: date-time + nullable: true observationUnitDbIds: type: array description: The unique id of an Observation Unit + nullable: true items: type: string observationUnitLevelCodes: @@ -4714,6 +5076,7 @@ components: type: array description: "The year or Phenotyping campaign of a multi-annual study (trees,\ \ grape, ...)" + nullable: true items: type: string studyDbIds: @@ -4802,6 +5165,7 @@ components: \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ \ your own risk. It may return large, unpaginated lists of observation\ \ data. Only set this value to True if you are sure you need to." + nullable: true example: false locationDbIds: type: array @@ -4816,16 +5180,19 @@ components: observationLevelRelationships: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevelRelationship" observationLevels: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevel" observationUnitDbIds: type: array description: The unique id of an observation unit + nullable: true items: type: string observationUnitLevelCodes: @@ -4903,6 +5270,7 @@ components: observationUnitNames: type: array description: The human readable identifier for an Observation Unit + nullable: true items: type: string observationVariableDbIds: @@ -4943,6 +5311,7 @@ components: type: array description: "The year or Phenotyping campaign of a multi-annual study (trees,\ \ grape, ...)" + nullable: true items: type: string studyDbIds: @@ -5082,6 +5451,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -5255,18 +5625,21 @@ components: A collection of unique identifiers for materials or germplasm within a genebank MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true items: type: string binomialNames: type: array description: List of the full binomial name (scientific name) to identify a germplasm + nullable: true items: type: string collections: type: array description: A specific panel/collection/population name this germplasm belongs to. + nullable: true items: type: string commonCropNames: @@ -5284,11 +5657,13 @@ components: type: array description: A familyCode representing the family this germplasm belongs to. + nullable: true items: type: string genus: type: array description: List of Genus names to identify germplasm + nullable: true items: type: string germplasmDbIds: @@ -5307,27 +5682,32 @@ components: germplasmPUIs: type: array description: List of Permanent Unique Identifiers to identify germplasm + nullable: true items: type: string includeFullTree: type: boolean description: "If this parameter is true, recursively include ALL of the\ \ nodes available in this pedigree tree" + nullable: true example: true includeParents: type: boolean description: "If this parameter is true, include the array of parents in\ \ the response" + nullable: true example: true includeProgeny: type: boolean description: "If this parameter is true, include the array of progeny in\ \ the response" + nullable: true example: true includeSiblings: type: boolean description: "If this parameter is true, include the array of siblings in\ \ the response" + nullable: true example: true instituteCodes: type: array @@ -5339,6 +5719,7 @@ components: \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ \ rules (v)\"." + nullable: true items: type: string pedigreeDepth: @@ -5374,6 +5755,7 @@ components: species: type: array description: List of Species names to identify germplasm + nullable: true items: type: string studyDbIds: @@ -5389,6 +5771,7 @@ components: synonyms: type: array description: List of alternative names or IDs used to reference this germplasm + nullable: true items: type: string trialDbIds: @@ -5599,9 +5982,6 @@ components: programDbId: type: string nullable: true - programName: - type: string - nullable: true sampleType: type: string description: "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" @@ -5614,21 +5994,9 @@ components: studyDbId: type: string nullable: true - studyName: - type: string - nullable: true - studyPUI: - type: string - nullable: true trialDbId: type: string nullable: true - trialName: - type: string - nullable: true - trialPUI: - type: string - nullable: true description: "A Plate represents the metadata for a collection of Samples. The\ \ physical Plate being represented might be a plastic tray full of Samples,\ \ or a group of Samples stored in individual containers ie bags, test tubes,\ @@ -5745,6 +6113,38 @@ components: PlateSearchRequest: type: object properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for @@ -5764,35 +6164,33 @@ components: nullable: true items: type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 plateBarcodes: type: array description: A unique identifier physically attached to the plate nullable: true items: type: string - plateNames: + plateDbIds: type: array - description: The human readable name of a plate of samples + description: The ID which uniquely identifies a plate of samples nullable: true items: type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - commonCropNames: + plateNames: type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." + description: The human readable name of a plate of samples + nullable: true items: type: string programDbIds: @@ -5805,9 +6203,12 @@ components: \ on a server." items: type: string - trialDbIds: + programNames: type: array - description: The ID which uniquely identifies a trial to search for + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string sampleDbIds: @@ -5816,37 +6217,36 @@ components: nullable: true items: type: string - plateDbIds: + sampleGroupDbIds: type: array - description: The ID which uniquely identifies a plate of samples + description: The unique identifier for a group of related Samples nullable: true items: type: string - studyDbIds: + sampleNames: type: array - description: List of study identifiers to search for + description: The human readable name of the sample + nullable: true items: type: string - trialNames: + studyDbIds: type: array - description: The human readable name of a trial to search for + description: List of study identifiers to search for items: type: string - sampleGroupDbIds: + studyNames: type: array - description: The unique identifier for a group of related Samples - nullable: true + description: List of study names to filter search results items: type: string - studyNames: + trialDbIds: type: array - description: List of study names to filter search results + description: The ID which uniquely identifies a trial to search for items: type: string - sampleNames: + trialNames: type: array - description: The human readable name of the sample - nullable: true + description: The human readable name of a trial to search for items: type: string description: "A Plate represents the metadata for a collection of Samples. The\ @@ -5964,7 +6364,6 @@ components: description: An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - nullable: true items: $ref: "#/components/schemas/ExternalReference" isDerived: @@ -5995,8 +6394,10 @@ components: description: The human readable name of a `Reference` within a `ReferenceSet`. referenceSetDbId: type: string + nullable: true referenceSetName: type: string + nullable: true sourceAccessions: type: array description: "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ)\ @@ -6009,12 +6410,12 @@ components: description: The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from. nullable: true - sourceGermplasmDbIds: + sourceGermplasm: type: array description: All known corresponding Germplasm nullable: true items: - type: string + $ref: "#/components/schemas/SourceGermplasm" sourceURI: type: string description: "The URI from which the sequence was obtained. Specifies a\ @@ -6024,12 +6425,6 @@ components: nullable: true species: $ref: "#/components/schemas/OntologyTerm" - variantDbIds: - type: array - description: variants - nullable: true - items: - type: string description: "A `Reference` is a canonical assembled contig, intended to act\ \ as a reference coordinate space for other genomic annotations. A single\ \ `Reference` might represent the human chromosome 1, for instance. `References`\ @@ -6089,6 +6484,7 @@ components: type: array description: "If specified, return the references for which the `accession`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string commonCropNames: @@ -6123,6 +6519,7 @@ components: \ same official sequence share the same coordinates and annotations, and\ \ can be replaced with the official sequence for certain use cases." format: boolean + nullable: true maxLength: type: integer description: The minimum length of this `References` sequence. @@ -6132,6 +6529,7 @@ components: type: array description: "If specified, return the references for which the `md5checksum`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string minLength: @@ -6161,12 +6559,14 @@ components: type: array description: A list of IDs which uniquely identify `References` within the given database server + nullable: true items: type: string referenceSetDbIds: type: array description: A list of IDs which uniquely identify `ReferenceSets` within the given database server + nullable: true items: type: string studyDbIds: @@ -6192,12 +6592,58 @@ components: ReferenceSearchRequest: type: object properties: + accessions: + type: array + description: "If specified, return the references for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + nullable: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for nullable: true items: type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string isDerived: type: boolean description: "A sequence X is said to be derived from source sequence Y,\ @@ -6206,10 +6652,16 @@ components: \ same official sequence share the same coordinates and annotations, and\ \ can be replaced with the official sequence for certain use cases." format: boolean - germplasmNames: + nullable: true + maxLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 90000 + md5checksums: type: array - description: List of human readable names to identify germplasm to search - for + description: "If specified, return the references for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." nullable: true items: type: string @@ -6218,25 +6670,17 @@ components: description: The minimum length of this `References` sequence. format: int32 example: 4000 - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -6247,15 +6691,26 @@ components: \ on a server." items: type: string - trialDbIds: + programNames: type: array - description: The ID which uniquely identifies a trial to search for + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: A list of IDs which uniquely identify `References` within the + given database server + nullable: true items: type: string referenceSetDbIds: type: array description: A list of IDs which uniquely identify `ReferenceSets` within the given database server + nullable: true items: type: string studyDbIds: @@ -6263,39 +6718,21 @@ components: description: List of study identifiers to search for items: type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - md5checksums: - type: array - description: "If specified, return the references for which the `md5checksum`\ - \ matches this string (case-sensitive, exact match)." - items: - type: string studyNames: type: array description: List of study names to filter search results items: type: string - referenceDbIds: + trialDbIds: type: array - description: A list of IDs which uniquely identify `References` within the - given database server + description: The ID which uniquely identifies a trial to search for items: type: string - accessions: + trialNames: type: array - description: "If specified, return the references for which the `accession`\ - \ matches this string (case-sensitive, exact match)." + description: The human readable name of a trial to search for items: type: string - maxLength: - type: integer - description: The minimum length of this `References` sequence. - format: int32 - example: 90000 description: "A `Reference` is a canonical assembled contig, intended to act\ \ as a reference coordinate space for other genomic annotations. A single\ \ `Reference` might represent the human chromosome 1, for instance. `References`\ @@ -6356,14 +6793,14 @@ components: `Reference` s in this set. Then sort that list, and take the MD5 hash of all the strings concatenated together. Express the hash as a lower-case hexadecimal string. - nullable: true - referenceDbId: - type: string - referenceName: - type: string + nullable: true referenceSetName: type: string description: The human readable name of a ReferenceSet + referencesDbId: + type: string + referencesName: + type: string sourceAccessions: type: array description: "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ)\ @@ -6493,27 +6930,20 @@ components: ReferenceSetSearchRequest: type: object properties: - germplasmDbIds: + accessions: type: array - description: List of IDs which uniquely identify germplasm to search for + description: "If set, return the reference sets for which the `accession`\ + \ matches this string (case-sensitive, exact match)." nullable: true items: type: string - germplasmNames: + assemblyPUIs: type: array - description: List of human readable names to identify germplasm to search - for + description: "If set, return the reference sets for which the `assemblyId`\ + \ matches this string (case-sensitive, exact match)." nullable: true items: type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string commonCropNames: type: array description: "The BrAPI Common Crop Name is the simple, generalized, widely\ @@ -6525,35 +6955,38 @@ components: \ of available crops on a server." items: type: string - programDbIds: + externalReferenceIDs: type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: type: string - trialDbIds: + externalReferenceIds: type: array - description: The ID which uniquely identifies a trial to search for + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) items: type: string - referenceSetDbIds: + externalReferenceSources: type: array - description: The `ReferenceSets` to search. - nullable: true + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) items: type: string - studyDbIds: + germplasmDbIds: type: array - description: List of study identifiers to search for + description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string - trialNames: + germplasmNames: type: array - description: The human readable name of a trial to search for + description: List of human readable names to identify germplasm to search + for + nullable: true items: type: string md5checksums: @@ -6563,23 +6996,59 @@ components: nullable: true items: type: string - assemblyPUIs: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: type: array - description: "If set, return the reference sets for which the `assemblyId`\ - \ matches this string (case-sensitive, exact match)." + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceSetDbIds: + type: array + description: The `ReferenceSets` to search. nullable: true items: type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string studyNames: type: array description: List of study names to filter search results items: type: string - accessions: + trialDbIds: type: array - description: "If set, return the reference sets for which the `accession`\ - \ matches this string (case-sensitive, exact match)." - nullable: true + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for items: type: string description: "A `ReferenceSet` is a set of `Reference` s which typically comprise\ @@ -6607,12 +7076,6 @@ components: properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" - callSetDbIds: - type: array - description: "" - nullable: true - items: - type: string column: type: integer description: The Column identifier for this `Sample` location in the `Plate` @@ -6623,27 +7086,14 @@ components: description: An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - nullable: true items: $ref: "#/components/schemas/ExternalReference" germplasmDbId: type: string nullable: true - germplasmName: - type: string - nullable: true - germplasmPUI: - type: string - nullable: true observationUnitDbId: type: string nullable: true - observationUnitName: - type: string - nullable: true - observationUnitPUI: - type: string - nullable: true plateDbId: type: string nullable: true @@ -6653,9 +7103,6 @@ components: programDbId: type: string nullable: true - programName: - type: string - nullable: true row: type: string description: The Row identifier for this `Sample` location in the `Plate` @@ -6670,7 +7117,7 @@ components: Description of a `Sample`
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing. nullable: true - sampleGroupId: + sampleGroupDbId: type: string description: The ID which uniquely identifies a group of `Samples` nullable: true @@ -6700,12 +7147,6 @@ components: studyDbId: type: string nullable: true - studyName: - type: string - nullable: true - studyPUI: - type: string - nullable: true takenBy: type: string description: The name or identifier of the entity which took the `Sample` @@ -6720,12 +7161,6 @@ components: trialDbId: type: string nullable: true - trialName: - type: string - nullable: true - trialPUI: - type: string - nullable: true well: type: string description: "The Well identifier for this `Sample` location in the `Plate`.\ @@ -6840,6 +7275,38 @@ components: SampleSearchRequest: type: object properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for @@ -6859,29 +7326,27 @@ components: nullable: true items: type: string - plateNames: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + plateDbIds: type: array - description: The human readable name of a `Plate` of `Samples` + description: The ID which uniquely identifies a `Plate` of `Samples` nullable: true items: type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - commonCropNames: + plateNames: type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." + description: The human readable name of a `Plate` of `Samples` + nullable: true items: type: string programDbIds: @@ -6894,9 +7359,12 @@ components: \ on a server." items: type: string - trialDbIds: + programNames: type: array - description: The ID which uniquely identifies a trial to search for + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string sampleDbIds: @@ -6905,37 +7373,36 @@ components: nullable: true items: type: string - plateDbIds: + sampleGroupDbIds: type: array - description: The ID which uniquely identifies a `Plate` of `Samples` + description: The unique identifier for a group of related `Samples` nullable: true items: type: string - studyDbIds: + sampleNames: type: array - description: List of study identifiers to search for + description: The human readable name of the `Sample` + nullable: true items: type: string - trialNames: + studyDbIds: type: array - description: The human readable name of a trial to search for + description: List of study identifiers to search for items: type: string - sampleGroupDbIds: + studyNames: type: array - description: The unique identifier for a group of related `Samples` - nullable: true + description: List of study names to filter search results items: type: string - studyNames: + trialDbIds: type: array - description: List of study names to filter search results + description: The ID which uniquely identifies a trial to search for items: type: string - sampleNames: + trialNames: type: array - description: The human readable name of the `Sample` - nullable: true + description: The human readable name of a trial to search for items: type: string description: "The identifiers and metadata associated with a physical piece\ @@ -7099,14 +7566,35 @@ components: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId SortOrder: type: string description: Sort order direction. Ascending/Descending. enum: - - asc - ASC - - desc - DESC + - asc + - desc + SourceGermplasm: + type: object + properties: + germplasmDbId: + type: string + description: "The ID which uniquely identifies a germplasm within the given\ + \ database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code\ + \ used to identify the biological material in the data file. Should be\ + \ unique within the Investigation. Can correspond to experimental plant\ + \ ID, inventory lot ID, etc. This material identification is different\ + \ from a BiosampleID which corresponds to Observation Unit or Samples\ + \ sections below." + germplasmName: + type: string + description: |- + Name of the germplasm. It can be the preferred name and does not have to be unique. + + MCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space. + description: A reference to a Germplasm StudyParameters: type: object properties: @@ -7216,15 +7704,17 @@ components: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId sortOrder: type: string description: Sort order direction. Ascending/Descending. nullable: true enum: - - asc - ASC - - desc - DESC + - asc + - desc studyCodes: type: array description: A short human readable code for a study @@ -7287,6 +7777,7 @@ components: \ a prior response to construct a query and move to the next or previous\ \ page respectively. " example: 33c27874 + deprecated: true TraitDataType: type: string description: |- @@ -7467,13 +7958,18 @@ components: formatted identifier. items: type: string + Value: + oneOf: + - type: boolean + format: boolean + - type: number + format: double + - type: string Variable: required: - - methodDbId - - methodName - - scaleDbId - - scaleName - - traitName + - method + - scale + - trait type: object properties: additionalInfo: @@ -7520,20 +8016,12 @@ components: description: 2 letter ISO 639-1 code for the language of submission of the variable. nullable: true - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string + method: + $ref: "#/components/schemas/Method" ontologyReference: $ref: "#/components/schemas/OntologyReference" - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string + scale: + $ref: "#/components/schemas/Scale" scientist: type: string description: Name of scientist submitting the variable. @@ -7554,12 +8042,8 @@ components: nullable: true items: type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + trait: + $ref: "#/components/schemas/Trait" description: "A unique combination of Trait, Method, and Scale to define a clear\ \ context for an Observation." VariableBaseClassParameters: @@ -7644,6 +8128,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -7725,10 +8210,20 @@ components: properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" - analysis: + alternateBases: type: array - description: Set of Analysis descriptors for this VariantSet + description: The bases that appear instead of the reference bases. Multiple + alternate alleles are possible. + nullable: true + items: + type: string + alternate_bases: + type: array + description: |- + **Deprecated in v2.1** Please use `alternateBases`. Github issue number #549 +
The bases that appear instead of the reference bases. Multiple alternate alleles are possible. nullable: true + deprecated: true items: type: string ciend: @@ -7769,7 +8264,6 @@ components: description: An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - nullable: true items: $ref: "#/components/schemas/ExternalReference" filtersApplied: @@ -7838,6 +8332,13 @@ components: nullable: true items: type: string + variantSetDbIds: + type: array + description: An array of `VariantSet` IDs this variant belongs to. This + also defines the `ReferenceSet` against which the `Variant` is to be interpreted. + nullable: true + items: + type: string variantType: type: string description: |- @@ -7858,6 +8359,8 @@ components: \ number #474 \n
Only return variant calls which belong to call sets\ \ with these IDs. If unspecified, return all variants and no variant call\ \ objects." + nullable: true + deprecated: true items: type: string commonCropNames: @@ -7900,15 +8403,19 @@ components: description: |- **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472
Only return variants on this reference. + nullable: true example: 120a2d5c + deprecated: true referenceDbIds: type: array description: The unique identifier representing a genotype `Reference` + nullable: true items: type: string referenceSetDbIds: type: array description: The unique identifier representing a genotype `ReferenceSet` + nullable: true items: type: string start: @@ -7943,39 +8450,28 @@ components: variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` + nullable: true items: type: string VariantSearchRequest: type: object properties: - referenceDbId: - type: string - description: |- - **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 -
Only return variants on this reference. - example: 120a2d5c - programNames: + callSetDbIds: type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: "**Deprecated in v2.1** Parameter unnecessary. Github issue\ + \ number #474 \n
Only return variant calls which belong to call sets\ + \ with these IDs. If unspecified, return all variants and no variant call\ + \ objects." + nullable: true + deprecated: true items: type: string - start: - type: integer - description: "The beginning of the window (0-based, inclusive) for which\ - \ overlapping variants should be returned. Genomic positions are non-negative\ - \ integers less than reference length. Requests spanning the join of circular\ - \ genomes are represented as two requests one on each side of the join\ - \ (position 0)." - format: int32 - example: 100 commonCropNames: type: array description: "The BrAPI Common Crop Name is the simple, generalized, widely\ @@ -7987,6 +8483,44 @@ components: \ of available crops on a server." items: type: string + end: + type: integer + description: "The end of the window (0-based, exclusive) for which overlapping\ + \ variants should be returned." + format: int32 + example: 1500 + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -7997,58 +8531,73 @@ components: \ on a server." items: type: string - trialDbIds: + programNames: type: array - description: The ID which uniquely identifies a trial to search for + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbId: + type: string + description: |- + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + nullable: true + example: 120a2d5c + deprecated: true + referenceDbIds: + type: array + description: The unique identifier representing a genotype `Reference` + nullable: true items: type: string referenceSetDbIds: type: array description: The unique identifier representing a genotype `ReferenceSet` + nullable: true items: type: string + start: + type: integer + description: "The beginning of the window (0-based, inclusive) for which\ + \ overlapping variants should be returned. Genomic positions are non-negative\ + \ integers less than reference length. Requests spanning the join of circular\ + \ genomes are represented as two requests one on each side of the join\ + \ (position 0)." + format: int32 + example: 100 studyDbIds: type: array description: List of study identifiers to search for items: type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - variantSetDbIds: + studyNames: type: array - description: A list of IDs which uniquely identify `VariantSets` + description: List of study names to filter search results items: type: string - studyNames: + trialDbIds: type: array - description: List of study names to filter search results + description: The ID which uniquely identifies a trial to search for items: type: string - referenceDbIds: + trialNames: type: array - description: The unique identifier representing a genotype `Reference` + description: The human readable name of a trial to search for items: type: string variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` + nullable: true items: type: string - end: - type: integer - description: "The end of the window (0-based, exclusive) for which overlapping\ - \ variants should be returned." - format: int32 - example: 1500 - callSetDbIds: + variantSetDbIds: type: array - description: "**Deprecated in v2.1** Parameter unnecessary. Github issue\ - \ number #474 \n
Only return variant calls which belong to call sets\ - \ with these IDs. If unspecified, return all variants and no variant call\ - \ objects." + description: A list of IDs which uniquely identify `VariantSets` + nullable: true items: type: string description: "A `Variant` represents a change in DNA sequence relative to some\ @@ -8077,7 +8626,6 @@ components: description: An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - nullable: true items: $ref: "#/components/schemas/ExternalReference" metadataFields: @@ -8094,15 +8642,6 @@ components: referenceSetName: type: string nullable: true - studyDbId: - type: string - nullable: true - studyName: - type: string - nullable: true - studyPUI: - type: string - nullable: true variantCount: type: integer description: The number of Variants included in this VariantSet @@ -8197,45 +8736,54 @@ components: VariantSetSearchRequest: type: object properties: - variantSetDbIds: - type: array - description: The unique identifier representing a VariantSet - items: - type: string - studyNames: + callSetDbIds: type: array - description: List of study names to filter search results + description: The unique identifier representing a CallSet items: type: string - referenceDbIds: + commonCropNames: type: array - description: The unique identifier representing a genotype Reference + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." items: type: string - programNames: + externalReferenceIDs: type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: type: string - variantDbIds: + externalReferenceIds: type: array - description: The unique identifier representing a Variant + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) items: type: string - commonCropNames: + externalReferenceSources: type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) items: type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -8246,14 +8794,17 @@ components: \ on a server." items: type: string - trialDbIds: + programNames: type: array - description: The ID which uniquely identifies a trial to search for + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string - callSetDbIds: + referenceDbIds: type: array - description: The unique identifier representing a CallSet + description: The unique identifier representing a genotype Reference items: type: string referenceSetDbIds: @@ -8266,11 +8817,31 @@ components: description: List of study identifiers to search for items: type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string trialNames: type: array description: The human readable name of a trial to search for items: type: string + variantDbIds: + type: array + description: The unique identifier representing a Variant + items: + type: string + variantSetDbIds: + type: array + description: The unique identifier representing a VariantSet + items: + type: string description: A VariantSet is a collection of variants and variant calls intended to be analyzed together. basePagination: @@ -8863,8 +9434,37 @@ components: properties: data: type: array + description: "The `data` array is part of the BrAPI standard List\ + \ Response JSON container. `data` will always contain the primary\ + \ list of objects being returned by a BrAPI endpoint. `data`\ + \ is also the only array impacted by the `metadata.pagination`\ + \ details. When the pagination parameters change, the `data`\ + \ array will reflect those changes in the JSON response." items: $ref: "#/components/schemas/Call" + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed + into a single occurrence (false) + nullable: true + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele + calls. + nullable: true + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele + calls. + nullable: true + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + nullable: true + example: "." LocationSingleResponse: description: OK content: @@ -9070,6 +9670,23 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/GenomeMap" + AlleleMatrixSingleResponse: + description: OK + content: + application/json: + schema: + title: AlleleMatrixSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/AlleleMatrix" PersonListResponse: description: OK content: diff --git a/Specification/Generated/BrAPI-Germplasm.yaml b/Specification/Generated/BrAPI-Germplasm.yaml index 2013039a..3200cf83 100644 --- a/Specification/Generated/BrAPI-Germplasm.yaml +++ b/Specification/Generated/BrAPI-Germplasm.yaml @@ -106,10 +106,11 @@ paths: $ref: "#/components/schemas/CrossNewRequest" example: "{_1={additionalInfo={}, crossAttributes=[{}], crossDbId=15187888,\ \ crossName=15a57676, crossType={}, crossingProject={}, externalReferences=[{}],\ - \ parent1={}, parent2={}, plannedCross={}, pollinationEvents=[{}],\ - \ observationUnits=[{}]}, _2={additionalInfo={}, crossAttributes=[{}],\ - \ crossDbId=15187889, crossName=15a57677, crossType={}, crossingProject={},\ - \ externalReferences=[{}], parent1={}, parent2={}, plannedCross={},\ + \ parent1={}, parent2={}, plannedCross={}, pollinationTimeStamp=2020-08-12T18:10:40.413Z,\ + \ pollinationEvents=[{}], observationUnits=[{}]}, _2={additionalInfo={},\ + \ crossAttributes=[{}], crossDbId=15187889, crossName=15a57677, crossType={},\ + \ crossingProject={}, externalReferences=[{}], parent1={}, parent2={},\ + \ plannedCross={}, pollinationTimeStamp=2020-08-12T18:10:40.413Z,\ \ pollinationEvents=[{}], observationUnits=[{}]}}" responses: "200": @@ -915,7 +916,7 @@ paths: schema: type: object additionalProperties: - $ref: "#/components/schemas/PlannedCross" + $ref: "#/components/schemas/PlannedCrossNewRequest" example: "{_1={additionalInfo={}, crossType={}, crossingProject={},\ \ externalReferences=[{}], parent1={}, parent2={}, plannedCrossDbId=47edd16c,\ \ plannedCrossName=487acf5a, status={}, crosses=[{}]}, _2={additionalInfo={},\ @@ -944,7 +945,7 @@ paths: schema: type: array items: - $ref: "#/components/schemas/PlannedCross" + $ref: "#/components/schemas/PlannedCrossNewRequest" responses: "200": $ref: "#/components/responses/PlannedCrossListResponse" @@ -1410,6 +1411,33 @@ paths: $ref: "#/components/responses/403Forbidden" "404": $ref: "#/components/responses/404NotFound" + /seedlots/{seedLotDbId}/transactions: + get: + tags: + - SeedLots + summary: Get a filtered list of SeedLotTransaction + description: Get a list of SeedLotTransaction + parameters: + - name: seedLotDbId + in: path + description: Unique DbId for the Seed Lot + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/SeedLotTransactionListResponse" + "404": + $ref: "#/components/responses/404NotFound" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" /search/germplasm: post: tags: @@ -1566,6 +1594,10 @@ paths: responses: "200": $ref: "#/components/responses/GermplasmListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1605,6 +1637,10 @@ paths: responses: "200": $ref: "#/components/responses/GermplasmAttributeListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1645,6 +1681,10 @@ paths: responses: "200": $ref: "#/components/responses/GermplasmAttributeValueListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1683,6 +1723,10 @@ paths: responses: "200": $ref: "#/components/responses/PedigreeNodeListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1767,21 +1811,41 @@ components: items: type: string dataMatrixAbbreviations: - type: array - description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ + type: string + description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ \ in the response." nullable: true - items: - type: string + example: "GT,RD" dataMatrixNames: - type: array - description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ - \ Depth' etc). This list controls which data matrices are returned in\ - \ the response." + type: string + description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ + \ 'Read Depth' etc). This list controls which data matrices are returned\ + \ in the response." + nullable: true + example: "Genotype,Read Depth" + dimensionCallSetPage: + type: integer + description: The requested page number for the CallSet dimension of the + matrix + format: int32 + nullable: true + dimensionCallSetPageSize: + type: integer + description: The requested page size for the CallSet dimension of the matrix + format: int32 + nullable: true + dimensionVariantPage: + type: integer + description: The requested page number for the Variant dimension of the + matrix + format: int32 + nullable: true + dimensionVariantPageSize: + type: integer + description: The requested page size for the Variant dimension of the matrix + format: int32 nullable: true - items: - type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single @@ -1850,6 +1914,7 @@ components: \ or not set (default), then the server should return all the matrix\n\ data as requested." example: true + default: false sampleDbIds: type: array description: A list of IDs which uniquely identify `Samples` within the @@ -1889,11 +1954,9 @@ components: Attribute: required: - attributeName - - methodDbId - - methodName - - scaleDbId - - scaleName - - traitName + - method + - scale + - trait type: object properties: additionalInfo: @@ -1961,20 +2024,12 @@ components: description: 2 letter ISO 639-1 code for the language of submission of the variable. nullable: true - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string + method: + $ref: "#/components/schemas/Method" ontologyReference: $ref: "#/components/schemas/OntologyReference" - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string + scale: + $ref: "#/components/schemas/Scale" scientist: type: string description: Name of scientist submitting the variable. @@ -1995,12 +2050,8 @@ components: nullable: true items: type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + trait: + $ref: "#/components/schemas/Trait" BiologicalStatusOfAccessionCode: type: string description: "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used\ @@ -2076,6 +2127,12 @@ components: occurrence (false) nullable: true example: true + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. sepPhased: type: string description: The string used as a separator for phased allele calls. @@ -2406,18 +2463,11 @@ components: germplasmName: type: string nullable: true - germplasmPUI: - type: string - nullable: true mixturePercentage: type: integer description: The percentage of the given germplasm in the seed lot mixture. format: int32 nullable: true - seedLotDbId: - type: string - seedLotName: - type: string description: "The mixture of germplasm present in the seed lot. \n
If this\ \ seed lot only contains a single germplasm, the response should contain the\ \ name and DbId of that germplasm with a mixturePercentage value of 100 \n\ @@ -2469,10 +2519,6 @@ components: type: string description: the value of a cross attribute nullable: true - crossDbId: - type: string - crossName: - type: string description: "A custom attribute associated with a cross. For example, if the\ \ crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative\ \ Humidity', 'crossAttributeValue':'80%'" @@ -2504,7 +2550,6 @@ components: description: An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - nullable: true items: $ref: "#/components/schemas/ExternalReference" parent1: @@ -2523,6 +2568,14 @@ components: nullable: true items: $ref: "#/components/schemas/PollinationEvent" + pollinationTimeStamp: + type: string + description: |- + **Deprecated in v2.1** Please use `pollinationEvents`. Github issue number #265 +
The timestamp when the pollination took place + format: date-time + nullable: true + deprecated: true description: The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present. @@ -2535,21 +2588,16 @@ components: germplasmName: type: string nullable: true - germplasmPUI: - type: string - nullable: true observationUnitDbId: type: string nullable: true observationUnitName: type: string nullable: true - observationUnitPUI: - type: string - nullable: true parentType: $ref: "#/components/schemas/ParentType" description: The identifying information gor the parent material of a cross. + nullable: true CrossRequest: type: object properties: @@ -2613,6 +2661,7 @@ components: description: "The type of cross make. Accepted values for this field are 'BIPARENTAL',\ \ 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED'\ \ and 'DOUBLE_HAPLOID'." + nullable: true enum: - BIPARENTAL - SELF @@ -2740,12 +2789,6 @@ components: The institute code for the donor institute
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard. nullable: true - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string description: Identifier assigned to an accession by the material donor. DonorInfo: type: object @@ -2809,6 +2852,7 @@ components: \ number #460
The external reference ID. Could be a simple string\ \ or a URI." nullable: true + deprecated: true referenceId: type: string description: The external reference ID. Could be a simple string or a URI. @@ -2824,6 +2868,7 @@ components: \ Github issue number #460 \n
List of external reference IDs. Could\ \ be a simple strings or a URIs. (use with `externalReferenceSources`\ \ parameter)" + deprecated: true items: type: string externalReferenceIds: @@ -2920,6 +2965,7 @@ components: type: string description: The literal string "Feature" example: Feature + default: Feature description: |- One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. @@ -2927,10 +2973,12 @@ components: A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + nullable: true GeoJSONGeometry: + nullable: true oneOf: - required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2942,13 +2990,14 @@ components: type: type: string description: The literal string "Point" + default: Point description: |- Copied from RFC 7946 Section 3.1.1 A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. - required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2964,6 +3013,7 @@ components: type: type: string description: The literal string "Polygon" + default: Polygon description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ @@ -2971,7 +3021,7 @@ components: \ MAY be included as an optional third element." GeoJSONPoint: required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2983,6 +3033,7 @@ components: type: type: string description: The literal string "Point" + default: Point description: |- Copied from RFC 7946 Section 3.1.1 @@ -2990,7 +3041,7 @@ components: easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. GeoJSONPolygon: required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -3006,6 +3057,7 @@ components: type: type: string description: The literal string "Polygon" + default: Polygon description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ @@ -3022,14 +3074,21 @@ components: type: string imageName: type: string + imagePUI: + type: string observationDbId: type: string + observationName: + type: string + observationPUI: + type: string observationUnit: $ref: "#/components/schemas/ObservationUnitPosition" type: type: string description: The literal string "Feature" example: Feature + default: Feature Germplasm: allOf: - $ref: "#/components/schemas/GermplasmNewRequest" @@ -3069,11 +3128,9 @@ components: GermplasmAttributeNewRequest: required: - attributeName - - methodDbId - - methodName - - scaleDbId - - scaleName - - traitName + - method + - scale + - trait type: object properties: additionalInfo: @@ -3095,12 +3152,6 @@ components: description: "The Permanent Unique Identifier of an Attribute, usually in\ \ the form of a URI" example: http://my-traits.com/trait/CO_123:0008012 - attributeValueDbIds: - type: array - description: attributeValues - nullable: true - items: - type: string commonCropName: type: string description: "Crop name (examples: \"Maize\", \"Wheat\")" @@ -3143,20 +3194,12 @@ components: description: 2 letter ISO 639-1 code for the language of submission of the variable. nullable: true - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string + method: + $ref: "#/components/schemas/Method" ontologyReference: $ref: "#/components/schemas/OntologyReference" - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string + scale: + $ref: "#/components/schemas/Scale" scientist: type: string description: Name of scientist submitting the variable. @@ -3177,12 +3220,8 @@ components: nullable: true items: type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + trait: + $ref: "#/components/schemas/Trait" description: "The Trait-Method-Scale definition for a variable, specifically\ \ variables related to Germplasm. Similar to an ObservationVariable, but related\ \ to a Germplasm instead of an ObservationUnit" @@ -3307,6 +3346,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -3384,41 +3424,41 @@ components: GermplasmAttributeSearchRequest: type: object properties: - germplasmNames: + attributeCategories: type: array - description: List of human readable names to identify germplasm to search - for + description: General category for the attribute. very similar to Trait class. nullable: true items: type: string - methodDbIds: - type: array - description: List of methods to filter search results - items: - type: string - programNames: + attributeDbIds: type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: List of Germplasm Attribute IDs to search for + nullable: true items: type: string - attributeDbIds: + attributeNames: type: array - description: List of Germplasm Attribute IDs to search for + description: List of human readable Germplasm Attribute names to search + for nullable: true items: type: string - trialNames: + attributePUIs: type: array - description: The human readable name of a trial to search for + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + nullable: true items: type: string - studyDbId: + commonCropNames: type: array - description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ - \ number #483 \n
The unique ID of a studies to filter on" + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." items: type: string dataTypes: @@ -3426,49 +3466,43 @@ components: description: List of scale data types to filter search results items: $ref: "#/components/schemas/TraitDataType" - attributeNames: - type: array - description: List of human readable Germplasm Attribute names to search - for - nullable: true - items: - type: string - methodPUIs: + externalReferenceIDs: type: array - description: "The Permanent Unique Identifier of a Method, usually in the\ - \ form of a URI" + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: type: string - scalePUIs: + externalReferenceIds: type: array - description: "The Permanent Unique Identifier of a Scale, usually in the\ - \ form of a URI" + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) items: type: string - traitAttributes: + externalReferenceSources: type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the attribute is the observed feature (or characteristic) of the entity\ - \ e.g., for \"grain colour\", attribute = \"colour\"" + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) items: type: string - scaleDbIds: + germplasmDbIds: type: array - description: The unique identifier for a Scale + description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string - traitEntityPUIs: + germplasmNames: type: array - description: "The Permanent Unique Identifier of a Trait Entity, usually\ - \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ - \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ - \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + description: List of human readable names to identify germplasm to search + for + nullable: true items: type: string - germplasmDbIds: + methodDbIds: type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true + description: List of methods to filter search results items: type: string methodNames: @@ -3478,41 +3512,28 @@ components:
MIAPPE V1.1 (DM-88) Method Name of the method of observation items: type: string - scaleNames: - type: array - description: |- - Name of the scale -
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable - items: - type: string - traitPUIs: + methodPUIs: type: array - description: "The Permanent Unique Identifier of a Trait, usually in the\ + description: "The Permanent Unique Identifier of a Method, usually in the\ \ form of a URI" items: type: string - traitClasses: - type: array - description: List of trait classes to filter search results - items: - type: string - attributeCategories: - type: array - description: General category for the attribute. very similar to Trait class. - nullable: true - items: - type: string - commonCropNames: + ontologyDbIds: type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." + description: List of ontology IDs to search for items: type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -3523,14 +3544,37 @@ components: \ on a server." items: type: string - trialDbIds: + programNames: type: array - description: The ID which uniquely identifies a trial to search for + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string - ontologyDbIds: + scaleDbIds: type: array - description: List of ontology IDs to search for + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -3543,16 +3587,43 @@ components: description: List of study names to filter search results items: type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string traitDbIds: type: array description: The unique identifier for a Trait items: type: string - attributePUIs: + traitEntities: type: array - description: "The Permanent Unique Identifier of an Attribute, usually in\ - \ the form of a URI" - nullable: true + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " items: type: string traitNames: @@ -3562,18 +3633,20 @@ components:
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation items: type: string - traitAttributePUIs: + traitPUIs: type: array - description: |- - The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI -
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" items: type: string - traitEntities: + trialDbIds: type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the entity is the part of the plant that the trait refers to e.g., for\ - \ \"grain colour\", entity = \"grain\"" + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for items: type: string description: "The Trait-Method-Scale definition for a variable, specifically\ @@ -3604,9 +3677,6 @@ components: attributeName: type: string nullable: true - attributePUI: - type: string - nullable: true determinedDate: type: string description: The date the value of this attribute was determined for a given @@ -3627,9 +3697,6 @@ components: germplasmName: type: string nullable: true - germplasmPUI: - type: string - nullable: true value: type: string description: The value of this attribute for a given germplasm @@ -3740,39 +3807,25 @@ components: GermplasmAttributeValueSearchRequest: type: object properties: - germplasmDbIds: + attributeDbIds: type: array - description: List of IDs which uniquely identify germplasm to search for + description: List of Germplasm Attribute IDs to search for nullable: true items: type: string - germplasmNames: + attributeNames: type: array - description: List of human readable names to identify germplasm to search + description: List of human readable Germplasm Attribute names to search for nullable: true items: type: string - methodDbIds: - type: array - description: List of methods to filter search results - nullable: true - items: - type: string - traitClasses: + attributeValueDbIds: type: array - description: List of trait classes to filter search results + description: List of Germplasm Attribute Value IDs to search for nullable: true items: type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string commonCropNames: type: array description: "The BrAPI Common Crop Name is the simple, generalized, widely\ @@ -3784,25 +3837,49 @@ components: \ of available crops on a server." items: type: string - programDbIds: + dataTypes: type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." + description: List of scale data types to filter search results + nullable: true + items: + $ref: "#/components/schemas/TraitDataType" + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: type: string - attributeValueDbIds: + externalReferenceIds: type: array - description: List of Germplasm Attribute Value IDs to search for + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for nullable: true items: type: string - attributeDbIds: + germplasmNames: type: array - description: List of Germplasm Attribute IDs to search for + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results nullable: true items: type: string @@ -3812,28 +3889,50 @@ components: nullable: true items: type: string - dataTypes: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: type: array - description: List of scale data types to filter search results - nullable: true + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." items: - $ref: "#/components/schemas/TraitDataType" - attributeNames: + type: string + programNames: type: array - description: List of human readable Germplasm Attribute names to search - for + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: List of scales to filter search results nullable: true items: type: string - traitDbIds: + traitClasses: type: array - description: List of trait unique ID to filter search results + description: List of trait classes to filter search results nullable: true items: type: string - scaleDbIds: + traitDbIds: type: array - description: List of scales to filter search results + description: List of trait unique ID to filter search results nullable: true items: type: string @@ -3842,22 +3941,23 @@ components: \ to the whole Germplasm instead of a single ObservationUnit." GermplasmChild: required: - - germplasmDbId - - germplasmName - - germplasmPUI + - childGermplasmDbId + - childGermplasmName - parentType type: object properties: - germplasmDbId: - type: string - germplasmName: + childGermplasmDbId: type: string - germplasmPUI: + childGermplasmName: type: string parentType: $ref: "#/components/schemas/ParentType" pedigreeNodeDbId: type: string + pedigreeNodeName: + type: string + pedigreeNodePUI: + type: string description: "A germplasm reference that is a direct child of this germplasm.\ \ These represent edges in the tree, connecting to other nodes." GermplasmMCPD: @@ -4151,8 +4251,6 @@ components: type: string germplasmName: type: string - germplasmPUI: - type: string instituteCode: type: string description: "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute\ @@ -4325,6 +4423,9 @@ components: breedingMethodName: type: string nullable: true + breedingMethodPUI: + type: string + nullable: true collection: type: string description: A specific panel/collection/population name this germplasm @@ -4428,12 +4529,6 @@ components: MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'. nullable: true - sampleDbIds: - type: array - description: samples - nullable: true - items: - type: string seedSource: type: string description: |- @@ -4520,12 +4615,6 @@ components: nullable: true coordinates: $ref: "#/components/schemas/GeoJSON" - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string description: "Information for material (orchard, natural sites, ...). Geographic\ \ identification of the plants from which seeds or cutting have been taken\ \ to produce that germplasm." @@ -4549,7 +4638,6 @@ components: required: - germplasmDbId - germplasmName - - germplasmPUI - parentType type: object properties: @@ -4557,12 +4645,8 @@ components: type: string germplasmName: type: string - germplasmPUI: - type: string parentType: $ref: "#/components/schemas/ParentType" - pedigreeNodeDbId: - type: string description: "A germplasm reference that is a direct parent of this germplasm.\ \ These represent edges in the tree, connecting to other nodes." GermplasmRequest: @@ -4712,12 +4796,6 @@ components: GermplasmSearchRequest: type: object properties: - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string accessionNumbers: type: array description: |- @@ -4727,27 +4805,20 @@ components: nullable: true items: type: string - germplasmNames: + binomialNames: type: array - description: List of human readable names to identify germplasm to search - for + description: List of the full binomial name (scientific name) to identify + a germplasm nullable: true items: type: string - synonyms: + collections: type: array - description: List of alternative names or IDs used to reference this germplasm + description: A specific panel/collection/population name this germplasm + belongs to. nullable: true items: type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string commonCropNames: type: array description: "The BrAPI Common Crop Name is the simple, generalized, widely\ @@ -4759,41 +4830,25 @@ components: \ of available crops on a server." items: type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - germplasmPUIs: - type: array - description: List of Permanent Unique Identifiers to identify germplasm - nullable: true - items: - type: string - parentDbIds: + externalReferenceIDs: type: array - description: Search for Germplasm with these parents - nullable: true + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: type: string - studyDbIds: + externalReferenceIds: type: array - description: List of study identifiers to search for + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) items: type: string - trialNames: + externalReferenceSources: type: array - description: The human readable name of a trial to search for + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) items: type: string familyCodes: @@ -4803,34 +4858,28 @@ components: nullable: true items: type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - collections: + genus: type: array - description: A specific panel/collection/population name this germplasm - belongs to. + description: List of Genus names to identify germplasm nullable: true items: type: string - genus: + germplasmDbIds: type: array - description: List of Genus names to identify germplasm + description: List of IDs which uniquely identify germplasm to search for nullable: true items: type: string - species: + germplasmNames: type: array - description: List of Species names to identify germplasm + description: List of human readable names to identify germplasm to search + for nullable: true items: type: string - binomialNames: + germplasmPUIs: type: array - description: List of the full binomial name (scientific name) to identify - a germplasm + description: List of Permanent Unique Identifiers to identify germplasm nullable: true items: type: string @@ -4847,12 +4896,79 @@ components: nullable: true items: type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + parentDbIds: + type: array + description: Search for Germplasm with these parents + nullable: true + items: + type: string progenyDbIds: type: array description: Search for Germplasm with these children nullable: true items: type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + nullable: true + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string description: "The conceptual identifiers and metadata describing a genetically\ \ unique organism that is noteworthy in some way. Depending on context, a\ \ Germplasm might be synonymous with Accession, Line, or Genotype. Note that\ @@ -5111,15 +5227,18 @@ components: abbreviations: type: array description: A list of shortened human readable names for a set of Locations + nullable: true items: type: string altitudeMax: type: number description: The maximum altitude to search for + nullable: true example: 200 altitudeMin: type: number description: The minimum altitude to search for + nullable: true example: 20 commonCropNames: type: array @@ -5138,21 +5257,25 @@ components: type: array description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ \ spec" + nullable: true items: type: string countryNames: type: array description: The full name of the country to search for + nullable: true items: type: string instituteAddresses: type: array description: The street address of the institute to search for + nullable: true items: type: string instituteNames: type: array description: The name of the institute to search for + nullable: true items: type: string locationDbIds: @@ -5169,6 +5292,7 @@ components: type: array description: "The type of location this represents (ex. Breeding Location,\ \ Storage Location, etc)" + nullable: true items: type: string parentLocationDbIds: @@ -5177,6 +5301,7 @@ components: \ defines the encompassing location that this location belongs to. \n\ For example, an Institution might have multiple Field Stations inside\ \ it and each Field Station might have multiple Fields." + nullable: true items: type: string parentLocationNames: @@ -5185,6 +5310,7 @@ components: \ defines the encompassing location that this location belongs to. \n\ For example, an Institution might have multiple Field Stations inside\ \ it and each Field Station might have multiple Fields." + nullable: true items: type: string programDbIds: @@ -5341,29 +5467,35 @@ components: observationDbIds: type: array description: The unique id of an Observation + nullable: true items: type: string observationLevelRelationships: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevelRelationship" observationLevels: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevel" observationTimeStampRangeEnd: type: string description: Timestamp range end format: date-time + nullable: true observationTimeStampRangeStart: type: string description: Timestamp range start format: date-time + nullable: true observationUnitDbIds: type: array description: The unique id of an Observation Unit + nullable: true items: type: string observationUnitLevelCodes: @@ -5476,6 +5608,7 @@ components: type: array description: "The year or Phenotyping campaign of a multi-annual study (trees,\ \ grape, ...)" + nullable: true items: type: string studyDbIds: @@ -5564,6 +5697,7 @@ components: \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ \ your own risk. It may return large, unpaginated lists of observation\ \ data. Only set this value to True if you are sure you need to." + nullable: true example: false locationDbIds: type: array @@ -5578,16 +5712,19 @@ components: observationLevelRelationships: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevelRelationship" observationLevels: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevel" observationUnitDbIds: type: array description: The unique id of an observation unit + nullable: true items: type: string observationUnitLevelCodes: @@ -5665,6 +5802,7 @@ components: observationUnitNames: type: array description: The human readable identifier for an Observation Unit + nullable: true items: type: string observationVariableDbIds: @@ -5705,6 +5843,7 @@ components: type: array description: "The year or Phenotyping campaign of a multi-annual study (trees,\ \ grape, ...)" + nullable: true items: type: string studyDbIds: @@ -5844,6 +5983,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -5990,24 +6130,24 @@ components: - FEMALE - SELF - POPULATION + - CLONAL PedigreeNode: required: - germplasmDbId - germplasmName - - germplasmPUI - - pedigreeNodeDbId type: object properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" breedingMethodDbId: type: string + nullable: true breedingMethodName: type: string + nullable: true crossingProjectDbId: type: string - crossingProjectName: - type: string + nullable: true crossingYear: type: integer description: The year the parents were originally crossed @@ -6022,7 +6162,6 @@ components: description: An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - nullable: true items: $ref: "#/components/schemas/ExternalReference" familyCode: @@ -6033,8 +6172,6 @@ components: type: string germplasmName: type: string - germplasmPUI: - type: string parents: type: array description: "A list of parent germplasm references in the pedigree tree\ @@ -6047,10 +6184,6 @@ components: nullable: true items: $ref: "#/components/schemas/GermplasmParent" - pedigreeNodeDbId: - type: string - description: The ID which uniquely identifies a pedigree node - nullable: true pedigreeString: type: string description: The string representation of the pedigree for this germplasm @@ -6068,7 +6201,7 @@ components: nullable: true items: $ref: "#/components/schemas/GermplasmChild" - siblingDbIds: + siblings: type: array description: "A list of sibling germplasm references in the pedigree tree\ \ for this germplasm. These represent edges in the tree, connecting to\ @@ -6077,7 +6210,7 @@ components: \ then this array should be empty, null, or not present in the response." nullable: true items: - type: string + $ref: "#/components/schemas/Germplasm" description: "A representation of a particular Germplasm within a pedigree tree,\ \ and all the links to its parents, siblings, and children. From a list of\ \ PedigreeNode objects, a client application should have all the information\ @@ -6091,18 +6224,21 @@ components: A collection of unique identifiers for materials or germplasm within a genebank MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true items: type: string binomialNames: type: array description: List of the full binomial name (scientific name) to identify a germplasm + nullable: true items: type: string collections: type: array description: A specific panel/collection/population name this germplasm belongs to. + nullable: true items: type: string commonCropNames: @@ -6120,11 +6256,13 @@ components: type: array description: A familyCode representing the family this germplasm belongs to. + nullable: true items: type: string genus: type: array description: List of Genus names to identify germplasm + nullable: true items: type: string germplasmDbIds: @@ -6143,27 +6281,32 @@ components: germplasmPUIs: type: array description: List of Permanent Unique Identifiers to identify germplasm + nullable: true items: type: string includeFullTree: type: boolean description: "If this parameter is true, recursively include ALL of the\ \ nodes available in this pedigree tree" + nullable: true example: true includeParents: type: boolean description: "If this parameter is true, include the array of parents in\ \ the response" + nullable: true example: true includeProgeny: type: boolean description: "If this parameter is true, include the array of progeny in\ \ the response" + nullable: true example: true includeSiblings: type: boolean description: "If this parameter is true, include the array of siblings in\ \ the response" + nullable: true example: true instituteCodes: type: array @@ -6175,6 +6318,7 @@ components: \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ \ rules (v)\"." + nullable: true items: type: string pedigreeDepth: @@ -6210,6 +6354,7 @@ components: species: type: array description: List of Species names to identify germplasm + nullable: true items: type: string studyDbIds: @@ -6225,6 +6370,7 @@ components: synonyms: type: array description: List of alternative names or IDs used to reference this germplasm + nullable: true items: type: string trialDbIds: @@ -6240,43 +6386,27 @@ components: PedigreeNodeSearchRequest: type: object properties: - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string accessionNumbers: type: array description: |- A collection of unique identifiers for materials or germplasm within a genebank MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for nullable: true items: type: string - includeParents: - type: boolean - description: "If this parameter is true, include the array of parents in\ - \ the response" - example: true - synonyms: + binomialNames: type: array - description: List of alternative names or IDs used to reference this germplasm + description: List of the full binomial name (scientific name) to identify + a germplasm + nullable: true items: type: string - programNames: + collections: type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: A specific panel/collection/population name this germplasm + belongs to. + nullable: true items: type: string commonCropNames: @@ -6290,106 +6420,167 @@ components: \ of available crops on a server." items: type: string - programDbIds: + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + nullable: true + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + nullable: true + items: + type: string + germplasmDbIds: type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." + description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string - trialDbIds: + germplasmNames: type: array - description: The ID which uniquely identifies a trial to search for + description: List of human readable names to identify germplasm to search + for + nullable: true items: type: string germplasmPUIs: type: array description: List of Permanent Unique Identifiers to identify germplasm + nullable: true items: type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - trialNames: + includeFullTree: + type: boolean + description: "If this parameter is true, recursively include ALL of the\ + \ nodes available in this pedigree tree" + nullable: true + example: true + includeParents: + type: boolean + description: "If this parameter is true, include the array of parents in\ + \ the response" + nullable: true + example: true + includeProgeny: + type: boolean + description: "If this parameter is true, include the array of progeny in\ + \ the response" + nullable: true + example: true + includeSiblings: + type: boolean + description: "If this parameter is true, include the array of siblings in\ + \ the response" + nullable: true + example: true + instituteCodes: type: array - description: The human readable name of a trial to search for + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + nullable: true items: type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + pedigreeDepth: + type: integer + description: "Recursively include this number of levels up the tree in the\ + \ response (parents, grand-parents, great-grand-parents, etc)" + format: int32 + example: 3 progenyDepth: type: integer description: "Recursively include this number of levels down the tree in\ \ the response (children, grand-children, great-grand-children, etc)" format: int32 example: 3 - familyCodes: + programDbIds: type: array - description: A familyCode representing the family this germplasm belongs - to. + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." items: type: string - includeProgeny: - type: boolean - description: "If this parameter is true, include the array of progeny in\ - \ the response" - example: true - studyNames: + programNames: type: array - description: List of study names to filter search results + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string - collections: + species: type: array - description: A specific panel/collection/population name this germplasm - belongs to. + description: List of Species names to identify germplasm + nullable: true items: type: string - genus: + studyDbIds: type: array - description: List of Genus names to identify germplasm + description: List of study identifiers to search for items: type: string - includeSiblings: - type: boolean - description: "If this parameter is true, include the array of siblings in\ - \ the response" - example: true - species: + studyNames: type: array - description: List of Species names to identify germplasm + description: List of study names to filter search results items: type: string - pedigreeDepth: - type: integer - description: "Recursively include this number of levels up the tree in the\ - \ response (parents, grand-parents, great-grand-parents, etc)" - format: int32 - example: 3 - binomialNames: + synonyms: type: array - description: List of the full binomial name (scientific name) to identify - a germplasm + description: List of alternative names or IDs used to reference this germplasm + nullable: true items: type: string - includeFullTree: - type: boolean - description: "If this parameter is true, recursively include ALL of the\ - \ nodes available in this pedigree tree" - example: true - instituteCodes: + trialDbIds: type: array - description: "The code for the institute that maintains the material. \n\ -
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ - \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ - \ country code of the country where the institute is located plus a number\ - \ (e.g. PER001). The current set of institute codes is available from\ - \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ - \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ - \ rules (v)\"." + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for items: type: string description: "A representation of a particular Germplasm within a pedigree tree,\ @@ -6478,8 +6669,19 @@ components: items: type: string PlannedCross: - required: - - plannedCrossDbId + allOf: + - $ref: "#/components/schemas/PlannedCrossNewRequest" + - required: + - plannedCrossDbId + type: object + properties: + plannedCrossDbId: + type: string + description: the unique identifier for a planned cross + description: Information regarding the intention to mate specific organisms + together to produce offspring with desired traits. A PlannedCross becomes + an actual Cross when the desired mating event actually occurs in the field. + PlannedCrossNewRequest: type: object properties: additionalInfo: @@ -6504,9 +6706,6 @@ components: $ref: "#/components/schemas/CrossParent" parent2: $ref: "#/components/schemas/CrossParent" - plannedCrossDbId: - type: string - description: the unique identifier for a planned cross plannedCrossName: type: string description: the human readable name for a planned cross @@ -6706,10 +6905,6 @@ components: PollinationEvent: type: object properties: - crossDbId: - type: string - crossName: - type: string pollinationNumber: type: string description: The unique identifier for this pollination event @@ -6845,6 +7040,7 @@ components: type: array description: "If specified, return the references for which the `accession`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string commonCropNames: @@ -6879,6 +7075,7 @@ components: \ same official sequence share the same coordinates and annotations, and\ \ can be replaced with the official sequence for certain use cases." format: boolean + nullable: true maxLength: type: integer description: The minimum length of this `References` sequence. @@ -6888,6 +7085,7 @@ components: type: array description: "If specified, return the references for which the `md5checksum`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string minLength: @@ -6917,12 +7115,14 @@ components: type: array description: A list of IDs which uniquely identify `References` within the given database server + nullable: true items: type: string referenceSetDbIds: type: array description: A list of IDs which uniquely identify `ReferenceSets` within the given database server + nullable: true items: type: string studyDbIds: @@ -7301,14 +7501,6 @@ components: type: string description: Description the storage location nullable: true - transactions: - type: array - description: "The complete history of transactions for this seed lot. This\ - \ includes seed increases, seed usage (planting), and trading with other\ - \ breeding programs." - nullable: true - items: - $ref: "#/components/schemas/SeedLotTransaction" units: type: string description: "A description of the things being counted in a SeedLot (seeds,\ @@ -7398,10 +7590,16 @@ components: nullable: true items: $ref: "#/components/schemas/ExternalReference" - seedLotDbId: + fromSeedLotDbId: type: string nullable: true - seedLotName: + fromSeedLotPUI: + type: string + nullable: true + toSeedLotDbId: + type: string + nullable: true + toSeedLotPUI: type: string nullable: true transactionDbId: @@ -7436,14 +7634,16 @@ components: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId SortOrder: type: string description: Sort order direction. Ascending/Descending. enum: - - asc - ASC - - desc - DESC + - asc + - desc StorageType: type: object properties: @@ -7472,12 +7672,6 @@ components: type: string description: A supplemental text description of the storage type nullable: true - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string description: The type of storage this germplasm is kept in at a genebank. StorageTypeCode: type: string @@ -7608,15 +7802,17 @@ components: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId sortOrder: type: string description: Sort order direction. Ascending/Descending. nullable: true enum: - - asc - ASC - - desc - DESC + - asc + - desc studyCodes: type: array description: A short human readable code for a study @@ -7659,12 +7855,6 @@ components: Synonym: type: object properties: - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string synonym: type: string description: Alternative name or ID used to reference this germplasm @@ -7680,12 +7870,6 @@ components: - taxonId type: object properties: - germplasmDbId: - type: string - germplasmName: - type: string - germplasmPUI: - type: string sourceName: type: string description: The human readable name of the taxonomy provider @@ -7721,6 +7905,7 @@ components: \ a prior response to construct a query and move to the next or previous\ \ page respectively. " example: 33c27874 + deprecated: true TraitDataType: type: string description: |- @@ -7903,11 +8088,9 @@ components: type: string Variable: required: - - methodDbId - - methodName - - scaleDbId - - scaleName - - traitName + - method + - scale + - trait type: object properties: additionalInfo: @@ -7954,20 +8137,12 @@ components: description: 2 letter ISO 639-1 code for the language of submission of the variable. nullable: true - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string + method: + $ref: "#/components/schemas/Method" ontologyReference: $ref: "#/components/schemas/OntologyReference" - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string + scale: + $ref: "#/components/schemas/Scale" scientist: type: string description: Name of scientist submitting the variable. @@ -7988,12 +8163,8 @@ components: nullable: true items: type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + trait: + $ref: "#/components/schemas/Trait" description: "A unique combination of Trait, Method, and Scale to define a clear\ \ context for an Observation." VariableBaseClassParameters: @@ -8078,6 +8249,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -8161,6 +8333,8 @@ components: \ number #474 \n
Only return variant calls which belong to call sets\ \ with these IDs. If unspecified, return all variants and no variant call\ \ objects." + nullable: true + deprecated: true items: type: string commonCropNames: @@ -8203,15 +8377,19 @@ components: description: |- **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472
Only return variants on this reference. + nullable: true example: 120a2d5c + deprecated: true referenceDbIds: type: array description: The unique identifier representing a genotype `Reference` + nullable: true items: type: string referenceSetDbIds: type: array description: The unique identifier representing a genotype `ReferenceSet` + nullable: true items: type: string start: @@ -8246,11 +8424,13 @@ components: variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` + nullable: true items: type: string VariantSetRequest: @@ -8701,6 +8881,30 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/Sample" + SeedLotTransactionListResponse: + description: OK + content: + application/json: + schema: + title: SeedLotTransactionListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/SeedLotTransaction" CallSetListResponse: description: OK content: @@ -8930,6 +9134,23 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/GenomeMap" + AlleleMatrixSingleResponse: + description: OK + content: + application/json: + schema: + title: AlleleMatrixSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/AlleleMatrix" PersonListResponse: description: OK content: @@ -9395,8 +9616,37 @@ components: properties: data: type: array + description: "The `data` array is part of the BrAPI standard List\ + \ Response JSON container. `data` will always contain the primary\ + \ list of objects being returned by a BrAPI endpoint. `data`\ + \ is also the only array impacted by the `metadata.pagination`\ + \ details. When the pagination parameters change, the `data`\ + \ array will reflect those changes in the JSON response." items: $ref: "#/components/schemas/Call" + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed + into a single occurrence (false) + nullable: true + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele + calls. + nullable: true + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele + calls. + nullable: true + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + nullable: true + example: "." BreedingMethodSingleResponse: description: OK content: diff --git a/Specification/Generated/BrAPI-Phenotyping.yaml b/Specification/Generated/BrAPI-Phenotyping.yaml index 443b6a1f..f2638c46 100644 --- a/Specification/Generated/BrAPI-Phenotyping.yaml +++ b/Specification/Generated/BrAPI-Phenotyping.yaml @@ -1693,6 +1693,10 @@ paths: responses: "200": $ref: "#/components/responses/ImageListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1731,6 +1735,10 @@ paths: responses: "200": $ref: "#/components/responses/ObservationListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1770,6 +1778,10 @@ paths: responses: "200": $ref: "#/components/responses/ObservationUnitListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1809,6 +1821,10 @@ paths: responses: "200": $ref: "#/components/responses/ObservationVariableListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "404": + $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1857,21 +1873,41 @@ components: items: type: string dataMatrixAbbreviations: - type: array - description: "`dataMatrixAbbreviations` is a comma seperated list of abbreviations\ + type: string + description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ \ in the response." nullable: true - items: - type: string + example: "GT,RD" dataMatrixNames: - type: array - description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ - \ Depth' etc). This list controls which data matrices are returned in\ - \ the response." + type: string + description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ + \ 'Read Depth' etc). This list controls which data matrices are returned\ + \ in the response." + nullable: true + example: "Genotype,Read Depth" + dimensionCallSetPage: + type: integer + description: The requested page number for the CallSet dimension of the + matrix + format: int32 + nullable: true + dimensionCallSetPageSize: + type: integer + description: The requested page size for the CallSet dimension of the matrix + format: int32 + nullable: true + dimensionVariantPage: + type: integer + description: The requested page number for the Variant dimension of the + matrix + format: int32 + nullable: true + dimensionVariantPageSize: + type: integer + description: The requested page size for the Variant dimension of the matrix + format: int32 nullable: true - items: - type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single @@ -1940,6 +1976,7 @@ components: \ or not set (default), then the server should return all the matrix\n\ data as requested." example: true + default: false sampleDbIds: type: array description: A list of IDs which uniquely identify `Samples` within the @@ -1979,11 +2016,9 @@ components: Attribute: required: - attributeName - - methodDbId - - methodName - - scaleDbId - - scaleName - - traitName + - method + - scale + - trait type: object properties: additionalInfo: @@ -2051,20 +2086,12 @@ components: description: 2 letter ISO 639-1 code for the language of submission of the variable. nullable: true - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string + method: + $ref: "#/components/schemas/Method" ontologyReference: $ref: "#/components/schemas/OntologyReference" - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string + scale: + $ref: "#/components/schemas/Scale" scientist: type: string description: Name of scientist submitting the variable. @@ -2085,12 +2112,8 @@ components: nullable: true items: type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + trait: + $ref: "#/components/schemas/Trait" CallRequest: type: object properties: @@ -2107,6 +2130,12 @@ components: occurrence (false) nullable: true example: true + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. sepPhased: type: string description: The string used as a separator for phased allele calls. @@ -2372,6 +2401,25 @@ components: Use `GET /programs` to find the list of available programs on a server. items: type: string + DataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text DocumentationLink: type: object properties: @@ -2379,12 +2427,10 @@ components: type: string description: The URL or URI to the documentation format: uri - nullable: true type: type: string description: "The type of documentation, which can be OBO Foundry, an RDF\ \ term or a webpage." - nullable: true enum: - OBO - RDF @@ -2414,6 +2460,17 @@ components: properties: additionalInfo: $ref: "#/components/schemas/AdditionalInfo" + date: + type: array + description: |- + **Deprecated in v2.1** Please use `eventDateRange.discreteDates`. Github issue number #440 +
A list of dates when the event occurred +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + nullable: true + deprecated: true + items: + type: string + format: date-time eventDateRange: $ref: "#/components/schemas/EventDateRange" eventDbId: @@ -2445,12 +2502,20 @@ components:
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology). nullable: true + observationUnitDbIds: + type: array + description: "A list of the affected observation units. If this parameter\ + \ is not given, it is understood that the event affected all units in\ + \ the study" + nullable: true + items: + type: string studyDbId: type: string + nullable: true studyName: type: string - studyPUI: - type: string + nullable: true description: "An event is discrete occurrence at a particular time in the experiment.\ \ Events may be the realization of Treatments or parts of Treatments, or may\ \ be confounding to Treatments. \n
ICASA Management Events allow for the\ @@ -2476,8 +2541,6 @@ components:
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. format: date-time nullable: true - eventDbId: - type: string startDate: type: string description: |- @@ -2489,6 +2552,7 @@ components: \ An Event can occur at one or more discrete time points (`discreteDates`)\ \ or an event can happen continuously over a longer period of time (`startDate`,\ \ `endDate`)" + nullable: true EventParameter: type: object properties: @@ -2504,14 +2568,14 @@ components: description is usually associated with the 'name' and 'code' of an event parameter. nullable: true - eventDbId: - type: string key: type: string description: "**Deprecated in v2.1** Please use `name`. Github issue number\ \ #440 \n
Specifies the relationship between the event\ \ and the given property. E.g. fertilizer, operator" + nullable: true example: operator + deprecated: true name: type: string description: |- @@ -2522,7 +2586,9 @@ components: type: string description: "**Deprecated in v2.1** Please use `code`. Github issue number\ \ #440 \nIf the 'value'\ @@ -2601,6 +2667,7 @@ components: \ number #460
The external reference ID. Could be a simple string\ \ or a URI." nullable: true + deprecated: true referenceId: type: string description: The external reference ID. Could be a simple string or a URI. @@ -2616,6 +2683,7 @@ components: \ Github issue number #460 \n
List of external reference IDs. Could\ \ be a simple strings or a URIs. (use with `externalReferenceSources`\ \ parameter)" + deprecated: true items: type: string externalReferenceIds: @@ -2712,6 +2780,7 @@ components: type: string description: The literal string "Feature" example: Feature + default: Feature description: |- One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. @@ -2719,10 +2788,12 @@ components: A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + nullable: true GeoJSONGeometry: + nullable: true oneOf: - required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2734,13 +2805,14 @@ components: type: type: string description: The literal string "Point" + default: Point description: |- Copied from RFC 7946 Section 3.1.1 A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. - required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2756,6 +2828,7 @@ components: type: type: string description: The literal string "Polygon" + default: Polygon description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ @@ -2763,7 +2836,7 @@ components: \ MAY be included as an optional third element." GeoJSONPoint: required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2775,6 +2848,7 @@ components: type: type: string description: The literal string "Point" + default: Point description: |- Copied from RFC 7946 Section 3.1.1 @@ -2782,7 +2856,7 @@ components: easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. GeoJSONPolygon: required: - - coordinateDbIds + - coordinates - type type: object properties: @@ -2798,6 +2872,7 @@ components: type: type: string description: The literal string "Polygon" + default: Polygon description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ \ The first two elements are longitude and latitude, or\neasting and northing,\ @@ -2814,14 +2889,21 @@ components: type: string imageName: type: string + imagePUI: + type: string observationDbId: type: string + observationName: + type: string + observationPUI: + type: string observationUnit: $ref: "#/components/schemas/ObservationUnitPosition" type: type: string description: The literal string "Feature" example: Feature + default: Feature GermplasmAttributeRequest: type: object properties: @@ -2943,6 +3025,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -3316,7 +3399,6 @@ components: description: An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. - nullable: true items: $ref: "#/components/schemas/ExternalReference" imageContent: @@ -3371,9 +3453,6 @@ components: observationUnitName: type: string nullable: true - observationUnitPUI: - type: string - nullable: true description: The metadata for an image file that is connected to some phenotypic observation data. ImageRequest: @@ -3489,87 +3568,100 @@ components: ImageSearchRequest: type: object properties: - imageFileSizeMax: - type: integer - description: A maximum image file size to search for. - format: int32 - example: 20000000 - imageFileNames: + commonCropNames: type: array - description: Image file names to search for. + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." items: type: string - imageTimeStampRangeStart: - type: string - description: The earliest timestamp to search for. - format: date-time - imageDbIds: + descriptiveOntologyTerms: type: array - description: A list of image Ids to search for + description: "A list of terms to formally describe the image to search for.\ + \ Each item could be a simple Tag, an Ontology reference Id, or a full\ + \ ontology URL." items: type: string - observationUnitDbIds: + externalReferenceIDs: type: array - description: A set of observation unit identifiers to search for. + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: type: string - imageNames: + externalReferenceIds: type: array - description: Human readable names to search for. + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) items: type: string - imageWidthMin: - type: integer - description: A minimum image width to search for. - format: int32 - example: 1280 - imageHeightMax: - type: integer - description: A maximum image height to search for. - format: int32 - example: 1080 - programNames: + externalReferenceSources: type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) items: type: string - commonCropNames: + imageDbIds: type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." + description: A list of image Ids to search for items: type: string - programDbIds: + imageFileNames: type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." + description: Image file names to search for. items: type: string - descriptiveOntologyTerms: + imageFileSizeMax: + type: integer + description: A maximum image file size to search for. + format: int32 + example: 20000000 + imageFileSizeMin: + type: integer + description: A minimum image file size to search for. + format: int32 + example: 1000 + imageHeightMax: + type: integer + description: A maximum image height to search for. + format: int32 + example: 1080 + imageHeightMin: + type: integer + description: A minimum image height to search for. + format: int32 + example: 720 + imageLocation: + $ref: "#/components/schemas/GeoJSONSearchArea" + imageNames: type: array - description: "A list of terms to formally describe the image to search for.\ - \ Each item could be a simple Tag, an Ontology reference Id, or a full\ - \ ontology URL." + description: Human readable names to search for. items: type: string - imageLocation: - $ref: "#/components/schemas/GeoJSONSearchArea" imageTimeStampRangeEnd: type: string description: The latest timestamp to search for. format: date-time + imageTimeStampRangeStart: + type: string + description: The earliest timestamp to search for. + format: date-time + imageWidthMax: + type: integer + description: A maximum image width to search for. + format: int32 + example: 1920 + imageWidthMin: + type: integer + description: A minimum image width to search for. + format: int32 + example: 1280 mimeTypes: type: array description: A set of image file types to search for. @@ -3581,26 +3673,45 @@ components: search for items: type: string - imageHeightMin: + observationUnitDbIds: + type: array + description: A set of observation unit identifiers to search for. + items: + type: string + page: type: integer - description: A minimum image height to search for. + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. format: int32 - example: 720 - imageFileSizeMin: + example: 0 + pageSize: type: integer - description: A minimum image file size to search for. + description: The size of the pages to be returned. Default is `1000`. format: int32 example: 1000 - imageWidthMax: - type: integer - description: A maximum image width to search for. - format: int32 - example: 1920 - description: The metadata for an image file that is connected to some phenotypic - observation data. - ListRequest: - type: object - properties: + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + description: The metadata for an image file that is connected to some phenotypic + observation data. + ListRequest: + type: object + properties: commonCropNames: type: array description: "The BrAPI Common Crop Name is the simple, generalized, widely\ @@ -3709,15 +3820,18 @@ components: abbreviations: type: array description: A list of shortened human readable names for a set of Locations + nullable: true items: type: string altitudeMax: type: number description: The maximum altitude to search for + nullable: true example: 200 altitudeMin: type: number description: The minimum altitude to search for + nullable: true example: 20 commonCropNames: type: array @@ -3736,21 +3850,25 @@ components: type: array description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ \ spec" + nullable: true items: type: string countryNames: type: array description: The full name of the country to search for + nullable: true items: type: string instituteAddresses: type: array description: The street address of the institute to search for + nullable: true items: type: string instituteNames: type: array description: The name of the institute to search for + nullable: true items: type: string locationDbIds: @@ -3767,6 +3885,7 @@ components: type: array description: "The type of location this represents (ex. Breeding Location,\ \ Storage Location, etc)" + nullable: true items: type: string parentLocationDbIds: @@ -3775,6 +3894,7 @@ components: \ defines the encompassing location that this location belongs to. \n\ For example, an Institution might have multiple Field Stations inside\ \ it and each Field Station might have multiple Fields." + nullable: true items: type: string parentLocationNames: @@ -3783,6 +3903,7 @@ components: \ defines the encompassing location that this location belongs to. \n\ For example, an Institution might have multiple Field Stations inside\ \ it and each Field Station might have multiple Fields." + nullable: true items: type: string programDbIds: @@ -3995,9 +4116,6 @@ components: germplasmName: type: string nullable: true - germplasmPUI: - type: string - nullable: true observationTimeStamp: type: string description: The date and time when this observation was made @@ -4009,9 +4127,6 @@ components: observationUnitName: type: string nullable: true - observationUnitPUI: - type: string - nullable: true observationVariableDbId: type: string nullable: true @@ -4027,13 +4142,13 @@ components: seasonName: type: string nullable: true - studyDbId: + seasonPUI: type: string nullable: true - studyName: + studyDbId: type: string nullable: true - studyPUI: + studyName: type: string nullable: true uploadedBy: @@ -4087,29 +4202,35 @@ components: observationDbIds: type: array description: The unique id of an Observation + nullable: true items: type: string observationLevelRelationships: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevelRelationship" observationLevels: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevel" observationTimeStampRangeEnd: type: string description: Timestamp range end format: date-time + nullable: true observationTimeStampRangeStart: type: string description: Timestamp range start format: date-time + nullable: true observationUnitDbIds: type: array description: The unique id of an Observation Unit + nullable: true items: type: string observationUnitLevelCodes: @@ -4222,6 +4343,7 @@ components: type: array description: "The year or Phenotyping campaign of a multi-annual study (trees,\ \ grape, ...)" + nullable: true items: type: string studyDbIds: @@ -4247,128 +4369,167 @@ components: ObservationSearchRequest: type: object properties: - germplasmDbIds: + commonCropNames: type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." items: type: string - locationDbIds: + externalReferenceIDs: type: array - description: The location ids to search for + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: type: string - locationNames: + externalReferenceIds: type: array - description: A human readable names to search for + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) items: type: string - germplasmNames: + externalReferenceSources: type: array - description: List of human readable names to identify germplasm to search - for - nullable: true + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) items: type: string - observationUnitDbIds: + germplasmDbIds: type: array - description: The unique id of an Observation Unit + description: List of IDs which uniquely identify germplasm to search for + nullable: true items: type: string - programNames: + germplasmNames: type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: List of human readable names to identify germplasm to search + for + nullable: true items: type: string - seasonDbIds: + locationDbIds: type: array - description: "The year or Phenotyping campaign of a multi-annual study (trees,\ - \ grape, ...)" + description: The location ids to search for items: type: string - commonCropNames: + locationNames: type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." + description: A human readable names to search for items: type: string - programDbIds: + observationDbIds: type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." + description: The unique id of an Observation + nullable: true items: type: string observationLevelRelationships: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevelRelationship" observationLevels: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevel" + observationTimeStampRangeEnd: + type: string + description: Timestamp range end + format: date-time + nullable: true + observationTimeStampRangeStart: + type: string + description: Timestamp range start + format: date-time + nullable: true + observationUnitDbIds: + type: array + description: The unique id of an Observation Unit + nullable: true + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string observationVariablePUIs: type: array description: "The Permanent Unique Identifier of an Observation Variable,\ \ usually in the form of a URI" items: type: string - trialDbIds: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: type: array - description: The ID which uniquely identifies a trial to search for + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." items: type: string - studyDbIds: + programNames: type: array - description: List of study identifiers to search for + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string - trialNames: + seasonDbIds: type: array - description: The human readable name of a trial to search for + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + nullable: true items: type: string - observationVariableNames: + studyDbIds: type: array - description: The names of Variables to search for + description: List of study identifiers to search for items: type: string - observationDbIds: + studyNames: type: array - description: The unique id of an Observation + description: List of study names to filter search results items: type: string - studyNames: + trialDbIds: type: array - description: List of study names to filter search results + description: The ID which uniquely identifies a trial to search for items: type: string - observationVariableDbIds: + trialNames: type: array - description: The DbIds of Variables to search for + description: The human readable name of a trial to search for items: type: string - observationTimeStampRangeStart: - type: string - description: Timestamp range start - format: date-time - observationTimeStampRangeEnd: - type: string - description: Timestamp range end - format: date-time description: A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. ObservationTreatment: @@ -4391,12 +4552,6 @@ components: \ all the plants targeted by a given experimental factor. " nullable: true example: test-factor:dia2020-2-nv.lf - observationUnitDbId: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string description: A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor. ObservationUnit: @@ -4415,6 +4570,7 @@ components: description: "A representation of the physical entity being observed during\ \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ \ but it could include things like Fields, Blocks, or Samples." + nullable: true ObservationUnitHierarchyLevel: type: object properties: @@ -4524,10 +4680,6 @@ components: nullable: true observationUnitDbId: type: string - observationUnitName: - type: string - observationUnitPUI: - type: string description: "Observation levels indicate the granularity level at which the\ \ measurements are taken. `levelName` \ndefines the level, `levelOrder` defines\ \ where that level exists in the hierarchy of levels. \n`levelOrder`s lower\ @@ -4549,6 +4701,9 @@ components: crossName: type: string nullable: true + crossPUI: + type: string + nullable: true externalReferences: type: array description: An array of external reference ids. These are references to @@ -4563,15 +4718,15 @@ components: germplasmName: type: string nullable: true - germplasmPUI: - type: string - nullable: true locationDbId: type: string nullable: true locationName: type: string nullable: true + locationPUI: + type: string + nullable: true observationUnitName: type: string description: A human readable name for an observation unit @@ -4591,19 +4746,22 @@ components: programName: type: string nullable: true + programPUI: + type: string + nullable: true seedLotDbId: type: string nullable: true seedLotName: type: string nullable: true - studyDbId: + seedLotPUI: type: string nullable: true - studyName: + studyDbId: type: string nullable: true - studyPUI: + studyName: type: string nullable: true treatments: @@ -4621,12 +4779,10 @@ components: trialName: type: string nullable: true - trialPUI: - type: string - nullable: true description: "A representation of the physical entity being observed during\ \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ \ but it could include things like Fields, Blocks, or Samples." + nullable: true ObservationUnitPosition: type: object properties: @@ -4669,12 +4825,6 @@ components: nullable: true items: $ref: "#/components/schemas/ObservationUnitLevelRelationship" - observationUnitDbId: - type: string - observationUnitName: - type: string - observationUnitPUI: - type: string positionCoordinateX: type: string description: The X position coordinate for an observation unit. Different @@ -4691,6 +4841,7 @@ components: $ref: "#/components/schemas/PositionCoordinateType" description: All positional and layout information related to this Observation Unit + nullable: true ObservationUnitRequest: type: object properties: @@ -4724,6 +4875,7 @@ components: \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ \ your own risk. It may return large, unpaginated lists of observation\ \ data. Only set this value to True if you are sure you need to." + nullable: true example: false locationDbIds: type: array @@ -4738,16 +4890,19 @@ components: observationLevelRelationships: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevelRelationship" observationLevels: type: array description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true items: $ref: "#/components/schemas/ObservationUnitLevel" observationUnitDbIds: type: array description: The unique id of an observation unit + nullable: true items: type: string observationUnitLevelCodes: @@ -4825,6 +4980,7 @@ components: observationUnitNames: type: array description: The human readable identifier for an Observation Unit + nullable: true items: type: string observationVariableDbIds: @@ -4865,6 +5021,7 @@ components: type: array description: "The year or Phenotyping campaign of a multi-annual study (trees,\ \ grape, ...)" + nullable: true items: type: string studyDbIds: @@ -4890,12 +5047,59 @@ components: ObservationUnitSearchRequest: type: object properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for nullable: true items: type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + includeObservations: + type: boolean + description: "Use this parameter to include a list of observations embedded\ + \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ + \ your own risk. It may return large, unpaginated lists of observation\ + \ data. Only set this value to True if you are sure you need to." + nullable: true + example: false locationDbIds: type: array description: The location ids to search for @@ -4906,48 +5110,57 @@ components: description: A human readable names to search for items: type: string - germplasmNames: + observationLevelRelationships: type: array - description: List of human readable names to identify germplasm to search - for + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships nullable: true items: - type: string - observationUnitNames: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: type: array - description: The human readable identifier for an Observation Unit + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true items: - type: string + $ref: "#/components/schemas/ObservationUnitLevel" observationUnitDbIds: type: array description: The unique id of an observation unit + nullable: true items: type: string - programNames: + observationUnitNames: type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + description: The human readable identifier for an Observation Unit + nullable: true items: type: string - seasonDbIds: + observationVariableDbIds: type: array - description: "The year or Phenotyping campaign of a multi-annual study (trees,\ - \ grape, ...)" + description: The DbIds of Variables to search for items: type: string - commonCropNames: + observationVariableNames: type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" items: type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -4958,57 +5171,39 @@ components: \ on a server." items: type: string - observationLevelRelationships: - type: array - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships - items: - $ref: "#/components/schemas/ObservationUnitLevelRelationship" - observationLevels: - type: array - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel - items: - $ref: "#/components/schemas/ObservationUnitLevel" - observationVariablePUIs: + programNames: type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string - trialDbIds: + seasonDbIds: type: array - description: The ID which uniquely identifies a trial to search for + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + nullable: true items: type: string - includeObservations: - type: boolean - description: "Use this parameter to include a list of observations embedded\ - \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ - \ your own risk. It may return large, unpaginated lists of observation\ - \ data. Only set this value to True if you are sure you need to." - example: false studyDbIds: type: array description: List of study identifiers to search for items: type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - observationVariableNames: + studyNames: type: array - description: The names of Variables to search for + description: List of study names to filter search results items: type: string - studyNames: + trialDbIds: type: array - description: List of study names to filter search results + description: The ID which uniquely identifies a trial to search for items: type: string - observationVariableDbIds: + trialNames: type: array - description: The DbIds of Variables to search for + description: The human readable name of a trial to search for items: type: string description: "A representation of the physical entity being observed during\ @@ -5029,12 +5224,10 @@ components: MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. ObservationVariableNewRequest: required: - - methodDbId - - methodName + - method - observationVariableName - - scaleDbId - - scaleName - - traitName + - scale + - trait type: object properties: additionalInfo: @@ -5081,12 +5274,8 @@ components: description: 2 letter ISO 639-1 code for the language of submission of the variable. nullable: true - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string + method: + $ref: "#/components/schemas/Method" observationVariableName: type: string description: |- @@ -5100,12 +5289,8 @@ components: nullable: true ontologyReference: $ref: "#/components/schemas/OntologyReference" - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string + scale: + $ref: "#/components/schemas/Scale" scientist: type: string description: Name of scientist submitting the variable. @@ -5126,12 +5311,8 @@ components: nullable: true items: type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + trait: + $ref: "#/components/schemas/Trait" ObservationVariableParameters: type: object properties: @@ -5249,6 +5430,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -5318,66 +5500,117 @@ components: description: The ID which uniquely identifies a trial to search for items: type: string - trialNames: + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ObservationVariableSearchRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: type: array - description: The human readable name of a trial to search for + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) items: type: string - ObservationVariableSearchRequest: - type: object - properties: methodDbIds: type: array description: List of methods to filter search results items: type: string - programNames: + methodNames: type: array description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation items: type: string - observationVariablePUIs: + methodPUIs: type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" items: type: string - trialNames: + observationVariableDbIds: type: array - description: The human readable name of a trial to search for + description: The DbIds of Variables to search for items: type: string - studyDbId: + observationVariableNames: type: array - description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ - \ number #483 \n
The unique ID of a studies to filter on" + description: The names of Variables to search for items: type: string - dataTypes: + observationVariablePUIs: type: array - description: List of scale data types to filter search results + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" items: - $ref: "#/components/schemas/TraitDataType" - methodPUIs: + type: string + ontologyDbIds: type: array - description: "The Permanent Unique Identifier of a Method, usually in the\ - \ form of a URI" + description: List of ontology IDs to search for items: type: string - scalePUIs: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: type: array - description: "The Permanent Unique Identifier of a Scale, usually in the\ - \ form of a URI" + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." items: type: string - traitAttributes: + programNames: type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the attribute is the observed feature (or characteristic) of the entity\ - \ e.g., for \"grain colour\", attribute = \"colour\"" + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. items: type: string scaleDbIds: @@ -5385,21 +5618,6 @@ components: description: The unique identifier for a Scale items: type: string - traitEntityPUIs: - type: array - description: "The Permanent Unique Identifier of a Trait Entity, usually\ - \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ - \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ - \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " - items: - type: string - methodNames: - type: array - description: |- - Human readable name for the method -
MIAPPE V1.1 (DM-88) Method Name of the method of observation - items: - type: string scaleNames: type: array description: |- @@ -5407,66 +5625,66 @@ components:
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable items: type: string - traitPUIs: + scalePUIs: type: array - description: "The Permanent Unique Identifier of a Trait, usually in the\ + description: "The Permanent Unique Identifier of a Scale, usually in the\ \ form of a URI" items: type: string - traitClasses: + studyDbId: type: array - description: List of trait classes to filter search results + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string - commonCropNames: + studyDbIds: type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." + description: List of study identifiers to search for items: type: string - programDbIds: + studyNames: type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." + description: List of study names to filter search results items: type: string - trialDbIds: + traitAttributePUIs: type: array - description: The ID which uniquely identifies a trial to search for + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" items: type: string - ontologyDbIds: + traitAttributes: type: array - description: List of ontology IDs to search for + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" items: type: string - studyDbIds: + traitClasses: type: array - description: List of study identifiers to search for + description: List of trait classes to filter search results items: type: string - observationVariableNames: + traitDbIds: type: array - description: The names of Variables to search for + description: The unique identifier for a Trait items: type: string - studyNames: + traitEntities: type: array - description: List of study names to filter search results + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" items: type: string - traitDbIds: + traitEntityPUIs: type: array - description: The unique identifier for a Trait + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " items: type: string traitNames: @@ -5476,23 +5694,20 @@ components:
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation items: type: string - observationVariableDbIds: + traitPUIs: type: array - description: The DbIds of Variables to search for + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" items: type: string - traitAttributePUIs: + trialDbIds: type: array - description: |- - The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI -
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + description: The ID which uniquely identifies a trial to search for items: type: string - traitEntities: + trialNames: type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the entity is the part of the plant that the trait refers to e.g., for\ - \ \"grain colour\", entity = \"grain\"" + description: The human readable name of a trial to search for items: type: string Ontology: @@ -5571,6 +5786,8 @@ components: type: string ontologyName: type: string + ontologyPUI: + type: string ontologyReferenceDbId: type: string description: The ID which uniquely identifies a ontology reference @@ -5587,6 +5804,7 @@ components: \ Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number -\ \ Accession number of the scale in a suitable controlled vocabulary (Crop\ \ Ontology)." + nullable: false OntologyRequest: type: object properties: @@ -5641,18 +5859,21 @@ components: A collection of unique identifiers for materials or germplasm within a genebank MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true items: type: string binomialNames: type: array description: List of the full binomial name (scientific name) to identify a germplasm + nullable: true items: type: string collections: type: array description: A specific panel/collection/population name this germplasm belongs to. + nullable: true items: type: string commonCropNames: @@ -5670,11 +5891,13 @@ components: type: array description: A familyCode representing the family this germplasm belongs to. + nullable: true items: type: string genus: type: array description: List of Genus names to identify germplasm + nullable: true items: type: string germplasmDbIds: @@ -5693,27 +5916,32 @@ components: germplasmPUIs: type: array description: List of Permanent Unique Identifiers to identify germplasm + nullable: true items: type: string includeFullTree: type: boolean description: "If this parameter is true, recursively include ALL of the\ \ nodes available in this pedigree tree" + nullable: true example: true includeParents: type: boolean description: "If this parameter is true, include the array of parents in\ \ the response" + nullable: true example: true includeProgeny: type: boolean description: "If this parameter is true, include the array of progeny in\ \ the response" + nullable: true example: true includeSiblings: type: boolean description: "If this parameter is true, include the array of siblings in\ \ the response" + nullable: true example: true instituteCodes: type: array @@ -5725,6 +5953,7 @@ components: \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ \ rules (v)\"." + nullable: true items: type: string pedigreeDepth: @@ -5760,6 +5989,7 @@ components: species: type: array description: List of Species names to identify germplasm + nullable: true items: type: string studyDbIds: @@ -5775,6 +6005,7 @@ components: synonyms: type: array description: List of alternative names or IDs used to reference this germplasm + nullable: true items: type: string trialDbIds: @@ -6180,6 +6411,7 @@ components: type: array description: "If specified, return the references for which the `accession`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string commonCropNames: @@ -6214,6 +6446,7 @@ components: \ same official sequence share the same coordinates and annotations, and\ \ can be replaced with the official sequence for certain use cases." format: boolean + nullable: true maxLength: type: integer description: The minimum length of this `References` sequence. @@ -6223,6 +6456,7 @@ components: type: array description: "If specified, return the references for which the `md5checksum`\ \ matches this string (case-sensitive, exact match)." + nullable: true items: type: string minLength: @@ -6252,12 +6486,14 @@ components: type: array description: A list of IDs which uniquely identify `References` within the given database server + nullable: true items: type: string referenceSetDbIds: type: array description: A list of IDs which uniquely identify `ReferenceSets` within the given database server + nullable: true items: type: string studyDbIds: @@ -6550,7 +6786,9 @@ components: \ other dataTypes when applicable." nullable: true validValues: - $ref: "#/components/schemas/ValidValues" + anyOf: + - $ref: "#/components/schemas/ValidValues" + - type: "null" description: "A Scale describes the units and acceptable values for an ObservationVariable.\ \ \n
For example, an ObservationVariable might be defined with a Trait\ \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ @@ -6705,14 +6943,16 @@ components: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId SortOrder: type: string description: Sort order direction. Ascending/Descending. enum: - - asc - ASC - - desc - DESC + - asc + - desc StudyParameters: type: object properties: @@ -6822,15 +7062,17 @@ components: - studyName - studyLocation - programName + - germplasmDbId + - observationVariableDbId sortOrder: type: string description: Sort order direction. Ascending/Descending. nullable: true enum: - - asc - ASC - - desc - DESC + - asc + - desc studyCodes: type: array description: A short human readable code for a study @@ -6893,6 +7135,7 @@ components: \ a prior response to construct a query and move to the next or previous\ \ page respectively. " example: 33c27874 + deprecated: true Trait: allOf: - $ref: "#/components/schemas/TraitNewRequest" @@ -7218,11 +7461,9 @@ components: \ options" Variable: required: - - methodDbId - - methodName - - scaleDbId - - scaleName - - traitName + - method + - scale + - trait type: object properties: additionalInfo: @@ -7269,20 +7510,12 @@ components: description: 2 letter ISO 639-1 code for the language of submission of the variable. nullable: true - methodDbId: - type: string - methodName: - type: string - methodPUI: - type: string + method: + $ref: "#/components/schemas/Method" ontologyReference: $ref: "#/components/schemas/OntologyReference" - scaleDbId: - type: string - scaleName: - type: string - scalePUI: - type: string + scale: + $ref: "#/components/schemas/Scale" scientist: type: string description: Name of scientist submitting the variable. @@ -7303,12 +7536,8 @@ components: nullable: true items: type: string - traitDbId: - type: string - traitName: - type: string - traitPUI: - type: string + trait: + $ref: "#/components/schemas/Trait" description: "A unique combination of Trait, Method, and Scale to define a clear\ \ context for an Observation." VariableBaseClassParameters: @@ -7393,6 +7622,7 @@ components: type: array description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true items: type: string studyDbIds: @@ -7476,6 +7706,8 @@ components: \ number #474 \n
Only return variant calls which belong to call sets\ \ with these IDs. If unspecified, return all variants and no variant call\ \ objects." + nullable: true + deprecated: true items: type: string commonCropNames: @@ -7518,15 +7750,19 @@ components: description: |- **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472
Only return variants on this reference. + nullable: true example: 120a2d5c + deprecated: true referenceDbIds: type: array description: The unique identifier representing a genotype `Reference` + nullable: true items: type: string referenceSetDbIds: type: array description: The unique identifier representing a genotype `ReferenceSet` + nullable: true items: type: string start: @@ -7561,11 +7797,13 @@ components: variantDbIds: type: array description: A list of IDs which uniquely identify `Variants` + nullable: true items: type: string variantSetDbIds: type: array description: A list of IDs which uniquely identify `VariantSets` + nullable: true items: type: string VariantSetRequest: @@ -8050,6 +8288,30 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/Sample" + SeedLotTransactionListResponse: + description: OK + content: + application/json: + schema: + title: SeedLotTransactionListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/SeedLotTransaction" CallSetListResponse: description: OK content: @@ -8368,6 +8630,23 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/GenomeMap" + AlleleMatrixSingleResponse: + description: OK + content: + application/json: + schema: + title: AlleleMatrixSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/AlleleMatrix" PersonListResponse: description: OK content: @@ -9021,8 +9300,37 @@ components: properties: data: type: array + description: "The `data` array is part of the BrAPI standard List\ + \ Response JSON container. `data` will always contain the primary\ + \ list of objects being returned by a BrAPI endpoint. `data`\ + \ is also the only array impacted by the `metadata.pagination`\ + \ details. When the pagination parameters change, the `data`\ + \ array will reflect those changes in the JSON response." items: $ref: "#/components/schemas/Call" + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed + into a single occurrence (false) + nullable: true + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele + calls. + nullable: true + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele + calls. + nullable: true + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + nullable: true + example: "." BreedingMethodSingleResponse: description: OK content: diff --git a/Specification/Generated/brapi_generated.graphqls b/Specification/Generated/brapi_generated.graphqls index 459fe2c8..94c89da9 100644 --- a/Specification/Generated/brapi_generated.graphqls +++ b/Specification/Generated/brapi_generated.graphqls @@ -118,80 +118,6 @@ interface ObservationUnitHierarchyLevel { levelOrder: Int } -""" -The exact level and level code of an observation unit. - -For more information on Observation Levels, please review the Observation Levels documentation. - -MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. -The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). -Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead." -""" -interface ObservationUnitLevel implements ObservationUnitHierarchyLevel { - """ - An ID code or number to represent a real thing that may or may not be an an observation unit. -
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. -
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. - """ - levelCode: String - """ - A name for this level - - **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** - - For more information on Observation Levels, please review the Observation Levels documentation. - """ - levelName: String - """ - `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers - are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). - - For more information on Observation Levels, please review the Observation Levels documentation. - """ - levelOrder: Int -} - -""" -Observation levels indicate the granularity level at which the measurements are taken. `levelName` -defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. -`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are -at the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify -this observation unit by each level of the hierarchy where it exists. - -For more information on Observation Levels, please review the Observation Levels documentation. - -**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** -""" -interface ObservationUnitLevelRelationship { - """ - An ID code or number to represent a real thing that may or may not be an an observation unit. -
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. -
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. - """ - levelCode: String - """ - A name for this level - - **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** - - For more information on Observation Levels, please review the Observation Levels documentation. - """ - levelName: String - """ - `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers - are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). - - For more information on Observation Levels, please review the Observation Levels documentation. - """ - levelOrder: Int - """ - The an observation unit -
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. -
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response. - """ - observationUnitDbIds: ID -} - "A unique combination of Trait, Method, and Scale to define a clear context for an Observation." interface Variable { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." @@ -251,6 +177,8 @@ interface Variable { union GeoJSONGeometry = GeoJSONPoint | GeoJSONPolygon +union Value = BooleanValue | NumberValue | StringValue + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." type AdditionalInfo { additionalInfo: AdditionalInfo @@ -334,6 +262,11 @@ type AvailableFormat { variantSetDbIds: ID } +"A value type wrapper for boolean" +type BooleanValue { + value: Boolean +} + "The techniques and protocol used to produce a Cross or Germplasm" type BreedingMethod { "A shortened version of the human readable name for a Breeding Method" @@ -364,11 +297,17 @@ type Call { If this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same. """ callSetDbIds: ID + genotype: ListValue "Genotype Metadata are additional layers of metadata associated with each genotype." genotypeMetadata: [GenotypeMetadata] "The value of this genotype call" genotypeValue: String """ + **Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491 +
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec. + """ + genotype_likelihood: [Float] + """ If this field is populated, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls on the same contig which have the same phase set string. """ @@ -380,8 +319,16 @@ type Call { } type CallListResponse { - data: [Call] - page: PageInfo + "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response." + dataDbId: [ID] + "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)" + expandHomozygotes: Boolean + "The string used as a separator for phased allele calls." + sepPhased: String + "The string used as a separator for unphased allele calls." + sepUnphased: String + "The string used as a representation for missing data." + unknownString: String } "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample" @@ -539,6 +486,11 @@ type Cross { plannedCrosDbIds: ID "The list of pollination events that occurred for this cross." pollinationEvents: [PollinationEvent] + """ + **Deprecated in v2.1** Please use `pollinationEvents`. Github issue number #265 +
The timestamp when the pollination took place + """ + pollinationTimeStamp: String } "A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'" @@ -726,8 +678,6 @@ MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept consta type EnvironmentParameter { "Human-readable value of the environment parameter (defined above) constant within the experiment" description: String - "Human-readable value of the environment parameter (defined above) constant within the experiment" - environmentParametersDbId: String """ Name of the environment parameter constant within the experiment @@ -759,6 +709,12 @@ An event is discrete occurrence at a particular time in the experiment. Events m type Event { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo + """ + **Deprecated in v2.1** Please use `eventDateRange.discreteDates`. Github issue number #440 +
A list of dates when the event occurred +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + """ + date: [String] "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" eventDateRange: EventDateRange "Internal database identifier" @@ -1158,7 +1114,7 @@ type Germplasm { } "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" -type GermplasmAttribute { +type GermplasmAttribute implements Attribute & Variable { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo "General category for the attribute. very similar to Trait class." @@ -1418,7 +1374,7 @@ type GermplasmOrigin { "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes." type GermplasmParent { "The parent germplasm" - parentGermplasmDbIds: ID + germplasmDbIds: ID """ The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. @@ -1522,8 +1478,6 @@ type KeyValuePair { "The date and time when this study was last modified" type LastUpdate { - "The ID which uniquely identifies a LastUpdate within the given database server" - lastUpdateDbId: String "Last update associated with a study" studyDbIds: ID "The timestamp of the update." @@ -1581,6 +1535,19 @@ type ListListResponse { page: PageInfo } +""" +**Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`. Github issue number #491 +
`ListValue` is a wrapper around a repeated field of values. +
The JSON representation for `ListValue` is JSON array. +""" +type ListValue { + """ + **Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`. Github issue number #491 +
Repeated field of dynamically typed values. + """ + values: [Value] +} + type ListsSearchResponse { data: [List] searchResultsDbId: String @@ -1874,6 +1841,11 @@ type Mutation { updateVariantSet(variantSetInput: VariantSetInput): VariantSet } +"A value type wrapper for number" +type NumberValue { + value: Float +} + "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." type Observation { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." @@ -1984,6 +1956,80 @@ type ObservationUnit { trialDbIds: ID } +""" +The exact level and level code of an observation unit. + +For more information on Observation Levels, please review the Observation Levels documentation. + +MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. +The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). +Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead." +""" +type ObservationUnitLevel implements ObservationUnitHierarchyLevel { + """ + An ID code or number to represent a real thing that may or may not be an an observation unit. +
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. +
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. + """ + levelCode: String + """ + A name for this level + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelName: String + """ + `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers + are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelOrder: Int +} + +""" +Observation levels indicate the granularity level at which the measurements are taken. `levelName` +defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. +`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are +at the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify +this observation unit by each level of the hierarchy where it exists. + +For more information on Observation Levels, please review the Observation Levels documentation. + +**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** +""" +type ObservationUnitLevelRelationship { + """ + An ID code or number to represent a real thing that may or may not be an an observation unit. +
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. +
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. + """ + levelCode: String + """ + A name for this level + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelName: String + """ + `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers + are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelOrder: Int + """ + The an observation unit +
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. +
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response. + """ + observationUnitDbIds: ID +} + type ObservationUnitListResponse { data: [ObservationUnit] page: PageInfo @@ -2228,8 +2274,6 @@ type PedigreeNode {
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response. """ parents: [GermplasmParent] - "The ID which uniquely identifies a pedigree node" - pedigreeNodeDbId: String "The string representation of the pedigree for this germplasm in PURDY notation" pedigreeString: String """ @@ -2637,7 +2681,7 @@ type Reference { "The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from." sourceDivergence: Float "All known corresponding Germplasm" - sourceGermplasmDbId: [ID] + sourceGermplasm: [SourceGermplasm] "The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the `getReferenceBases()` method to obtain sequence bases for a `Reference` instead of attempting to retrieve this URI." sourceURI: String "An ontology term describing an attribute." @@ -2751,7 +2795,7 @@ type Sample { """ sampleDescription: String "The ID which uniquely identifies a group of `Samples`" - sampleGroupId: String + sampleGroupDbId: String "The human readable name of the `Sample`" sampleName: String """ @@ -2944,6 +2988,23 @@ type SeedLotsSearchResponse { searchResultsDbId: String } +"A reference to a Germplasm" +type SourceGermplasm { + """ + The ID which uniquely identifies a germplasm within the given database server +
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. + """ + germplasmDbId: String + """ + Name of the germplasm. It can be the preferred name and does not have to be unique. + + MCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space. + """ + germplasmName: String + "The Reference associated with this Source Germplasm" + referenceDbIds: ID +} + "The type of storage this germplasm is kept in at a genebank." type StorageType { """ @@ -2968,6 +3029,11 @@ type StorageType { germplasmDbIds: ID } +"A value type wrapper for string" +type StringValue { + value: String +} + type StudiesSearchResponse { data: [Study] searchResultsDbId: String @@ -3247,8 +3313,13 @@ type Variant { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfo alleleMatrices(alleleMatrixInput: AlleleMatrixInput, paging: PageInput): AlleleMatrixListResponse - "Set of Analysis descriptors for this VariantSet" - analysis: [String] + "The bases that appear instead of the reference bases. Multiple alternate alleles are possible." + alternateBases: [String] + """ + **Deprecated in v2.1** Please use `alternateBases`. Github issue number #549 +
The bases that appear instead of the reference bases. Multiple alternate alleles are possible. + """ + alternate_bases: [String] calls(callsInput: CallsInput, paging: PageInput): CallListResponse "Similar to \"cipos\", but for the variant's end position (which is derived from start + svlen)." ciend: [Int] @@ -3300,7 +3371,7 @@ type Variant { "A human readable name associated with a `Variant`" variantNames: [String] "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted." - variantSet(paging: PageInput, variantSetsInput: VariantSetsInput): VariantSetListResponse + variantSets(paging: PageInput, variantSetsInput: VariantSetsInput): VariantSetListResponse """ The "variant_type" is used to denote e.g. structural variants. Examples: @@ -3555,6 +3626,7 @@ enum MlsStatus { "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. " enum ParentType { + CLONAL FEMALE MALE POPULATION @@ -3624,7 +3696,9 @@ enum SampleType { "Name of the field to sort by." enum SortBy { + germplasmDbId locationDbId + observationVariableDbId programDbId programName seasonDbId @@ -3770,11 +3844,17 @@ input CallInput { If this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same. """ callSet: CallSetInput + genotype: ListValueInput "Genotype Metadata are additional layers of metadata associated with each genotype." genotypeMetadata: [GenotypeMetadataInput] "The value of this genotype call" genotypeValue: String """ + **Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491 +
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec. + """ + genotype_likelihood: [Float] + """ If this field is populated, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls on the same contig which have the same phase set string. """ @@ -3861,6 +3941,12 @@ input CallsInput { callSetDbIds: [String] "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)" expandHomozygotes: Boolean + """ + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + """ + pageToken: String "The string used as a separator for phased allele calls." sepPhased: String "The string used as a separator for unphased allele calls." @@ -4001,6 +4087,11 @@ input CrossInput { plannedCross: PlannedCrossInput "The list of pollination events that occurred for this cross." pollinationEvents: [PollinationEventInput] + """ + **Deprecated in v2.1** Please use `pollinationEvents`. Github issue number #265 +
The timestamp when the pollination took place + """ + pollinationTimeStamp: String } "The identifying information gor the parent material of a cross." @@ -4233,8 +4324,6 @@ MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept consta input EnvironmentParameterInput { "Human-readable value of the environment parameter (defined above) constant within the experiment" description: String - "Human-readable value of the environment parameter (defined above) constant within the experiment" - environmentParametersDbId: String """ Name of the environment parameter constant within the experiment @@ -4287,6 +4376,12 @@ An event is discrete occurrence at a particular time in the experiment. Events m input EventInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput + """ + **Deprecated in v2.1** Please use `eventDateRange.discreteDates`. Github issue number #440 +
A list of dates when the event occurred +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + """ + date: [String] "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" eventDateRange: EventDateRangeInput "Internal database identifier" @@ -5130,7 +5225,7 @@ input GermplasmOriginInput { "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes." input GermplasmParentInput { "The parent germplasm" - parentGermplasm: GermplasmInput + germplasm: GermplasmInput """ The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. @@ -5271,8 +5366,6 @@ input InstituteInput { "The date and time when this study was last modified" input LastUpdateInput { - "The ID which uniquely identifies a LastUpdate within the given database server" - lastUpdateDbId: String "Last update associated with a study" study: StudyInput "The timestamp of the update." @@ -5325,6 +5418,19 @@ input ListInput { listType: ListType } +""" +**Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`. Github issue number #491 +
`ListValue` is a wrapper around a repeated field of values. +
The JSON representation for `ListValue` is JSON array. +""" +input ListValueInput { + """ + **Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`. Github issue number #491 +
Repeated field of dynamically typed values. + """ + values: [ValueInput] +} + input ListsInput { """ The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. @@ -6387,8 +6493,6 @@ input PedigreeNodeInput {
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response. """ parents: [GermplasmParentInput] - "The ID which uniquely identifies a pedigree node" - pedigreeNodeDbId: String "The string representation of the pedigree for this germplasm in PURDY notation" pedigreeString: String """ @@ -6824,7 +6928,7 @@ input ReferenceInput { "The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from." sourceDivergence: Float "All known corresponding Germplasm" - sourceGermplasm: [GermplasmInput] + sourceGermplasm: [SourceGermplasmInput] "The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the `getReferenceBases()` method to obtain sequence bases for a `Reference` instead of attempting to retrieve this URI." sourceURI: String "An ontology term describing an attribute." @@ -7004,7 +7108,7 @@ input SampleInput { """ sampleDescription: String "The ID which uniquely identifies a group of `Samples`" - sampleGroupId: String + sampleGroupDbId: String "The human readable name of the `Sample`" sampleName: String """ @@ -7294,6 +7398,23 @@ input SeedLotsInput { seedLotDbIds: [String] } +"A reference to a Germplasm" +input SourceGermplasmInput { + """ + The ID which uniquely identifies a germplasm within the given database server +
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. + """ + germplasmDbId: String + """ + Name of the germplasm. It can be the preferred name and does not have to be unique. + + MCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space. + """ + germplasmName: String + "The Reference associated with this Source Germplasm" + reference: ReferenceInput +} + "The type of storage this germplasm is kept in at a genebank." input StorageTypeInput { """ @@ -7753,13 +7874,27 @@ input ValidValuesInput { scale: ScaleInput } +input ValueInput { + "Field for possible type 'Boolean'" + boolean: Boolean + "Field for possible type 'Float'" + float: Float + "Field for possible type 'String'" + string: String +} + "A `Variant` represents a change in DNA sequence relative to some reference. For example, a variant could represent a classic marker, a SNP, or an insertion. This is equivalent to a row in VCF." input VariantInput { "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." additionalInfo: AdditionalInfoInput alleleMatrices: [AlleleMatrixInput] - "Set of Analysis descriptors for this VariantSet" - analysis: [String] + "The bases that appear instead of the reference bases. Multiple alternate alleles are possible." + alternateBases: [String] + """ + **Deprecated in v2.1** Please use `alternateBases`. Github issue number #549 +
The bases that appear instead of the reference bases. Multiple alternate alleles are possible. + """ + alternate_bases: [String] calls: [CallInput] "Similar to \"cipos\", but for the variant's end position (which is derived from start + svlen)." ciend: [Int] @@ -7811,7 +7946,7 @@ input VariantInput { "A human readable name associated with a `Variant`" variantNames: [String] "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted." - variantSet: [VariantSetInput] + variantSets: [VariantSetInput] """ The "variant_type" is used to denote e.g. structural variants. Examples: diff --git a/Specification/Generated/brapi_generated.json b/Specification/Generated/brapi_generated.json index f4f58ac8..56c257bf 100644 --- a/Specification/Generated/brapi_generated.json +++ b/Specification/Generated/brapi_generated.json @@ -5,6 +5,203 @@ "version" : "2.1" }, "paths" : { + "/allelematrix" : { + "get" : { + "tags" : [ + "AlleleMatrix" + ], + "summary" : "Get a filtered list of AlleleMatrix", + "description" : "Get a list of AlleleMatrix", + "parameters" : [ + { + "name" : "preview", + "in" : "query", + "description" : "Default Value = false\n
\nIf 'preview' is set to true, then the server should only return the lists of 'callSetDbIds', \n'variantDbIds', and 'variantSetDbIds'. The server should not return any matrix data. This\nis intended to be a preview and give the client a sense of how large the matrix returned will be\n
\nIf 'preview' is set to false or not set (default), then the server should return all the matrix\ndata as requested.", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "dimensionVariantPage", + "in" : "query", + "description" : "The requested page number for the Variant dimension of the matrix", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "dimensionVariantPageSize", + "in" : "query", + "description" : "The requested page size for the Variant dimension of the matrix", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "dimensionCallSetPage", + "in" : "query", + "description" : "The requested page number for the CallSet dimension of the matrix", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "dimensionCallSetPageSize", + "in" : "query", + "description" : "The requested page size for the CallSet dimension of the matrix", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "dataMatrixNames", + "in" : "query", + "description" : "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "dataMatrixAbbreviations", + "in" : "query", + "description" : "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "positionRange", + "in" : "query", + "description" : "The postion range to search\n
\nUses the format \":-\" where is the chromosome name, is \nthe starting position of the range, and is the ending position of the range", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmName", + "in" : "query", + "description" : "A list of human readable `Germplasm` names", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmPUI", + "in" : "query", + "description" : "A list of permanent unique identifiers associated with `Germplasm`", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Germplasm` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "callSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "expandHomozygotes", + "in" : "query", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "sepPhased", + "in" : "query", + "description" : "The string used as a separator for phased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sepUnphased", + "in" : "query", + "description" : "The string used as a separator for unphased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "unknownString", + "in" : "query", + "description" : "The string used as a representation for missing data.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/AlleleMatrixSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, "/breedingmethods" : { "get" : { "tags" : [ @@ -110,6 +307,15 @@ "type" : "string" } }, + { + "name" : "pageToken", + "in" : "query", + "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { "$ref" : "#/components/parameters/pageToken" }, @@ -342,7 +548,7 @@ "additionalProperties" : { "$ref" : "#/components/schemas/CrossNewRequest" }, - "example" : "{_1={additionalInfo={}, crossAttributes=[{}], crossDbId=15187888, crossName=15a57676, crossType={}, crossingProject={}, externalReferences=[{}], parent1={}, parent2={}, plannedCross={}, pollinationEvents=[{}], observationUnits=[{}]}, _2={additionalInfo={}, crossAttributes=[{}], crossDbId=15187889, crossName=15a57677, crossType={}, crossingProject={}, externalReferences=[{}], parent1={}, parent2={}, plannedCross={}, pollinationEvents=[{}], observationUnits=[{}]}}" + "example" : "{_1={additionalInfo={}, crossAttributes=[{}], crossDbId=15187888, crossName=15a57676, crossType={}, crossingProject={}, externalReferences=[{}], parent1={}, parent2={}, plannedCross={}, pollinationTimeStamp=2020-08-12T18:10:40.413Z, pollinationEvents=[{}], observationUnits=[{}]}, _2={additionalInfo={}, crossAttributes=[{}], crossDbId=15187889, crossName=15a57677, crossType={}, crossingProject={}, externalReferences=[{}], parent1={}, parent2={}, plannedCross={}, pollinationTimeStamp=2020-08-12T18:10:40.413Z, pollinationEvents=[{}], observationUnits=[{}]}}" } } } @@ -3352,7 +3558,7 @@ "schema" : { "type" : "object", "additionalProperties" : { - "$ref" : "#/components/schemas/PlannedCross" + "$ref" : "#/components/schemas/PlannedCrossNewRequest" }, "example" : "{_1={additionalInfo={}, crossType={}, crossingProject={}, externalReferences=[{}], parent1={}, parent2={}, plannedCrossDbId=47edd16c, plannedCrossName=487acf5a, status={}, crosses=[{}]}, _2={additionalInfo={}, crossType={}, crossingProject={}, externalReferences=[{}], parent1={}, parent2={}, plannedCrossDbId=47edd16d, plannedCrossName=487acf5b, status={}, crosses=[{}]}}" } @@ -3391,7 +3597,7 @@ "schema" : { "type" : "array", "items" : { - "$ref" : "#/components/schemas/PlannedCross" + "$ref" : "#/components/schemas/PlannedCrossNewRequest" } } } @@ -4144,7 +4350,7 @@ "additionalProperties" : { "$ref" : "#/components/schemas/SampleNewRequest" }, - "example" : "{_1={additionalInfo={}, callSets=[{}], column=10, externalReferences=[{}], germplasm={}, observationUnit={}, plate={}, program={}, row=00358167, sampleBarcode=6a6db74b, sampleDescription=3388964f, sampleDbId=079d6d5e, sampleGroupId=70fcb311, sampleName=082a6b4c, samplePUI=08863647, sampleTimestamp=2020-08-12T18:10:40.413Z, sampleType=0889ec7d, study={}, takenBy=599da043, tissueType=4d105e22, trial={}, well=06bc78f3}, _2={additionalInfo={}, callSets=[{}], column=20, externalReferences=[{}], germplasm={}, observationUnit={}, plate={}, program={}, row=00358168, sampleBarcode=6a6db74c, sampleDescription=33889650, sampleDbId=079d6d5f, sampleGroupId=70fcb312, sampleName=082a6b4d, samplePUI=08863648, sampleTimestamp=2020-08-12T18:10:40.413Z, sampleType=0889ec7e, study={}, takenBy=599da044, tissueType=4d105e23, trial={}, well=06bc78f4}}" + "example" : "{_1={additionalInfo={}, callSets=[{}], column=10, externalReferences=[{}], germplasm={}, observationUnit={}, plate={}, program={}, row=00358167, sampleBarcode=6a6db74b, sampleDescription=3388964f, sampleDbId=079d6d5e, sampleGroupDbId=2455eef3, sampleName=082a6b4c, samplePUI=08863647, sampleTimestamp=2020-08-12T18:10:40.413Z, sampleType=0889ec7d, study={}, takenBy=599da043, tissueType=4d105e22, trial={}, well=06bc78f3}, _2={additionalInfo={}, callSets=[{}], column=20, externalReferences=[{}], germplasm={}, observationUnit={}, plate={}, program={}, row=00358168, sampleBarcode=6a6db74c, sampleDescription=33889650, sampleDbId=079d6d5f, sampleGroupDbId=2455eef4, sampleName=082a6b4d, samplePUI=08863648, sampleTimestamp=2020-08-12T18:10:40.413Z, sampleType=0889ec7e, study={}, takenBy=599da044, tissueType=4d105e23, trial={}, well=06bc78f4}}" } } } @@ -4724,7 +4930,9 @@ "studyType", "studyName", "studyLocation", - "programName" + "programName", + "germplasmDbId", + "observationVariableDbId" ] } }, @@ -4737,10 +4945,10 @@ "type" : "string", "description" : "Sort order direction. Ascending/Descending.", "enum" : [ - "asc", "ASC", - "desc", - "DESC" + "DESC", + "asc", + "desc" ] } }, @@ -5540,6 +5748,9 @@ "200" : { "$ref" : "#/components/responses/CallListResponse" }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -5548,9 +5759,6 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" - }, - "404" : { - "$ref" : "#/components/responses/404NotFound" } } } @@ -5713,6 +5921,9 @@ "200" : { "$ref" : "#/components/responses/LinkageGroupListResponse" }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -5721,9 +5932,6 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" - }, - "404" : { - "$ref" : "#/components/responses/404NotFound" } } } @@ -7394,6 +7602,52 @@ } } }, + "/seedlots/{seedLotDbId}/transactions" : { + "get" : { + "tags" : [ + "SeedLots" + ], + "summary" : "Get a filtered list of SeedLotTransaction", + "description" : "Get a list of SeedLotTransaction", + "parameters" : [ + { + "name" : "seedLotDbId", + "in" : "path", + "description" : "Unique DbId for the Seed Lot", + "required" : true, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotTransactionListResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, "/studies/{studyDbId}" : { "get" : { "tags" : [ @@ -7765,6 +8019,9 @@ "200" : { "$ref" : "#/components/responses/CallListResponse" }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -7773,9 +8030,6 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" - }, - "404" : { - "$ref" : "#/components/responses/404NotFound" } } } @@ -7890,6 +8144,9 @@ "200" : { "$ref" : "#/components/responses/CallListResponse" }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -7898,9 +8155,6 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" - }, - "404" : { - "$ref" : "#/components/responses/404NotFound" } } } @@ -7954,6 +8208,9 @@ "200" : { "$ref" : "#/components/responses/CallSetListResponse" }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -7962,9 +8219,6 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" - }, - "404" : { - "$ref" : "#/components/responses/404NotFound" } } } @@ -8012,6 +8266,9 @@ "200" : { "$ref" : "#/components/responses/VariantListResponse" }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -8020,9 +8277,6 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" - }, - "404" : { - "$ref" : "#/components/responses/404NotFound" } } } @@ -8050,7 +8304,7 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/AlleleMatrixListResponse" + "$ref" : "#/components/responses/AlleleMatrixSingleResponse" }, "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" @@ -9010,7 +9264,13 @@ ], "responses" : { "200" : { - "$ref" : "#/components/responses/AlleleMatrixListResponse" + "$ref" : "#/components/responses/AlleleMatrixSingleResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -9055,6 +9315,12 @@ "200" : { "$ref" : "#/components/responses/CallListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9098,6 +9364,12 @@ "200" : { "$ref" : "#/components/responses/CallSetListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9141,6 +9413,12 @@ "200" : { "$ref" : "#/components/responses/GermplasmListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9184,6 +9462,12 @@ "200" : { "$ref" : "#/components/responses/GermplasmAttributeListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9227,6 +9511,12 @@ "200" : { "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9270,6 +9560,12 @@ "200" : { "$ref" : "#/components/responses/ImageListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9313,6 +9609,12 @@ "200" : { "$ref" : "#/components/responses/ListListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9356,6 +9658,12 @@ "200" : { "$ref" : "#/components/responses/LocationListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9399,6 +9707,12 @@ "200" : { "$ref" : "#/components/responses/MarkerPositionListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9442,6 +9756,12 @@ "200" : { "$ref" : "#/components/responses/ObservationListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9485,6 +9805,12 @@ "200" : { "$ref" : "#/components/responses/ObservationUnitListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9528,6 +9854,12 @@ "200" : { "$ref" : "#/components/responses/ObservationVariableListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9571,6 +9903,12 @@ "200" : { "$ref" : "#/components/responses/PedigreeNodeListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9614,6 +9952,12 @@ "200" : { "$ref" : "#/components/responses/PersonListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9657,6 +10001,12 @@ "200" : { "$ref" : "#/components/responses/PlateListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9700,6 +10050,12 @@ "200" : { "$ref" : "#/components/responses/ProgramListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9743,6 +10099,12 @@ "200" : { "$ref" : "#/components/responses/ReferenceListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9786,6 +10148,12 @@ "200" : { "$ref" : "#/components/responses/ReferenceSetListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9829,6 +10197,12 @@ "200" : { "$ref" : "#/components/responses/SampleListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9872,6 +10246,12 @@ "200" : { "$ref" : "#/components/responses/StudyListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9915,6 +10295,12 @@ "200" : { "$ref" : "#/components/responses/TrialListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9958,6 +10344,12 @@ "200" : { "$ref" : "#/components/responses/VariantListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -10001,6 +10393,12 @@ "200" : { "$ref" : "#/components/responses/VariantSetListResponse" }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -10053,8 +10451,19 @@ "nullable" : true }, "AlleleMatrix" : { + "required" : [ + "callSetDbIds", + "variantSetDbIds" + ], "type" : "object", "properties" : { + "callSetDbIds" : { + "type" : "array", + "description" : "A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case.", + "items" : { + "type" : "string" + } + }, "dataMatrices" : { "type" : "array", "description" : "The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows.", @@ -10090,6 +10499,21 @@ "type" : "string", "description" : "The string used as a representation for missing data.", "nullable" : true + }, + "variantDbIds" : { + "type" : "array", + "description" : "A list of unique identifiers for the Variants contained in the matrix response. This array should match the ordering for rows in the matrix.", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "A list of unique identifiers for the VariantSets contained in the matrix response. A VariantSet is a data set originating from a sequencing event. Often, users will only be interested in data from a single VariantSet, but in some cases a user might be interested in a matrix with data from multiple VariantSets.", + "items" : { + "type" : "string" + } } }, "description" : "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." @@ -10131,20 +10555,40 @@ } }, "dataMatrixAbbreviations" : { - "type" : "array", - "description" : "`dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "type" : "string", + "description" : "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", "nullable" : true, - "items" : { - "type" : "string" - } + "example" : "GT,RD" }, "dataMatrixNames" : { - "type" : "array", - "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "type" : "string", + "description" : "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", "nullable" : true, - "items" : { - "type" : "string" - } + "example" : "Genotype,Read Depth" + }, + "dimensionCallSetPage" : { + "type" : "integer", + "description" : "The requested page number for the CallSet dimension of the matrix", + "format" : "int32", + "nullable" : true + }, + "dimensionCallSetPageSize" : { + "type" : "integer", + "description" : "The requested page size for the CallSet dimension of the matrix", + "format" : "int32", + "nullable" : true + }, + "dimensionVariantPage" : { + "type" : "integer", + "description" : "The requested page number for the Variant dimension of the matrix", + "format" : "int32", + "nullable" : true + }, + "dimensionVariantPageSize" : { + "type" : "integer", + "description" : "The requested page size for the Variant dimension of the matrix", + "format" : "int32", + "nullable" : true }, "expandHomozygotes" : { "type" : "boolean", @@ -10218,7 +10662,8 @@ "preview" : { "type" : "boolean", "description" : "Default Value = false\n
\nIf 'preview' is set to true, then the server should only return the lists of 'callSetDbIds', \n'variantDbIds', and 'variantSetDbIds'. The server should not return any matrix data. This\nis intended to be a preview and give the client a sense of how large the matrix returned will be\n
\nIf 'preview' is set to false or not set (default), then the server should return all the matrix\ndata as requested.", - "example" : true + "example" : true, + "default" : false }, "sampleDbIds" : { "type" : "array", @@ -10267,19 +10712,63 @@ "AlleleMatrixSearchRequest" : { "type" : "object", "properties" : { - "germplasmDbIds" : { + "callSetDbIds" : { "type" : "array", - "description" : "A list of IDs which uniquely identify `Germplasm` within the given database server", - "nullable" : true, + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", "items" : { "type" : "string" } }, - "preview" : { + "dataMatrixAbbreviations" : { + "type" : "string", + "description" : "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "nullable" : true, + "example" : "GT,RD" + }, + "dataMatrixNames" : { + "type" : "string", + "description" : "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "nullable" : true, + "example" : "Genotype,Read Depth" + }, + "dimensionCallSetPage" : { + "type" : "integer", + "description" : "The requested page number for the CallSet dimension of the matrix", + "format" : "int32", + "nullable" : true + }, + "dimensionCallSetPageSize" : { + "type" : "integer", + "description" : "The requested page size for the CallSet dimension of the matrix", + "format" : "int32", + "nullable" : true + }, + "dimensionVariantPage" : { + "type" : "integer", + "description" : "The requested page number for the Variant dimension of the matrix", + "format" : "int32", + "nullable" : true + }, + "dimensionVariantPageSize" : { + "type" : "integer", + "description" : "The requested page size for the Variant dimension of the matrix", + "format" : "int32", + "nullable" : true + }, + "expandHomozygotes" : { "type" : "boolean", - "description" : "Default Value = false\n
\nIf 'preview' is set to true, then the server should only return the lists of 'callSetDbIds', \n'variantDbIds', and 'variantSetDbIds'. The server should not return any matrix data. This\nis intended to be a preview and give the client a sense of how large the matrix returned will be\n
\nIf 'preview' is set to false or not set (default), then the server should return all the matrix\ndata as requested.", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "nullable" : true, "example" : true }, + "germplasmDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Germplasm` within the given database server", + "nullable" : true, + "items" : { + "type" : "string" + } + }, "germplasmNames" : { "type" : "array", "description" : "A list of human readable `Germplasm` names", @@ -10288,6 +10777,14 @@ "type" : "string" } }, + "germplasmPUIs" : { + "type" : "array", + "description" : "A list of permanent unique identifiers associated with `Germplasm`", + "nullable" : true, + "items" : { + "type" : "string" + } + }, "pagination" : { "type" : "array", "description" : "Pagination for the matrix", @@ -10319,20 +10816,6 @@ } } }, - "unknownString" : { - "type" : "string", - "description" : "The string used as a representation for missing data.", - "nullable" : true, - "example" : "." - }, - "germplasmPUIs" : { - "type" : "array", - "description" : "A list of permanent unique identifiers associated with `Germplasm`", - "nullable" : true, - "items" : { - "type" : "string" - } - }, "positionRanges" : { "type" : "array", "description" : "The postion range to search\n
\nUses the format \":-\" where is the chromosome name, is \nthe starting position of the range, and is the ending position of the range", @@ -10341,6 +10824,12 @@ "type" : "string" } }, + "preview" : { + "type" : "boolean", + "description" : "Default Value = false\n
\nIf 'preview' is set to true, then the server should only return the lists of 'callSetDbIds', \n'variantDbIds', and 'variantSetDbIds'. The server should not return any matrix data. This\nis intended to be a preview and give the client a sense of how large the matrix returned will be\n
\nIf 'preview' is set to false or not set (default), then the server should return all the matrix\ndata as requested.", + "example" : true, + "default" : false + }, "sampleDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Samples` within the given database server", @@ -10349,27 +10838,23 @@ "type" : "string" } }, - "variantSetDbIds" : { - "type" : "array", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "sepPhased" : { + "type" : "string", + "description" : "The string used as a separator for phased allele calls.", "nullable" : true, - "items" : { - "type" : "string" - } + "example" : "|" }, - "dataMatrixAbbreviations" : { - "type" : "array", - "description" : "`dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "sepUnphased" : { + "type" : "string", + "description" : "The string used as a separator for unphased allele calls.", "nullable" : true, - "items" : { - "type" : "string" - } + "example" : "/" }, - "expandHomozygotes" : { - "type" : "boolean", - "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "unknownString" : { + "type" : "string", + "description" : "The string used as a representation for missing data.", "nullable" : true, - "example" : true + "example" : "." }, "variantDbIds" : { "type" : "array", @@ -10379,32 +10864,13 @@ "type" : "string" } }, - "callSetDbIds" : { - "type" : "array", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "items" : { - "type" : "string" - } - }, - "dataMatrixNames" : { + "variantSetDbIds" : { "type" : "array", - "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", "nullable" : true, "items" : { "type" : "string" } - }, - "sepPhased" : { - "type" : "string", - "description" : "The string used as a separator for phased allele calls.", - "nullable" : true, - "example" : "|" - }, - "sepUnphased" : { - "type" : "string", - "description" : "The string used as a separator for unphased allele calls.", - "nullable" : true, - "example" : "/" } }, "description" : "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." @@ -10454,12 +10920,6 @@ "description" : "The time at which this record was last updated, in ISO 8601 format.", "format" : "date-time", "nullable" : true - }, - "variantSetDbId" : { - "type" : "string" - }, - "variantSetName" : { - "type" : "string" } }, "description" : "An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used." @@ -10467,11 +10927,9 @@ "Attribute" : { "required" : [ "attributeName", - "methodDbId", - "methodName", - "scaleDbId", - "scaleName", - "traitName" + "method", + "scale", + "trait" ], "type" : "object", "properties" : { @@ -10549,26 +11007,14 @@ "description" : "2 letter ISO 639-1 code for the language of submission of the variable.", "nullable" : true }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" + "method" : { + "$ref" : "#/components/schemas/Method" }, "ontologyReference" : { "$ref" : "#/components/schemas/OntologyReference" }, - "scaleDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" + "scale" : { + "$ref" : "#/components/schemas/Scale" }, "scientist" : { "type" : "string", @@ -10594,14 +11040,8 @@ "type" : "string" } }, - "traitDbId" : { - "type" : "string" - }, - "traitName" : { - "type" : "string" - }, - "traitPUI" : { - "type" : "string" + "trait" : { + "$ref" : "#/components/schemas/Trait" } } }, @@ -10657,12 +11097,6 @@ "type" : "string", "description" : "The string used as a representation for missing data.", "nullable" : true - }, - "variantSetDbId" : { - "type" : "string" - }, - "variantSetName" : { - "type" : "string" } }, "description" : "Each 'availableFormat' object is a pairing of dataFormat and fileFormat. These must be communicated in pairs because they are not independent parameters and sometimes one influences the other." @@ -10739,6 +11173,14 @@ "callSetName" : { "type" : "string" }, + "genotype" : { + "deprecated" : true, + "allOf" : [ + { + "$ref" : "#/components/schemas/ListValue" + } + ] + }, "genotypeMetadata" : { "type" : "array", "description" : "Genotype Metadata are additional layers of metadata associated with each genotype.", @@ -10750,6 +11192,15 @@ "type" : "string", "description" : "The value of this genotype call" }, + "genotype_likelihood" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `genotypeMetadata`. Github issue number #491 \n
The genotype likelihood for this variant call. Each array entry represents how likely a specific genotype is for this call as log10(P(data | genotype)), analogous to the GL tag in the VCF spec. The value ordering is defined by the GL tag in the VCF spec.", + "deprecated" : true, + "items" : { + "type" : "number", + "format" : "double" + } + }, "phaseSet" : { "type" : "string", "description" : "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string." @@ -10757,6 +11208,9 @@ "variantDbId" : { "type" : "string" }, + "variantName" : { + "type" : "string" + }, "variantSetDbId" : { "type" : "string" }, @@ -10783,6 +11237,10 @@ "nullable" : true, "example" : true }, + "pageToken" : { + "type" : "string", + "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response." + }, "sepPhased" : { "type" : "string", "description" : "The string used as a separator for phased allele calls.", @@ -10822,41 +11280,35 @@ "CallSearchRequest" : { "type" : "object", "properties" : { - "variantSetDbIds" : { + "callSetDbIds" : { "type" : "array", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", "nullable" : true, "items" : { "type" : "string" } }, - "unknownString" : { - "type" : "string", - "description" : "The string used as a representation for missing data.", - "nullable" : true, - "example" : "." - }, "expandHomozygotes" : { "type" : "boolean", "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", "nullable" : true, "example" : true }, - "variantDbIds" : { - "type" : "array", - "description" : "A list of IDs which uniquely identify `Variant` within the given database server", - "nullable" : true, - "items" : { - "type" : "string" - } + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 }, - "callSetDbIds" : { - "type" : "array", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", - "nullable" : true, - "items" : { - "type" : "string" - } + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "pageToken" : { + "type" : "string", + "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response." }, "sepPhased" : { "type" : "string", @@ -10869,6 +11321,28 @@ "description" : "The string used as a separator for unphased allele calls.", "nullable" : true, "example" : "/" + }, + "unknownString" : { + "type" : "string", + "description" : "The string used as a representation for missing data.", + "nullable" : true, + "example" : "." + }, + "variantDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Variant` within the given database server", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "nullable" : true, + "items" : { + "type" : "string" + } } }, "description" : "A `Call` represents the determination of genotype with respect to a particular `Variant`. \n\nIt may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named RS_1234 in a call set with the name NA_12345." @@ -10900,7 +11374,6 @@ "externalReferences" : { "type" : "array", "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "nullable" : true, "items" : { "$ref" : "#/components/schemas/ExternalReference" } @@ -10909,31 +11382,23 @@ "type" : "string", "nullable" : true }, - "sampleName" : { - "type" : "string", - "nullable" : true - }, - "samplePUI" : { - "type" : "string", - "nullable" : true - }, "studyDbId" : { "type" : "string", "nullable" : true }, - "studyName" : { - "type" : "string", - "nullable" : true - }, - "studyPUI" : { - "type" : "string", - "nullable" : true - }, "updated" : { "type" : "string", "description" : "The time at which this call set was last updated", "format" : "date-time", "nullable" : true + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "The IDs of the variantSets this callSet has calls in.", + "nullable" : true, + "items" : { + "type" : "string" + } } }, "description" : "A CallSet is a collection of Calls that were generated by the same analysis of the same Sample" @@ -11051,106 +11516,140 @@ "CallSetSearchRequest" : { "type" : "object", "properties" : { - "germplasmDbIds" : { + "callSetDbIds" : { "type" : "array", - "description" : "List of IDs which uniquely identify germplasm to search for", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", "nullable" : true, "items" : { "type" : "string" } }, - "germplasmNames" : { + "callSetNames" : { "type" : "array", - "description" : "List of human readable names to identify germplasm to search for", + "description" : "A list of human readable names associated with `CallSets`", "nullable" : true, "items" : { "type" : "string" } }, - "programNames" : { + "commonCropNames" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "commonCropNames" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "programDbIds" : { + "externalReferenceIds" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "trialDbIds" : { + "externalReferenceSources" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "sampleDbIds" : { + "germplasmDbIds" : { "type" : "array", - "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "description" : "List of IDs which uniquely identify germplasm to search for", "nullable" : true, "items" : { "type" : "string" } }, - "studyDbIds" : { + "germplasmNames" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "trialNames" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "variantSetDbIds" : { + "programNames" : { "type" : "array", - "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", - "nullable" : true, + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "callSetNames" : { + "sampleDbIds" : { "type" : "array", - "description" : "A list of human readable names associated with `CallSets`", + "description" : "A list of IDs which uniquely identify `Samples` within the given database server", "nullable" : true, "items" : { "type" : "string" } }, - "studyNames" : { + "sampleNames" : { + "type" : "array", + "description" : "A list of human readable names associated with `Samples`", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { "type" : "array", "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "sampleNames" : { + "trialDbIds" : { "type" : "array", - "description" : "A list of human readable names associated with `Samples`", - "nullable" : true, + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } }, - "callSetDbIds" : { + "trialNames" : { "type" : "array", - "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", "nullable" : true, "items" : { "type" : "string" @@ -11381,21 +11880,11 @@ "type" : "string", "nullable" : true }, - "germplasmPUI" : { - "type" : "string", - "nullable" : true - }, "mixturePercentage" : { "type" : "integer", "description" : "The percentage of the given germplasm in the seed lot mixture.", "format" : "int32", "nullable" : true - }, - "seedLotDbId" : { - "type" : "string" - }, - "seedLotName" : { - "type" : "string" } }, "description" : "The mixture of germplasm present in the seed lot. \n
If this seed lot only contains a single germplasm, the response should contain the name and DbId of that germplasm with a mixturePercentage value of 100 \n
If the seed lot contains a mixture of different germplasm, the response should contain the name and DbId every germplasm present. The mixturePercentage field should contain the ratio of each germplasm in the total mixture. All of the mixturePercentage values in this array should sum to equal 100." @@ -11453,12 +11942,6 @@ "type" : "string", "description" : "the value of a cross attribute", "nullable" : true - }, - "crossDbId" : { - "type" : "string" - }, - "crossName" : { - "type" : "string" } }, "description" : "A custom attribute associated with a cross. For example, if the crossing event occurred on a humid day, a user might record 'crossAttributeName':'Relative Humidity', 'crossAttributeValue':'80%'" @@ -11496,7 +11979,6 @@ "externalReferences" : { "type" : "array", "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "nullable" : true, "items" : { "$ref" : "#/components/schemas/ExternalReference" } @@ -11522,6 +12004,13 @@ "items" : { "$ref" : "#/components/schemas/PollinationEvent" } + }, + "pollinationTimeStamp" : { + "type" : "string", + "description" : "**Deprecated in v2.1** Please use `pollinationEvents`. Github issue number #265\n
The timestamp when the pollination took place", + "format" : "date-time", + "nullable" : true, + "deprecated" : true } }, "description" : "The identifiers and metadata represent that specific organisms have mated to produce offspring with particular traits or genes. The offspring of a Cross might be developed into a Germplasm if the desired traits are present." @@ -11537,10 +12026,6 @@ "type" : "string", "nullable" : true }, - "germplasmPUI" : { - "type" : "string", - "nullable" : true - }, "observationUnitDbId" : { "type" : "string", "nullable" : true @@ -11549,15 +12034,12 @@ "type" : "string", "nullable" : true }, - "observationUnitPUI" : { - "type" : "string", - "nullable" : true - }, "parentType" : { "$ref" : "#/components/schemas/ParentType" } }, - "description" : "The identifying information gor the parent material of a cross." + "description" : "The identifying information gor the parent material of a cross.", + "nullable" : true }, "CrossRequest" : { "type" : "object", @@ -11624,6 +12106,7 @@ "CrossType" : { "type" : "string", "description" : "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'.", + "nullable" : true, "enum" : [ "BIPARENTAL", "SELF", @@ -11846,12 +12329,15 @@ }, "DataType" : { "type" : "string", - "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", + "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", "enum" : [ - "string", - "integer", - "float", - "boolean" + "Code", + "Date", + "Duration", + "Nominal", + "Numerical", + "Ordinal", + "Text" ] }, "DatasetAuthorships" : { @@ -11876,15 +12362,6 @@ "type" : "string", "description" : "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository.", "nullable" : true - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" } }, "description" : "License and citation information for the data in this trial" @@ -11903,13 +12380,11 @@ "URL" : { "type" : "string", "description" : "The URL or URI to the documentation", - "format" : "uri", - "nullable" : true + "format" : "uri" }, "type" : { "type" : "string", "description" : "The type of documentation, which can be OBO Foundry, an RDF term or a webpage.", - "nullable" : true, "enum" : [ "OBO", "RDF", @@ -11940,15 +12415,6 @@ "type" : "string", "description" : "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", "nullable" : true - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" } }, "description" : "Identifier assigned to an accession by the material donor." @@ -11986,7 +12452,6 @@ "EnvironmentParameter" : { "required" : [ "description", - "environmentParametersDbId", "parameterName" ], "type" : "object", @@ -11995,10 +12460,6 @@ "type" : "string", "description" : "Human-readable value of the environment parameter (defined above) constant within the experiment" }, - "environmentParametersDbId" : { - "type" : "string", - "description" : "Human-readable value of the environment parameter (defined above) constant within the experiment" - }, "parameterName" : { "type" : "string", "description" : "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. " @@ -12008,15 +12469,6 @@ "description" : "URI pointing to an ontology class for the parameter", "nullable" : true }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, "unit" : { "type" : "string", "description" : "Unit of the value for this parameter", @@ -12050,6 +12502,16 @@ "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, + "date" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `eventDateRange.discreteDates`. Github issue number #440\n
A list of dates when the event occurred\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", + "nullable" : true, + "deprecated" : true, + "items" : { + "type" : "string", + "format" : "date-time" + } + }, "eventDateRange" : { "$ref" : "#/components/schemas/EventDateRange" }, @@ -12079,14 +12541,21 @@ "description" : "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology).", "nullable" : true }, + "observationUnitDbIds" : { + "type" : "array", + "description" : "A list of the affected observation units. If this parameter is not given, it is understood that the event affected all units in the study", + "nullable" : true, + "items" : { + "type" : "string" + } + }, "studyDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" + "type" : "string", + "nullable" : true } }, "description" : "An event is discrete occurrence at a particular time in the experiment. Events may be the realization of Treatments or parts of Treatments, or may be confounding to Treatments. \n
ICASA Management Events allow for the following types -> planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other" @@ -12109,9 +12578,6 @@ "format" : "date-time", "nullable" : true }, - "eventDbId" : { - "type" : "string" - }, "startDate" : { "type" : "string", "description" : "The beginning of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event.", @@ -12119,7 +12585,8 @@ "nullable" : true } }, - "description" : "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" + "description" : "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)", + "nullable" : true }, "EventParameter" : { "type" : "object", @@ -12134,13 +12601,12 @@ "description" : "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter.", "nullable" : true }, - "eventDbId" : { - "type" : "string" - }, "key" : { "type" : "string", "description" : "**Deprecated in v2.1** Please use `name`. Github issue number #440 \n
Specifies the relationship between the event and the given property. E.g. fertilizer, operator", - "example" : "operator" + "nullable" : true, + "example" : "operator", + "deprecated" : true }, "name" : { "type" : "string", @@ -12150,7 +12616,9 @@ "rdfValue" : { "type" : "string", "description" : "**Deprecated in v2.1** Please use `code`. Github issue number #440 \nThe external reference ID. Could be a simple string or a URI.", - "nullable" : true + "nullable" : true, + "deprecated" : true }, "referenceId" : { "type" : "string", @@ -12277,6 +12738,7 @@ "externalReferenceIDs" : { "type" : "array", "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } @@ -12502,16 +12964,19 @@ "type" : { "type" : "string", "description" : "The literal string \"Feature\"", - "example" : "Feature" + "example" : "Feature", + "default" : "Feature" } }, - "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "nullable" : true }, "GeoJSONGeometry" : { + "nullable" : true, "oneOf" : [ { "required" : [ - "coordinateDbIds", + "coordinates", "type" ], "type" : "object", @@ -12525,14 +12990,15 @@ }, "type" : { "type" : "string", - "description" : "The literal string \"Point\"" + "description" : "The literal string \"Point\"", + "default" : "Point" } }, "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." }, { "required" : [ - "coordinateDbIds", + "coordinates", "type" ], "type" : "object", @@ -12552,7 +13018,8 @@ }, "type" : { "type" : "string", - "description" : "The literal string \"Polygon\"" + "description" : "The literal string \"Polygon\"", + "default" : "Polygon" } }, "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." @@ -12561,7 +13028,7 @@ }, "GeoJSONPoint" : { "required" : [ - "coordinateDbIds", + "coordinates", "type" ], "type" : "object", @@ -12575,14 +13042,15 @@ }, "type" : { "type" : "string", - "description" : "The literal string \"Point\"" + "description" : "The literal string \"Point\"", + "default" : "Point" } }, "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." }, "GeoJSONPolygon" : { "required" : [ - "coordinateDbIds", + "coordinates", "type" ], "type" : "object", @@ -12602,7 +13070,8 @@ }, "type" : { "type" : "string", - "description" : "The literal string \"Polygon\"" + "description" : "The literal string \"Polygon\"", + "default" : "Polygon" } }, "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element." @@ -12622,16 +13091,26 @@ "imageName" : { "type" : "string" }, + "imagePUI" : { + "type" : "string" + }, "observationDbId" : { "type" : "string" }, + "observationName" : { + "type" : "string" + }, + "observationPUI" : { + "type" : "string" + }, "observationUnit" : { "$ref" : "#/components/schemas/ObservationUnitPosition" }, "type" : { "type" : "string", "description" : "The literal string \"Feature\"", - "example" : "Feature" + "example" : "Feature", + "default" : "Feature" } } }, @@ -12675,11 +13154,9 @@ "GermplasmAttributeNewRequest" : { "required" : [ "attributeName", - "methodDbId", - "methodName", - "scaleDbId", - "scaleName", - "traitName" + "method", + "scale", + "trait" ], "type" : "object", "properties" : { @@ -12706,14 +13183,6 @@ "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", "example" : "http://my-traits.com/trait/CO_123:0008012" }, - "attributeValueDbIds" : { - "type" : "array", - "description" : "attributeValues", - "nullable" : true, - "items" : { - "type" : "string" - } - }, "commonCropName" : { "type" : "string", "description" : "Crop name (examples: \"Maize\", \"Wheat\")", @@ -12761,26 +13230,14 @@ "description" : "2 letter ISO 639-1 code for the language of submission of the variable.", "nullable" : true }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" + "method" : { + "$ref" : "#/components/schemas/Method" }, "ontologyReference" : { "$ref" : "#/components/schemas/OntologyReference" }, - "scaleDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" + "scale" : { + "$ref" : "#/components/schemas/Scale" }, "scientist" : { "type" : "string", @@ -12806,14 +13263,8 @@ "type" : "string" } }, - "traitDbId" : { - "type" : "string" - }, - "traitName" : { - "type" : "string" - }, - "traitPUI" : { - "type" : "string" + "trait" : { + "$ref" : "#/components/schemas/Trait" } }, "description" : "The Trait-Method-Scale definition for a variable, specifically variables related to Germplasm. Similar to an ObservationVariable, but related to a Germplasm instead of an ObservationUnit" @@ -12949,6 +13400,7 @@ "studyDbId" : { "type" : "array", "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "deprecated" : true, "items" : { "type" : "string" } @@ -13042,46 +13494,41 @@ "GermplasmAttributeSearchRequest" : { "type" : "object", "properties" : { - "germplasmNames" : { + "attributeCategories" : { "type" : "array", - "description" : "List of human readable names to identify germplasm to search for", + "description" : "General category for the attribute. very similar to Trait class.", "nullable" : true, "items" : { "type" : "string" } }, - "methodDbIds" : { - "type" : "array", - "description" : "List of methods to filter search results", - "items" : { - "type" : "string" - } - }, - "programNames" : { + "attributeDbIds" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of Germplasm Attribute IDs to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "attributeDbIds" : { + "attributeNames" : { "type" : "array", - "description" : "List of Germplasm Attribute IDs to search for", + "description" : "List of human readable Germplasm Attribute names to search for", "nullable" : true, "items" : { "type" : "string" } }, - "trialNames" : { + "attributePUIs" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", + "nullable" : true, "items" : { "type" : "string" } }, - "studyDbId" : { + "commonCropNames" : { "type" : "array", - "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } @@ -13093,117 +13540,123 @@ "$ref" : "#/components/schemas/TraitDataType" } }, - "attributeNames" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "List of human readable Germplasm Attribute names to search for", - "nullable" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "methodPUIs" : { + "externalReferenceIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "scalePUIs" : { + "externalReferenceSources" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "traitAttributes" : { + "germplasmDbIds" : { "type" : "array", - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "scaleDbIds" : { + "germplasmNames" : { "type" : "array", - "description" : "The unique identifier for a Scale", + "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "traitEntityPUIs" : { + "methodDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "description" : "List of methods to filter search results", "items" : { "type" : "string" } }, - "germplasmDbIds" : { + "methodNames" : { "type" : "array", - "description" : "List of IDs which uniquely identify germplasm to search for", - "nullable" : true, + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", "items" : { "type" : "string" } }, - "methodNames" : { + "methodPUIs" : { "type" : "array", - "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", "items" : { "type" : "string" } }, - "scaleNames" : { + "ontologyDbIds" : { "type" : "array", - "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "description" : "List of ontology IDs to search for", "items" : { "type" : "string" } }, - "traitPUIs" : { - "type" : "array", - "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", - "items" : { - "type" : "string" - } + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 }, - "traitClasses" : { + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { "type" : "array", - "description" : "List of trait classes to filter search results", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "attributeCategories" : { + "programNames" : { "type" : "array", - "description" : "General category for the attribute. very similar to Trait class.", - "nullable" : true, + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "commonCropNames" : { + "scaleDbIds" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "The unique identifier for a Scale", "items" : { "type" : "string" } }, - "programDbIds" : { + "scaleNames" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", "items" : { "type" : "string" } }, - "trialDbIds" : { + "scalePUIs" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", "items" : { "type" : "string" } }, - "ontologyDbIds" : { + "studyDbId" : { "type" : "array", - "description" : "List of ontology IDs to search for", + "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "deprecated" : true, "items" : { "type" : "string" } @@ -13222,6 +13675,27 @@ "type" : "string" } }, + "traitAttributePUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } + }, + "traitAttributes" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "items" : { + "type" : "string" + } + }, + "traitClasses" : { + "type" : "array", + "description" : "List of trait classes to filter search results", + "items" : { + "type" : "string" + } + }, "traitDbIds" : { "type" : "array", "description" : "The unique identifier for a Trait", @@ -13229,10 +13703,16 @@ "type" : "string" } }, - "attributePUIs" : { + "traitEntities" : { "type" : "array", - "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", - "nullable" : true, + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "items" : { + "type" : "string" + } + }, + "traitEntityPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", "items" : { "type" : "string" } @@ -13244,16 +13724,23 @@ "type" : "string" } }, - "traitAttributePUIs" : { + "traitPUIs" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", "items" : { "type" : "string" } }, - "traitEntities" : { + "trialDbIds" : { "type" : "array", - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } @@ -13295,10 +13782,6 @@ "type" : "string", "nullable" : true }, - "attributePUI" : { - "type" : "string", - "nullable" : true - }, "determinedDate" : { "type" : "string", "description" : "The date the value of this attribute was determined for a given germplasm", @@ -13321,10 +13804,6 @@ "type" : "string", "nullable" : true }, - "germplasmPUI" : { - "type" : "string", - "nullable" : true - }, "value" : { "type" : "string", "description" : "The value of this attribute for a given germplasm", @@ -13450,70 +13929,86 @@ "GermplasmAttributeValueSearchRequest" : { "type" : "object", "properties" : { - "germplasmDbIds" : { + "attributeDbIds" : { "type" : "array", - "description" : "List of IDs which uniquely identify germplasm to search for", + "description" : "List of Germplasm Attribute IDs to search for", "nullable" : true, "items" : { "type" : "string" } }, - "germplasmNames" : { + "attributeNames" : { "type" : "array", - "description" : "List of human readable names to identify germplasm to search for", + "description" : "List of human readable Germplasm Attribute names to search for", "nullable" : true, "items" : { "type" : "string" } }, - "methodDbIds" : { + "attributeValueDbIds" : { "type" : "array", - "description" : "List of methods to filter search results", + "description" : "List of Germplasm Attribute Value IDs to search for", "nullable" : true, "items" : { "type" : "string" } }, - "traitClasses" : { + "commonCropNames" : { "type" : "array", - "description" : "List of trait classes to filter search results", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "dataTypes" : { + "type" : "array", + "description" : "List of scale data types to filter search results", "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "externalReferenceIDs" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "programNames" : { + "externalReferenceIds" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "commonCropNames" : { + "externalReferenceSources" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "programDbIds" : { + "germplasmDbIds" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "attributeValueDbIds" : { + "germplasmNames" : { "type" : "array", - "description" : "List of Germplasm Attribute Value IDs to search for", + "description" : "List of human readable names to identify germplasm to search for", "nullable" : true, "items" : { "type" : "string" } }, - "attributeDbIds" : { + "methodDbIds" : { "type" : "array", - "description" : "List of Germplasm Attribute IDs to search for", + "description" : "List of methods to filter search results", "nullable" : true, "items" : { "type" : "string" @@ -13527,33 +14022,51 @@ "type" : "string" } }, - "dataTypes" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { "type" : "array", - "description" : "List of scale data types to filter search results", - "nullable" : true, + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { - "$ref" : "#/components/schemas/TraitDataType" + "type" : "string" } }, - "attributeNames" : { + "programNames" : { "type" : "array", - "description" : "List of human readable Germplasm Attribute names to search for", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "scaleDbIds" : { + "type" : "array", + "description" : "List of scales to filter search results", "nullable" : true, "items" : { "type" : "string" } }, - "traitDbIds" : { + "traitClasses" : { "type" : "array", - "description" : "List of trait unique ID to filter search results", + "description" : "List of trait classes to filter search results", "nullable" : true, "items" : { "type" : "string" } }, - "scaleDbIds" : { + "traitDbIds" : { "type" : "array", - "description" : "List of scales to filter search results", + "description" : "List of trait unique ID to filter search results", "nullable" : true, "items" : { "type" : "string" @@ -13564,20 +14077,16 @@ }, "GermplasmChild" : { "required" : [ - "germplasmDbId", - "germplasmName", - "germplasmPUI", + "childGermplasmDbId", + "childGermplasmName", "parentType" ], "type" : "object", "properties" : { - "germplasmDbId" : { + "childGermplasmDbId" : { "type" : "string" }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { + "childGermplasmName" : { "type" : "string" }, "parentType" : { @@ -13585,6 +14094,12 @@ }, "pedigreeNodeDbId" : { "type" : "string" + }, + "pedigreeNodeName" : { + "type" : "string" + }, + "pedigreeNodePUI" : { + "type" : "string" } }, "description" : "A germplasm reference that is a direct child of this germplasm. These represent edges in the tree, connecting to other nodes." @@ -13831,9 +14346,6 @@ "germplasmName" : { "type" : "string" }, - "germplasmPUI" : { - "type" : "string" - }, "instituteCode" : { "type" : "string", "description" : "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", @@ -13974,6 +14486,10 @@ "type" : "string", "nullable" : true }, + "breedingMethodPUI" : { + "type" : "string", + "nullable" : true + }, "collection" : { "type" : "string", "description" : "A specific panel/collection/population name this germplasm belongs to.", @@ -14056,14 +14572,6 @@ "description" : "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'.", "nullable" : true }, - "sampleDbIds" : { - "type" : "array", - "description" : "samples", - "nullable" : true, - "items" : { - "type" : "string" - } - }, "seedSource" : { "type" : "string", "description" : "An identifier for the source of the biological material\n
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: \"mother_accession X father_accession\", or, if father is unknown, as \"mother_accession X UNKNOWN\". For in situ material, the region of provenance may be used when an accession is not available.", @@ -14131,15 +14639,6 @@ }, "coordinates" : { "$ref" : "#/components/schemas/GeoJSON" - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" } }, "description" : "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm." @@ -14169,7 +14668,6 @@ "required" : [ "germplasmDbId", "germplasmName", - "germplasmPUI", "parentType" ], "type" : "object", @@ -14180,14 +14678,8 @@ "germplasmName" : { "type" : "string" }, - "germplasmPUI" : { - "type" : "string" - }, "parentType" : { "$ref" : "#/components/schemas/ParentType" - }, - "pedigreeNodeDbId" : { - "type" : "string" } }, "description" : "A germplasm reference that is a direct parent of this germplasm. These represent edges in the tree, connecting to other nodes." @@ -14353,14 +14845,6 @@ "GermplasmSearchRequest" : { "type" : "object", "properties" : { - "germplasmDbIds" : { - "type" : "array", - "description" : "List of IDs which uniquely identify germplasm to search for", - "nullable" : true, - "items" : { - "type" : "string" - } - }, "accessionNumbers" : { "type" : "array", "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", @@ -14369,111 +14853,141 @@ "type" : "string" } }, - "germplasmNames" : { + "binomialNames" : { "type" : "array", - "description" : "List of human readable names to identify germplasm to search for", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", "nullable" : true, "items" : { "type" : "string" } }, - "synonyms" : { + "collections" : { "type" : "array", - "description" : "List of alternative names or IDs used to reference this germplasm", + "description" : "A specific panel/collection/population name this germplasm belongs to.", "nullable" : true, "items" : { "type" : "string" } }, - "programNames" : { + "commonCropNames" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "commonCropNames" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "programDbIds" : { + "externalReferenceIds" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "trialDbIds" : { + "externalReferenceSources" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "germplasmPUIs" : { + "familyCodes" : { "type" : "array", - "description" : "List of Permanent Unique Identifiers to identify germplasm", + "description" : "A familyCode representing the family this germplasm belongs to.", "nullable" : true, "items" : { "type" : "string" } }, - "parentDbIds" : { + "genus" : { "type" : "array", - "description" : "Search for Germplasm with these parents", + "description" : "List of Genus names to identify germplasm", "nullable" : true, "items" : { "type" : "string" } }, - "studyDbIds" : { + "germplasmDbIds" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "trialNames" : { + "germplasmNames" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "familyCodes" : { + "germplasmPUIs" : { "type" : "array", - "description" : "A familyCode representing the family this germplasm belongs to.", + "description" : "List of Permanent Unique Identifiers to identify germplasm", "nullable" : true, "items" : { "type" : "string" } }, - "studyNames" : { + "instituteCodes" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "nullable" : true, "items" : { "type" : "string" } }, - "collections" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "parentDbIds" : { "type" : "array", - "description" : "A specific panel/collection/population name this germplasm belongs to.", + "description" : "Search for Germplasm with these parents", "nullable" : true, "items" : { "type" : "string" } }, - "genus" : { + "progenyDbIds" : { "type" : "array", - "description" : "List of Genus names to identify germplasm", + "description" : "Search for Germplasm with these children", "nullable" : true, "items" : { "type" : "string" } }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, "species" : { "type" : "array", "description" : "List of Species names to identify germplasm", @@ -14482,29 +14996,41 @@ "type" : "string" } }, - "binomialNames" : { + "studyDbIds" : { "type" : "array", - "description" : "List of the full binomial name (scientific name) to identify a germplasm", - "nullable" : true, + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } }, - "instituteCodes" : { + "studyNames" : { "type" : "array", - "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", - "nullable" : true, + "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "progenyDbIds" : { + "synonyms" : { "type" : "array", - "description" : "Search for Germplasm with these children", + "description" : "List of alternative names or IDs used to reference this germplasm", "nullable" : true, "items" : { "type" : "string" } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } } }, "description" : "The conceptual identifiers and metadata describing a genetically unique organism that is noteworthy in some way. Depending on context, a Germplasm might be synonymous with Accession, Line, or Genotype. Note that Germplasm is conceptual data, not necessarily associated to a real physical object, so Seed/Inventory Lots and Observation Units become physical instantiations of a particular Germplasm. Note a Germplasm is unique and noteworthy, so a Cross may or may not create a new Germplasm, since not every Cross is unique or noteworthy." @@ -14514,8 +15040,7 @@ "properties" : { "PUI" : { "type" : "string", - "description" : "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology.", - "nullable" : true + "description" : "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology." }, "description" : { "type" : "string", @@ -14523,7 +15048,8 @@ "nullable" : true } }, - "description" : "Short description of the facility in which the study was carried out." + "description" : "Short description of the facility in which the study was carried out.", + "nullable" : true }, "Image" : { "allOf" : [ @@ -14572,7 +15098,6 @@ "externalReferences" : { "type" : "array", "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "nullable" : true, "items" : { "$ref" : "#/components/schemas/ExternalReference" } @@ -14636,10 +15161,6 @@ "observationUnitName" : { "type" : "string", "nullable" : true - }, - "observationUnitPUI" : { - "type" : "string", - "nullable" : true } }, "description" : "The metadata for an image file that is connected to some phenotypic observation data." @@ -14771,93 +15292,112 @@ "ImageSearchRequest" : { "type" : "object", "properties" : { - "imageFileSizeMax" : { - "type" : "integer", - "description" : "A maximum image file size to search for.", - "format" : "int32", - "example" : 20000000 - }, - "imageFileNames" : { + "commonCropNames" : { "type" : "array", - "description" : "Image file names to search for.", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "imageTimeStampRangeStart" : { - "type" : "string", - "description" : "The earliest timestamp to search for.", - "format" : "date-time" - }, - "imageDbIds" : { + "descriptiveOntologyTerms" : { "type" : "array", - "description" : "A list of image Ids to search for", + "description" : "A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", "items" : { "type" : "string" } }, - "observationUnitDbIds" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "A set of observation unit identifiers to search for.", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "imageNames" : { + "externalReferenceIds" : { "type" : "array", - "description" : "Human readable names to search for.", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "imageWidthMin" : { - "type" : "integer", - "description" : "A minimum image width to search for.", - "format" : "int32", - "example" : 1280 - }, - "imageHeightMax" : { - "type" : "integer", - "description" : "A maximum image height to search for.", - "format" : "int32", - "example" : 1080 - }, - "programNames" : { + "externalReferenceSources" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "commonCropNames" : { + "imageDbIds" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "A list of image Ids to search for", "items" : { "type" : "string" } }, - "programDbIds" : { + "imageFileNames" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "Image file names to search for.", "items" : { "type" : "string" } }, - "descriptiveOntologyTerms" : { + "imageFileSizeMax" : { + "type" : "integer", + "description" : "A maximum image file size to search for.", + "format" : "int32", + "example" : 20000000 + }, + "imageFileSizeMin" : { + "type" : "integer", + "description" : "A minimum image file size to search for.", + "format" : "int32", + "example" : 1000 + }, + "imageHeightMax" : { + "type" : "integer", + "description" : "A maximum image height to search for.", + "format" : "int32", + "example" : 1080 + }, + "imageHeightMin" : { + "type" : "integer", + "description" : "A minimum image height to search for.", + "format" : "int32", + "example" : 720 + }, + "imageLocation" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + }, + "imageNames" : { "type" : "array", - "description" : "A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", + "description" : "Human readable names to search for.", "items" : { "type" : "string" } }, - "imageLocation" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" - }, "imageTimeStampRangeEnd" : { "type" : "string", "description" : "The latest timestamp to search for.", "format" : "date-time" }, + "imageTimeStampRangeStart" : { + "type" : "string", + "description" : "The earliest timestamp to search for.", + "format" : "date-time" + }, + "imageWidthMax" : { + "type" : "integer", + "description" : "A maximum image width to search for.", + "format" : "int32", + "example" : 1920 + }, + "imageWidthMin" : { + "type" : "integer", + "description" : "A minimum image width to search for.", + "format" : "int32", + "example" : 1280 + }, "mimeTypes" : { "type" : "array", "description" : "A set of image file types to search for.", @@ -14872,23 +15412,38 @@ "type" : "string" } }, - "imageHeightMin" : { + "observationUnitDbIds" : { + "type" : "array", + "description" : "A set of observation unit identifiers to search for.", + "items" : { + "type" : "string" + } + }, + "page" : { "type" : "integer", - "description" : "A minimum image height to search for.", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", "format" : "int32", - "example" : 720 + "example" : 0 }, - "imageFileSizeMin" : { + "pageSize" : { "type" : "integer", - "description" : "A minimum image file size to search for.", + "description" : "The size of the pages to be returned. Default is `1000`.", "format" : "int32", "example" : 1000 }, - "imageWidthMax" : { - "type" : "integer", - "description" : "A maximum image width to search for.", - "format" : "int32", - "example" : 1920 + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } } }, "description" : "The metadata for an image file that is connected to some phenotypic observation data." @@ -14918,24 +15473,8 @@ "description" : "The details of an Institute or other simular entity." }, "LastUpdate" : { - "required" : [ - "lastUpdateDbId" - ], "type" : "object", "properties" : { - "lastUpdateDbId" : { - "type" : "string", - "description" : "The ID which uniquely identifies a LastUpdate within the given database server" - }, - "studyDbId" : { - "type" : "string" - }, - "studyName" : { - "type" : "string" - }, - "studyPUI" : { - "type" : "string" - }, "timestamp" : { "type" : "string", "description" : "The timestamp of the update.", @@ -14948,7 +15487,8 @@ "nullable" : true } }, - "description" : "The date and time when this study was last modified" + "description" : "The date and time when this study was last modified", + "nullable" : true }, "LinkageGroup" : { "type" : "object", @@ -15051,6 +15591,9 @@ "description" : "Human readable name of a List Owner. (usually a user or person)", "nullable" : true }, + "listOwnerPersonDbId" : { + "type" : "string" + }, "listSize" : { "type" : "integer", "description" : "The number of elements in a List", @@ -15064,9 +15607,6 @@ }, "listType" : { "$ref" : "#/components/schemas/ListType" - }, - "personDbId" : { - "type" : "string" } }, "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." @@ -15167,19 +15707,6 @@ "ListSearchRequest" : { "type" : "object", "properties" : { - "dateCreatedRangeStart" : { - "type" : "string", - "description" : "Define the beginning for an interval of time and only include Lists that are created within this interval.", - "format" : "date-time", - "nullable" : true - }, - "programNames" : { - "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "items" : { - "type" : "string" - } - }, "commonCropNames" : { "type" : "array", "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", @@ -15187,12 +15714,17 @@ "type" : "string" } }, - "programDbIds" : { - "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "items" : { - "type" : "string" - } + "dateCreatedRangeEnd" : { + "type" : "string", + "description" : "Define the end for an interval of time and only include Lists that are created within this interval.", + "format" : "date-time", + "nullable" : true + }, + "dateCreatedRangeStart" : { + "type" : "string", + "description" : "Define the beginning for an interval of time and only include Lists that are created within this interval.", + "format" : "date-time", + "nullable" : true }, "dateModifiedRangeEnd" : { "type" : "string", @@ -15200,22 +15732,33 @@ "format" : "date-time", "nullable" : true }, - "listSources" : { + "dateModifiedRangeStart" : { + "type" : "string", + "description" : "Define the beginning for an interval of time and only include Lists that are modified within this interval.", + "format" : "date-time", + "nullable" : true + }, + "externalReferenceIDs" : { "type" : "array", - "description" : "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", - "nullable" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "listType" : { - "$ref" : "#/components/schemas/ListType" + "externalReferenceIds" : { + "type" : "array", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items" : { + "type" : "string" + } }, - "dateCreatedRangeEnd" : { - "type" : "string", - "description" : "Define the end for an interval of time and only include Lists that are created within this interval.", - "format" : "date-time", - "nullable" : true + "externalReferenceSources" : { + "type" : "array", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "items" : { + "type" : "string" + } }, "listDbIds" : { "type" : "array", @@ -15233,6 +15776,14 @@ "type" : "string" } }, + "listOwnerNames" : { + "type" : "array", + "description" : "An array of names for the people or entities who are responsible for a set of Lists", + "nullable" : true, + "items" : { + "type" : "string" + } + }, "listOwnerPersonDbIds" : { "type" : "array", "description" : "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", @@ -15241,19 +15792,42 @@ "type" : "string" } }, - "dateModifiedRangeStart" : { - "type" : "string", - "description" : "Define the beginning for an interval of time and only include Lists that are modified within this interval.", - "format" : "date-time", - "nullable" : true - }, - "listOwnerNames" : { + "listSources" : { "type" : "array", - "description" : "An array of names for the people or entities who are responsible for a set of Lists", + "description" : "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", "nullable" : true, "items" : { "type" : "string" } + }, + "listType" : { + "$ref" : "#/components/schemas/ListType" + }, + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } } }, "description" : "A List represents a collection of other BrAPI data objects. Typically these are custom lists generated by a user to keep track of interesting data. For example, a user might build a List of Germplasm that they have manually marked for further study." @@ -15274,6 +15848,32 @@ "samples" ] }, + "ListValue" : { + "type" : "object", + "properties" : { + "values" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`. Github issue number #491 \n
Repeated field of dynamically typed values.", + "deprecated" : true, + "items" : { + "oneOf" : [ + { + "type" : "boolean", + "format" : "boolean" + }, + { + "type" : "number", + "format" : "double" + }, + { + "type" : "string" + } + ] + } + } + }, + "description" : "**Deprecated in v2.1** Please use `genotypeValue` or `genotypeMetadata`. Github issue number #491 \n
`ListValue` is a wrapper around a repeated field of values.\n
The JSON representation for `ListValue` is JSON array." + }, "Location" : { "allOf" : [ { @@ -15373,17 +15973,25 @@ "description" : "The full name of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study.", "nullable" : true }, - "locationDbId" : { + "locationName" : { "type" : "string", + "description" : "A human readable name for a Location\n
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place." + }, + "locationType" : { + "type" : "string", + "description" : "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)", "nullable" : true }, - "locationName" : { + "parentLocationDbId" : { "type" : "string", "nullable" : true }, - "locationType" : { + "parentLocationName" : { + "type" : "string", + "nullable" : true + }, + "parentLocationPUI" : { "type" : "string", - "description" : "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)", "nullable" : true }, "siteStatus" : { @@ -15429,6 +16037,7 @@ "abbreviations" : { "type" : "array", "description" : "A list of shortened human readable names for a set of Locations", + "nullable" : true, "items" : { "type" : "string" } @@ -15436,11 +16045,13 @@ "altitudeMax" : { "type" : "number", "description" : "The maximum altitude to search for", + "nullable" : true, "example" : 200 }, "altitudeMin" : { "type" : "number", "description" : "The minimum altitude to search for", + "nullable" : true, "example" : 20 }, "commonCropNames" : { @@ -15456,6 +16067,7 @@ "countryCodes" : { "type" : "array", "description" : "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec", + "nullable" : true, "items" : { "type" : "string" } @@ -15463,6 +16075,7 @@ "countryNames" : { "type" : "array", "description" : "The full name of the country to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -15470,6 +16083,7 @@ "instituteAddresses" : { "type" : "array", "description" : "The street address of the institute to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -15477,6 +16091,7 @@ "instituteNames" : { "type" : "array", "description" : "The name of the institute to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -15498,6 +16113,7 @@ "locationTypes" : { "type" : "array", "description" : "The type of location this represents (ex. Breeding Location, Storage Location, etc)", + "nullable" : true, "items" : { "type" : "string" } @@ -15505,6 +16121,7 @@ "parentLocationDbIds" : { "type" : "array", "description" : "The unique identifier for a Location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "nullable" : true, "items" : { "type" : "string" } @@ -15512,6 +16129,7 @@ "parentLocationNames" : { "type" : "array", "description" : "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "nullable" : true, "items" : { "type" : "string" } @@ -15535,16 +16153,40 @@ "LocationSearchRequest" : { "type" : "object", "properties" : { - "locationDbIds" : { + "abbreviations" : { "type" : "array", - "description" : "The location ids to search for", + "description" : "A list of shortened human readable names for a set of Locations", + "nullable" : true, "items" : { "type" : "string" } }, - "locationNames" : { + "altitudeMax" : { + "type" : "number", + "description" : "The maximum altitude to search for", + "nullable" : true, + "example" : 200 + }, + "altitudeMin" : { + "type" : "number", + "description" : "The minimum altitude to search for", + "nullable" : true, + "example" : 20 + }, + "commonCropNames" : { "type" : "array", - "description" : "A human readable names to search for", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "coordinates" : { + "$ref" : "#/components/schemas/GeoJSONSearchArea" + }, + "countryCodes" : { + "type" : "array", + "description" : "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec", + "nullable" : true, "items" : { "type" : "string" } @@ -15552,35 +16194,37 @@ "countryNames" : { "type" : "array", "description" : "The full name of the country to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "coordinates" : { - "$ref" : "#/components/schemas/GeoJSONSearchArea" - }, - "programNames" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "altitudeMax" : { - "type" : "number", - "description" : "The maximum altitude to search for", - "example" : 200 + "externalReferenceIds" : { + "type" : "array", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items" : { + "type" : "string" + } }, - "commonCropNames" : { + "externalReferenceSources" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "programDbIds" : { + "instituteAddresses" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The street address of the institute to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -15588,20 +16232,21 @@ "instituteNames" : { "type" : "array", "description" : "The name of the institute to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "countryCodes" : { + "locationDbIds" : { "type" : "array", - "description" : "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec", + "description" : "The location ids to search for", "items" : { "type" : "string" } }, - "parentLocationNames" : { + "locationNames" : { "type" : "array", - "description" : "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "description" : "A human readable names to search for", "items" : { "type" : "string" } @@ -15609,32 +16254,49 @@ "locationTypes" : { "type" : "array", "description" : "The type of location this represents (ex. Breeding Location, Storage Location, etc)", + "nullable" : true, "items" : { "type" : "string" } }, + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, "parentLocationDbIds" : { "type" : "array", "description" : "The unique identifier for a Location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "nullable" : true, "items" : { "type" : "string" } }, - "instituteAddresses" : { + "parentLocationNames" : { "type" : "array", - "description" : "The street address of the institute to search for", + "description" : "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "nullable" : true, "items" : { "type" : "string" } }, - "altitudeMin" : { - "type" : "number", - "description" : "The minimum altitude to search for", - "example" : 20 + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } }, - "abbreviations" : { + "programNames" : { "type" : "array", - "description" : "A list of shortened human readable names for a set of Locations", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } @@ -15670,6 +16332,10 @@ "variantDbId" : { "type" : "string", "nullable" : true + }, + "variantName" : { + "type" : "string", + "nullable" : true } }, "description" : "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." @@ -15728,14 +16394,6 @@ "type" : "string" } }, - "variantDbIds" : { - "type" : "array", - "description" : "A list of IDs which uniquely identify `Variants` within the given database server", - "nullable" : true, - "items" : { - "type" : "string" - } - }, "mapDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `GenomeMaps` within the given database server", @@ -15757,6 +16415,26 @@ "format" : "int32", "nullable" : true, "example" : 250 + }, + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "variantDbIds" : { + "type" : "array", + "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "nullable" : true, + "items" : { + "type" : "string" + } } }, "description" : "A MarkerPosition describes a particular genetic marker at a specific position on a GenomeMap. A collection of MarkerPositions make up the data to represent a full GenomeMap." @@ -15767,7 +16445,6 @@ "dataType" : { "type" : "string", "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", - "nullable" : true, "enum" : [ "string", "integer", @@ -15777,19 +16454,11 @@ }, "fieldAbbreviation" : { "type" : "string", - "description" : "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"", - "nullable" : true + "description" : "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"" }, "fieldName" : { "type" : "string", - "description" : "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"", - "nullable" : true - }, - "variantSetDbId" : { - "type" : "string" - }, - "variantSetName" : { - "type" : "string" + "description" : "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"" } }, "description" : "Indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard " @@ -15974,10 +16643,6 @@ "type" : "string", "nullable" : true }, - "germplasmPUI" : { - "type" : "string", - "nullable" : true - }, "observationTimeStamp" : { "type" : "string", "description" : "The date and time when this observation was made", @@ -15992,10 +16657,6 @@ "type" : "string", "nullable" : true }, - "observationUnitPUI" : { - "type" : "string", - "nullable" : true - }, "observationVariableDbId" : { "type" : "string", "nullable" : true @@ -16016,15 +16677,15 @@ "type" : "string", "nullable" : true }, - "studyDbId" : { + "seasonPUI" : { "type" : "string", "nullable" : true }, - "studyName" : { + "studyDbId" : { "type" : "string", "nullable" : true }, - "studyPUI" : { + "studyName" : { "type" : "string", "nullable" : true }, @@ -16084,6 +16745,7 @@ "observationDbIds" : { "type" : "array", "description" : "The unique id of an Observation", + "nullable" : true, "items" : { "type" : "string" } @@ -16091,6 +16753,7 @@ "observationLevelRelationships" : { "type" : "array", "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "nullable" : true, "items" : { "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" } @@ -16098,6 +16761,7 @@ "observationLevels" : { "type" : "array", "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "nullable" : true, "items" : { "$ref" : "#/components/schemas/ObservationUnitLevel" } @@ -16105,16 +16769,19 @@ "observationTimeStampRangeEnd" : { "type" : "string", "description" : "Timestamp range end", - "format" : "date-time" + "format" : "date-time", + "nullable" : true }, "observationTimeStampRangeStart" : { "type" : "string", "description" : "Timestamp range start", - "format" : "date-time" + "format" : "date-time", + "nullable" : true }, "observationUnitDbIds" : { "type" : "array", "description" : "The unique id of an Observation Unit", + "nullable" : true, "items" : { "type" : "string" } @@ -16206,6 +16873,7 @@ "seasonDbIds" : { "type" : "array", "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "nullable" : true, "items" : { "type" : "string" } @@ -16243,67 +16911,69 @@ "ObservationSearchRequest" : { "type" : "object", "properties" : { - "germplasmDbIds" : { + "commonCropNames" : { "type" : "array", - "description" : "List of IDs which uniquely identify germplasm to search for", - "nullable" : true, + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "locationDbIds" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "The location ids to search for", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "locationNames" : { + "externalReferenceIds" : { "type" : "array", - "description" : "A human readable names to search for", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "germplasmNames" : { + "externalReferenceSources" : { "type" : "array", - "description" : "List of human readable names to identify germplasm to search for", - "nullable" : true, + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "observationUnitDbIds" : { + "germplasmDbIds" : { "type" : "array", - "description" : "The unique id of an Observation Unit", + "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "programNames" : { + "germplasmNames" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "seasonDbIds" : { + "locationDbIds" : { "type" : "array", - "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "description" : "The location ids to search for", "items" : { "type" : "string" } }, - "commonCropNames" : { + "locationNames" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "A human readable names to search for", "items" : { "type" : "string" } }, - "programDbIds" : { + "observationDbIds" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The unique id of an Observation", + "nullable" : true, "items" : { "type" : "string" } @@ -16311,6 +16981,7 @@ "observationLevelRelationships" : { "type" : "array", "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "nullable" : true, "items" : { "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" } @@ -16318,48 +16989,89 @@ "observationLevels" : { "type" : "array", "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "nullable" : true, "items" : { "$ref" : "#/components/schemas/ObservationUnitLevel" } }, - "observationVariablePUIs" : { + "observationTimeStampRangeEnd" : { + "type" : "string", + "description" : "Timestamp range end", + "format" : "date-time", + "nullable" : true + }, + "observationTimeStampRangeStart" : { + "type" : "string", + "description" : "Timestamp range start", + "format" : "date-time", + "nullable" : true + }, + "observationUnitDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "description" : "The unique id of an Observation Unit", + "nullable" : true, "items" : { "type" : "string" } }, - "trialDbIds" : { + "observationVariableDbIds" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "The DbIds of Variables to search for", "items" : { "type" : "string" } }, - "studyDbIds" : { + "observationVariableNames" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "The names of Variables to search for", "items" : { "type" : "string" } }, - "trialNames" : { + "observationVariablePUIs" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", "items" : { "type" : "string" } }, - "observationVariableNames" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { "type" : "array", - "description" : "The names of Variables to search for", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "observationDbIds" : { + "programNames" : { "type" : "array", - "description" : "The unique id of an Observation", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "seasonDbIds" : { + "type" : "array", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } @@ -16371,22 +17083,19 @@ "type" : "string" } }, - "observationVariableDbIds" : { + "trialDbIds" : { "type" : "array", - "description" : "The DbIds of Variables to search for", + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } }, - "observationTimeStampRangeStart" : { - "type" : "string", - "description" : "Timestamp range start", - "format" : "date-time" - }, - "observationTimeStampRangeEnd" : { - "type" : "string", - "description" : "Timestamp range end", - "format" : "date-time" + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } } }, "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." @@ -16405,15 +17114,6 @@ "description" : "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. ", "nullable" : true, "example" : "test-factor:dia2020-2-nv.lf" - }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" } }, "description" : "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor." @@ -16434,7 +17134,8 @@ "description" : "The ID which uniquely identifies an observation unit\n\nMIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. " } }, - "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples.", + "nullable" : true } ] }, @@ -16498,12 +17199,6 @@ }, "observationUnitDbId" : { "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" } }, "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** " @@ -16522,6 +17217,10 @@ "type" : "string", "nullable" : true }, + "crossPUI" : { + "type" : "string", + "nullable" : true + }, "externalReferences" : { "type" : "array", "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -16538,15 +17237,15 @@ "type" : "string", "nullable" : true }, - "germplasmPUI" : { + "locationDbId" : { "type" : "string", "nullable" : true }, - "locationDbId" : { + "locationName" : { "type" : "string", "nullable" : true }, - "locationName" : { + "locationPUI" : { "type" : "string", "nullable" : true }, @@ -16571,6 +17270,10 @@ "type" : "string", "nullable" : true }, + "programPUI" : { + "type" : "string", + "nullable" : true + }, "seedLotDbId" : { "type" : "string", "nullable" : true @@ -16579,15 +17282,15 @@ "type" : "string", "nullable" : true }, - "studyDbId" : { + "seedLotPUI" : { "type" : "string", "nullable" : true }, - "studyName" : { + "studyDbId" : { "type" : "string", "nullable" : true }, - "studyPUI" : { + "studyName" : { "type" : "string", "nullable" : true }, @@ -16606,13 +17309,10 @@ "trialName" : { "type" : "string", "nullable" : true - }, - "trialPUI" : { - "type" : "string", - "nullable" : true } }, - "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples.", + "nullable" : true }, "ObservationUnitPosition" : { "type" : "object", @@ -16646,15 +17346,6 @@ "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" } }, - "observationUnitDbId" : { - "type" : "string" - }, - "observationUnitName" : { - "type" : "string" - }, - "observationUnitPUI" : { - "type" : "string" - }, "positionCoordinateX" : { "type" : "string", "description" : "The X position coordinate for an observation unit. Different systems may use different coordinate systems.", @@ -16672,7 +17363,8 @@ "$ref" : "#/components/schemas/PositionCoordinateType" } }, - "description" : "All positional and layout information related to this Observation Unit" + "description" : "All positional and layout information related to this Observation Unit", + "nullable" : true }, "ObservationUnitRequest" : { "type" : "object", @@ -16703,6 +17395,7 @@ "includeObservations" : { "type" : "boolean", "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", + "nullable" : true, "example" : false }, "locationDbIds" : { @@ -16722,6 +17415,7 @@ "observationLevelRelationships" : { "type" : "array", "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "nullable" : true, "items" : { "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" } @@ -16729,6 +17423,7 @@ "observationLevels" : { "type" : "array", "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "nullable" : true, "items" : { "$ref" : "#/components/schemas/ObservationUnitLevel" } @@ -16736,6 +17431,7 @@ "observationUnitDbIds" : { "type" : "array", "description" : "The unique id of an observation unit", + "nullable" : true, "items" : { "type" : "string" } @@ -16792,6 +17488,7 @@ "observationUnitNames" : { "type" : "array", "description" : "The human readable identifier for an Observation Unit", + "nullable" : true, "items" : { "type" : "string" } @@ -16834,6 +17531,7 @@ "seasonDbIds" : { "type" : "array", "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "nullable" : true, "items" : { "type" : "string" } @@ -16854,31 +17552,74 @@ }, "trialDbIds" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } + } + } + }, + "ObservationUnitSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "externalReferenceIDs" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, + "items" : { + "type" : "string" + } + }, + "externalReferenceIds" : { + "type" : "array", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items" : { + "type" : "string" + } + }, + "externalReferenceSources" : { + "type" : "array", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "trialNames" : { + "germplasmDbIds" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } - } - } - }, - "ObservationUnitSearchRequest" : { - "type" : "object", - "properties" : { - "germplasmDbIds" : { + }, + "germplasmNames" : { "type" : "array", - "description" : "List of IDs which uniquely identify germplasm to search for", + "description" : "List of human readable names to identify germplasm to search for", "nullable" : true, "items" : { "type" : "string" } }, + "includeObservations" : { + "type" : "boolean", + "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", + "nullable" : true, + "example" : false + }, "locationDbIds" : { "type" : "array", "description" : "The location ids to search for", @@ -16893,120 +17634,117 @@ "type" : "string" } }, - "germplasmNames" : { + "observationLevelRelationships" : { "type" : "array", - "description" : "List of human readable names to identify germplasm to search for", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", "nullable" : true, "items" : { - "type" : "string" + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" } }, - "observationUnitNames" : { + "observationLevels" : { "type" : "array", - "description" : "The human readable identifier for an Observation Unit", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "nullable" : true, "items" : { - "type" : "string" + "$ref" : "#/components/schemas/ObservationUnitLevel" } }, "observationUnitDbIds" : { "type" : "array", "description" : "The unique id of an observation unit", + "nullable" : true, "items" : { "type" : "string" } }, - "programNames" : { + "observationUnitNames" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The human readable identifier for an Observation Unit", + "nullable" : true, "items" : { "type" : "string" } }, - "seasonDbIds" : { + "observationVariableDbIds" : { "type" : "array", - "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "description" : "The DbIds of Variables to search for", "items" : { "type" : "string" } }, - "commonCropNames" : { + "observationVariableNames" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "The names of Variables to search for", "items" : { "type" : "string" } }, - "programDbIds" : { + "observationVariablePUIs" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", "items" : { "type" : "string" } }, - "observationLevelRelationships" : { - "type" : "array", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", - "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" - } + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 }, - "observationLevels" : { - "type" : "array", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", - "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevel" - } + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 }, - "observationVariablePUIs" : { + "programDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "trialDbIds" : { + "programNames" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "includeObservations" : { - "type" : "boolean", - "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", - "example" : false - }, - "studyDbIds" : { + "seasonDbIds" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "nullable" : true, "items" : { "type" : "string" } }, - "trialNames" : { + "studyDbIds" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } }, - "observationVariableNames" : { + "studyNames" : { "type" : "array", - "description" : "The names of Variables to search for", + "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "studyNames" : { + "trialDbIds" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } }, - "observationVariableDbIds" : { + "trialNames" : { "type" : "array", - "description" : "The DbIds of Variables to search for", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } @@ -17035,12 +17773,10 @@ }, "ObservationVariableNewRequest" : { "required" : [ - "methodDbId", - "methodName", + "method", "observationVariableName", - "scaleDbId", - "scaleName", - "traitName" + "scale", + "trait" ], "type" : "object", "properties" : { @@ -17094,14 +17830,8 @@ "description" : "2 letter ISO 639-1 code for the language of submission of the variable.", "nullable" : true }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" + "method" : { + "$ref" : "#/components/schemas/Method" }, "observationVariableName" : { "type" : "string", @@ -17115,14 +17845,8 @@ "ontologyReference" : { "$ref" : "#/components/schemas/OntologyReference" }, - "scaleDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" + "scale" : { + "$ref" : "#/components/schemas/Scale" }, "scientist" : { "type" : "string", @@ -17148,14 +17872,8 @@ "type" : "string" } }, - "traitDbId" : { - "type" : "string" - }, - "traitName" : { - "type" : "string" - }, - "traitPUI" : { - "type" : "string" + "trait" : { + "$ref" : "#/components/schemas/Trait" } } }, @@ -17289,6 +18007,7 @@ "studyDbId" : { "type" : "array", "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "deprecated" : true, "items" : { "type" : "string" } @@ -17382,46 +18101,54 @@ "ObservationVariableSearchRequest" : { "type" : "object", "properties" : { - "methodDbIds" : { + "commonCropNames" : { "type" : "array", - "description" : "List of methods to filter search results", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "programNames" : { + "dataTypes" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of scale data types to filter search results", + "items" : { + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "externalReferenceIDs" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "observationVariablePUIs" : { + "externalReferenceIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "trialNames" : { + "externalReferenceSources" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "studyDbId" : { + "methodDbIds" : { "type" : "array", - "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "description" : "List of methods to filter search results", "items" : { "type" : "string" } }, - "dataTypes" : { + "methodNames" : { "type" : "array", - "description" : "List of scale data types to filter search results", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", "items" : { - "$ref" : "#/components/schemas/TraitDataType" + "type" : "string" } }, "methodPUIs" : { @@ -17431,107 +18158,120 @@ "type" : "string" } }, - "scalePUIs" : { + "observationVariableDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "description" : "The DbIds of Variables to search for", "items" : { "type" : "string" } }, - "traitAttributes" : { + "observationVariableNames" : { "type" : "array", - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "description" : "The names of Variables to search for", "items" : { "type" : "string" } }, - "scaleDbIds" : { + "observationVariablePUIs" : { "type" : "array", - "description" : "The unique identifier for a Scale", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", "items" : { "type" : "string" } }, - "traitEntityPUIs" : { + "ontologyDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "description" : "List of ontology IDs to search for", "items" : { "type" : "string" } }, - "methodNames" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { "type" : "array", - "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "scaleNames" : { + "programNames" : { "type" : "array", - "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "traitPUIs" : { + "scaleDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "description" : "The unique identifier for a Scale", "items" : { "type" : "string" } }, - "traitClasses" : { + "scaleNames" : { "type" : "array", - "description" : "List of trait classes to filter search results", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", "items" : { "type" : "string" } }, - "commonCropNames" : { + "scalePUIs" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", "items" : { "type" : "string" } }, - "programDbIds" : { + "studyDbId" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "deprecated" : true, "items" : { "type" : "string" } }, - "trialDbIds" : { + "studyDbIds" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } }, - "ontologyDbIds" : { + "studyNames" : { "type" : "array", - "description" : "List of ontology IDs to search for", + "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "studyDbIds" : { + "traitAttributePUIs" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", "items" : { "type" : "string" } }, - "observationVariableNames" : { + "traitAttributes" : { "type" : "array", - "description" : "The names of Variables to search for", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", "items" : { "type" : "string" } }, - "studyNames" : { + "traitClasses" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "List of trait classes to filter search results", "items" : { "type" : "string" } @@ -17543,6 +18283,20 @@ "type" : "string" } }, + "traitEntities" : { + "type" : "array", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "items" : { + "type" : "string" + } + }, + "traitEntityPUIs" : { + "type" : "array", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "items" : { + "type" : "string" + } + }, "traitNames" : { "type" : "array", "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", @@ -17550,23 +18304,23 @@ "type" : "string" } }, - "observationVariableDbIds" : { + "traitPUIs" : { "type" : "array", - "description" : "The DbIds of Variables to search for", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", "items" : { "type" : "string" } }, - "traitAttributePUIs" : { + "trialDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } }, - "traitEntities" : { + "trialNames" : { "type" : "array", - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } @@ -17674,6 +18428,9 @@ "ontologyName" : { "type" : "string" }, + "ontologyPUI" : { + "type" : "string" + }, "ontologyReferenceDbId" : { "type" : "string", "description" : "The ID which uniquely identifies a ontology reference", @@ -17685,7 +18442,8 @@ "nullable" : true } }, - "description" : "MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)." + "description" : "MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology \nMIAPPE V1.1 (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\nMIAPPE V1.1 (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", + "nullable" : false }, "OntologyRequest" : { "type" : "object", @@ -17785,15 +18543,14 @@ "MALE", "FEMALE", "SELF", - "POPULATION" + "POPULATION", + "CLONAL" ] }, "PedigreeNode" : { "required" : [ "germplasmDbId", - "germplasmName", - "germplasmPUI", - "pedigreeNodeDbId" + "germplasmName" ], "type" : "object", "properties" : { @@ -17801,16 +18558,16 @@ "$ref" : "#/components/schemas/AdditionalInfo" }, "breedingMethodDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "breedingMethodName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "crossingProjectDbId" : { - "type" : "string" - }, - "crossingProjectName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "crossingYear" : { "type" : "integer", @@ -17826,7 +18583,6 @@ "externalReferences" : { "type" : "array", "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "nullable" : true, "items" : { "$ref" : "#/components/schemas/ExternalReference" } @@ -17842,9 +18598,6 @@ "germplasmName" : { "type" : "string" }, - "germplasmPUI" : { - "type" : "string" - }, "parents" : { "type" : "array", "description" : "A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. \n
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response.", @@ -17853,11 +18606,6 @@ "$ref" : "#/components/schemas/GermplasmParent" } }, - "pedigreeNodeDbId" : { - "type" : "string", - "description" : "The ID which uniquely identifies a pedigree node", - "nullable" : true - }, "pedigreeString" : { "type" : "string", "description" : "The string representation of the pedigree for this germplasm in PURDY notation", @@ -17871,12 +18619,12 @@ "$ref" : "#/components/schemas/GermplasmChild" } }, - "siblingDbIds" : { + "siblings" : { "type" : "array", "description" : "A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Siblings share at least one parent with the given germplasm. \n
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response.", "nullable" : true, "items" : { - "type" : "string" + "$ref" : "#/components/schemas/Germplasm" } } }, @@ -17888,6 +18636,7 @@ "accessionNumbers" : { "type" : "array", "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "nullable" : true, "items" : { "type" : "string" } @@ -17895,6 +18644,7 @@ "binomialNames" : { "type" : "array", "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -17902,6 +18652,7 @@ "collections" : { "type" : "array", "description" : "A specific panel/collection/population name this germplasm belongs to.", + "nullable" : true, "items" : { "type" : "string" } @@ -17916,6 +18667,7 @@ "familyCodes" : { "type" : "array", "description" : "A familyCode representing the family this germplasm belongs to.", + "nullable" : true, "items" : { "type" : "string" } @@ -17923,6 +18675,7 @@ "genus" : { "type" : "array", "description" : "List of Genus names to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -17946,6 +18699,7 @@ "germplasmPUIs" : { "type" : "array", "description" : "List of Permanent Unique Identifiers to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -17953,26 +18707,31 @@ "includeFullTree" : { "type" : "boolean", "description" : "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", + "nullable" : true, "example" : true }, "includeParents" : { "type" : "boolean", "description" : "If this parameter is true, include the array of parents in the response", + "nullable" : true, "example" : true }, "includeProgeny" : { "type" : "boolean", "description" : "If this parameter is true, include the array of progeny in the response", + "nullable" : true, "example" : true }, "includeSiblings" : { "type" : "boolean", "description" : "If this parameter is true, include the array of siblings in the response", + "nullable" : true, "example" : true }, "instituteCodes" : { "type" : "array", "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "nullable" : true, "items" : { "type" : "string" } @@ -18006,6 +18765,7 @@ "species" : { "type" : "array", "description" : "List of Species names to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -18027,6 +18787,7 @@ "synonyms" : { "type" : "array", "description" : "List of alternative names or IDs used to reference this germplasm", + "nullable" : true, "items" : { "type" : "string" } @@ -18050,162 +18811,209 @@ "PedigreeNodeSearchRequest" : { "type" : "object", "properties" : { - "germplasmDbIds" : { + "accessionNumbers" : { "type" : "array", - "description" : "List of IDs which uniquely identify germplasm to search for", + "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", "nullable" : true, "items" : { "type" : "string" } }, - "accessionNumbers" : { + "binomialNames" : { "type" : "array", - "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "nullable" : true, "items" : { "type" : "string" } }, - "germplasmNames" : { + "collections" : { "type" : "array", - "description" : "List of human readable names to identify germplasm to search for", + "description" : "A specific panel/collection/population name this germplasm belongs to.", "nullable" : true, "items" : { "type" : "string" } }, - "includeParents" : { - "type" : "boolean", - "description" : "If this parameter is true, include the array of parents in the response", - "example" : true - }, - "synonyms" : { + "commonCropNames" : { "type" : "array", - "description" : "List of alternative names or IDs used to reference this germplasm", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "programNames" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "commonCropNames" : { + "externalReferenceIds" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "programDbIds" : { + "externalReferenceSources" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "trialDbIds" : { + "familyCodes" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "A familyCode representing the family this germplasm belongs to.", + "nullable" : true, "items" : { "type" : "string" } }, - "germplasmPUIs" : { + "genus" : { "type" : "array", - "description" : "List of Permanent Unique Identifiers to identify germplasm", + "description" : "List of Genus names to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } }, - "studyDbIds" : { + "germplasmDbIds" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "trialNames" : { + "germplasmNames" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "progenyDepth" : { - "type" : "integer", - "description" : "Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc)", - "format" : "int32", - "example" : 3 - }, - "familyCodes" : { + "germplasmPUIs" : { "type" : "array", - "description" : "A familyCode representing the family this germplasm belongs to.", + "description" : "List of Permanent Unique Identifiers to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } }, + "includeFullTree" : { + "type" : "boolean", + "description" : "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", + "nullable" : true, + "example" : true + }, + "includeParents" : { + "type" : "boolean", + "description" : "If this parameter is true, include the array of parents in the response", + "nullable" : true, + "example" : true + }, "includeProgeny" : { "type" : "boolean", "description" : "If this parameter is true, include the array of progeny in the response", + "nullable" : true, "example" : true }, - "studyNames" : { + "includeSiblings" : { + "type" : "boolean", + "description" : "If this parameter is true, include the array of siblings in the response", + "nullable" : true, + "example" : true + }, + "instituteCodes" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "nullable" : true, "items" : { "type" : "string" } }, - "collections" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "pedigreeDepth" : { + "type" : "integer", + "description" : "Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc)", + "format" : "int32", + "example" : 3 + }, + "progenyDepth" : { + "type" : "integer", + "description" : "Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc)", + "format" : "int32", + "example" : 3 + }, + "programDbIds" : { "type" : "array", - "description" : "A specific panel/collection/population name this germplasm belongs to.", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "genus" : { + "programNames" : { "type" : "array", - "description" : "List of Genus names to identify germplasm", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "includeSiblings" : { - "type" : "boolean", - "description" : "If this parameter is true, include the array of siblings in the response", - "example" : true - }, "species" : { "type" : "array", "description" : "List of Species names to identify germplasm", + "nullable" : true, "items" : { "type" : "string" } }, - "pedigreeDepth" : { - "type" : "integer", - "description" : "Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc)", - "format" : "int32", - "example" : 3 + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } }, - "binomialNames" : { + "studyNames" : { "type" : "array", - "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "includeFullTree" : { - "type" : "boolean", - "description" : "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", - "example" : true + "synonyms" : { + "type" : "array", + "description" : "List of alternative names or IDs used to reference this germplasm", + "nullable" : true, + "items" : { + "type" : "string" + } }, - "instituteCodes" : { + "trialDbIds" : { "type" : "array", - "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } @@ -18383,10 +19191,9 @@ "PersonSearchRequest" : { "type" : "object", "properties" : { - "middleNames" : { + "commonCropNames" : { "type" : "array", - "description" : "Persons middle name", - "nullable" : true, + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } @@ -18399,70 +19206,105 @@ "type" : "string" } }, - "userIDs" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, + "items" : { + "type" : "string" + } + }, + "externalReferenceIds" : { + "type" : "array", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items" : { + "type" : "string" + } + }, + "externalReferenceSources" : { + "type" : "array", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "items" : { + "type" : "string" + } + }, + "firstNames" : { + "type" : "array", + "description" : "Persons first name", "nullable" : true, "items" : { "type" : "string" } }, - "personDbIds" : { + "lastNames" : { "type" : "array", - "description" : "Unique ID for this person", + "description" : "Persons last name", "nullable" : true, "items" : { "type" : "string" } }, - "programNames" : { + "mailingAddresses" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "physical address of this person", + "nullable" : true, "items" : { "type" : "string" } }, - "commonCropNames" : { + "middleNames" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "Persons middle name", + "nullable" : true, "items" : { "type" : "string" } }, - "programDbIds" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "personDbIds" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "Unique ID for this person", + "nullable" : true, "items" : { "type" : "string" } }, - "firstNames" : { + "phoneNumbers" : { "type" : "array", - "description" : "Persons first name", + "description" : "phone number of this person", "nullable" : true, "items" : { "type" : "string" } }, - "lastNames" : { + "programDbIds" : { "type" : "array", - "description" : "Persons last name", - "nullable" : true, + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "mailingAddresses" : { + "programNames" : { "type" : "array", - "description" : "physical address of this person", - "nullable" : true, + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "phoneNumbers" : { + "userIDs" : { "type" : "array", - "description" : "phone number of this person", + "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", "nullable" : true, "items" : { "type" : "string" @@ -18472,9 +19314,26 @@ "description" : "A generic object used to maintain the metadata needed to describe a human. The Person might be a software user, a field technician, or a primary contact for a Program." }, "PlannedCross" : { - "required" : [ - "plannedCrossDbId" - ], + "allOf" : [ + { + "$ref" : "#/components/schemas/PlannedCrossNewRequest" + }, + { + "required" : [ + "plannedCrossDbId" + ], + "type" : "object", + "properties" : { + "plannedCrossDbId" : { + "type" : "string", + "description" : "the unique identifier for a planned cross" + } + }, + "description" : "Information regarding the intention to mate specific organisms together to produce offspring with desired traits. A PlannedCross becomes an actual Cross when the desired mating event actually occurs in the field." + } + ] + }, + "PlannedCrossNewRequest" : { "type" : "object", "properties" : { "additionalInfo" : { @@ -18505,10 +19364,6 @@ "parent2" : { "$ref" : "#/components/schemas/CrossParent" }, - "plannedCrossDbId" : { - "type" : "string", - "description" : "the unique identifier for a planned cross" - }, "plannedCrossName" : { "type" : "string", "description" : "the human readable name for a planned cross", @@ -18666,10 +19521,6 @@ "type" : "string", "nullable" : true }, - "programName" : { - "type" : "string", - "nullable" : true - }, "sampleType" : { "type" : "string", "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", @@ -18685,25 +19536,9 @@ "type" : "string", "nullable" : true }, - "studyName" : { - "type" : "string", - "nullable" : true - }, - "studyPUI" : { - "type" : "string", - "nullable" : true - }, "trialDbId" : { "type" : "string", "nullable" : true - }, - "trialName" : { - "type" : "string", - "nullable" : true - }, - "trialPUI" : { - "type" : "string", - "nullable" : true } }, "description" : "A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis." @@ -18837,6 +19672,35 @@ "PlateSearchRequest" : { "type" : "object", "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "externalReferenceIDs" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, + "items" : { + "type" : "string" + } + }, + "externalReferenceIds" : { + "type" : "array", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items" : { + "type" : "string" + } + }, + "externalReferenceSources" : { + "type" : "array", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "items" : { + "type" : "string" + } + }, "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", @@ -18861,6 +19725,18 @@ "type" : "string" } }, + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, "plateBarcodes" : { "type" : "array", "description" : "A unique identifier physically attached to the plate", @@ -18869,24 +19745,18 @@ "type" : "string" } }, - "plateNames" : { + "plateDbIds" : { "type" : "array", - "description" : "The human readable name of a plate of samples", + "description" : "The ID which uniquely identifies a plate of samples", "nullable" : true, "items" : { "type" : "string" } }, - "programNames" : { - "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "items" : { - "type" : "string" - } - }, - "commonCropNames" : { + "plateNames" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "The human readable name of a plate of samples", + "nullable" : true, "items" : { "type" : "string" } @@ -18898,9 +19768,9 @@ "type" : "string" } }, - "trialDbIds" : { + "programNames" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } @@ -18913,47 +19783,46 @@ "type" : "string" } }, - "plateDbIds" : { + "sampleGroupDbIds" : { "type" : "array", - "description" : "The ID which uniquely identifies a plate of samples", + "description" : "The unique identifier for a group of related Samples", "nullable" : true, "items" : { "type" : "string" } }, - "studyDbIds" : { + "sampleNames" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "The human readable name of the sample", + "nullable" : true, "items" : { "type" : "string" } }, - "trialNames" : { + "studyDbIds" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } }, - "sampleGroupDbIds" : { + "studyNames" : { "type" : "array", - "description" : "The unique identifier for a group of related Samples", - "nullable" : true, + "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "studyNames" : { + "trialDbIds" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } }, - "sampleNames" : { + "trialNames" : { "type" : "array", - "description" : "The human readable name of the sample", - "nullable" : true, + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } @@ -18964,12 +19833,6 @@ "PollinationEvent" : { "type" : "object", "properties" : { - "crossDbId" : { - "type" : "string" - }, - "crossName" : { - "type" : "string" - }, "pollinationNumber" : { "type" : "string", "description" : "The unique identifier for this pollination event", @@ -19061,13 +19924,17 @@ "description" : "Information describing the grant or funding source for this program", "nullable" : true }, - "objective" : { + "leadPersonDbId" : { + "type" : "string", + "nullable" : true + }, + "leadPersonName" : { "type" : "string", - "description" : "The primary objective of the program", "nullable" : true }, - "personDbId" : { + "objective" : { "type" : "string", + "description" : "The primary objective of the program", "nullable" : true }, "programName" : { @@ -19077,7 +19944,6 @@ "programType" : { "type" : "string", "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", - "nullable" : true, "enum" : [ "STANDARD", "PROJECT" @@ -19179,39 +20045,39 @@ "ProgramSearchRequest" : { "type" : "object", "properties" : { - "leadPersonNames" : { + "abbreviations" : { "type" : "array", - "description" : "The names of the program leader to search for", + "description" : "A list of shortened human readable names for a set of Programs", "nullable" : true, "items" : { "type" : "string" } }, - "programNames" : { + "commonCropNames" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "commonCropNames" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "programDbIds" : { + "externalReferenceIds" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "objectives" : { + "externalReferenceSources" : { "type" : "array", - "description" : "A program objective to search for", - "nullable" : true, + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } @@ -19224,6 +20090,48 @@ "type" : "string" } }, + "leadPersonNames" : { + "type" : "array", + "description" : "The names of the program leader to search for", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "objectives" : { + "type" : "array", + "description" : "A program objective to search for", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, "programTypes" : { "type" : "array", "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", @@ -19236,14 +20144,6 @@ "PROJECT" ] } - }, - "abbreviations" : { - "type" : "array", - "description" : "A list of shortened human readable names for a set of Programs", - "nullable" : true, - "items" : { - "type" : "string" - } } }, "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies." @@ -19268,15 +20168,6 @@ "type" : "string", "description" : "The publication reference.", "nullable" : true - }, - "trialDbId" : { - "type" : "string" - }, - "trialName" : { - "type" : "string" - }, - "trialPUI" : { - "type" : "string" } }, "description" : "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended." @@ -19299,7 +20190,6 @@ "externalReferences" : { "type" : "array", "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "nullable" : true, "items" : { "$ref" : "#/components/schemas/ExternalReference" } @@ -19329,10 +20219,12 @@ "description" : "The human readable name of a `Reference` within a `ReferenceSet`." }, "referenceSetDbId" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "referenceSetName" : { - "type" : "string" + "type" : "string", + "nullable" : true }, "sourceAccessions" : { "type" : "array", @@ -19347,12 +20239,12 @@ "description" : "The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from.", "nullable" : true }, - "sourceGermplasmDbIds" : { + "sourceGermplasm" : { "type" : "array", "description" : "All known corresponding Germplasm", "nullable" : true, "items" : { - "type" : "string" + "$ref" : "#/components/schemas/SourceGermplasm" } }, "sourceURI" : { @@ -19362,14 +20254,6 @@ }, "species" : { "$ref" : "#/components/schemas/OntologyTerm" - }, - "variantDbIds" : { - "type" : "array", - "description" : "variants", - "nullable" : true, - "items" : { - "type" : "string" - } } }, "description" : "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." @@ -19424,6 +20308,7 @@ "accessions" : { "type" : "array", "description" : "If specified, return the references for which the `accession` matches this string (case-sensitive, exact match).", + "nullable" : true, "items" : { "type" : "string" } @@ -19454,7 +20339,8 @@ "isDerived" : { "type" : "boolean", "description" : "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", - "format" : "boolean" + "format" : "boolean", + "nullable" : true }, "maxLength" : { "type" : "integer", @@ -19465,6 +20351,7 @@ "md5checksums" : { "type" : "array", "description" : "If specified, return the references for which the `md5checksum` matches this string (case-sensitive, exact match).", + "nullable" : true, "items" : { "type" : "string" } @@ -19492,6 +20379,7 @@ "referenceDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `References` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -19499,6 +20387,7 @@ "referenceSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `ReferenceSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -19536,6 +20425,43 @@ "ReferenceSearchRequest" : { "type" : "object", "properties" : { + "accessions" : { + "type" : "array", + "description" : "If specified, return the references for which the `accession` matches this string (case-sensitive, exact match).", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "externalReferenceIDs" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, + "items" : { + "type" : "string" + } + }, + "externalReferenceIds" : { + "type" : "array", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items" : { + "type" : "string" + } + }, + "externalReferenceSources" : { + "type" : "array", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "items" : { + "type" : "string" + } + }, "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", @@ -19544,11 +20470,6 @@ "type" : "string" } }, - "isDerived" : { - "type" : "boolean", - "description" : "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", - "format" : "boolean" - }, "germplasmNames" : { "type" : "array", "description" : "List of human readable names to identify germplasm to search for", @@ -19557,36 +20478,62 @@ "type" : "string" } }, - "minLength" : { + "isDerived" : { + "type" : "boolean", + "description" : "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", + "format" : "boolean", + "nullable" : true + }, + "maxLength" : { "type" : "integer", "description" : "The minimum length of this `References` sequence.", "format" : "int32", - "example" : 4000 + "example" : 90000 }, - "programNames" : { + "md5checksums" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "If specified, return the references for which the `md5checksum` matches this string (case-sensitive, exact match).", + "nullable" : true, "items" : { "type" : "string" } }, - "commonCropNames" : { + "minLength" : { + "type" : "integer", + "description" : "The minimum length of this `References` sequence.", + "format" : "int32", + "example" : 4000 + }, + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "programDbIds" : { + "programNames" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "trialDbIds" : { + "referenceDbIds" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "A list of IDs which uniquely identify `References` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -19594,6 +20541,7 @@ "referenceSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `ReferenceSets` within the given database server", + "nullable" : true, "items" : { "type" : "string" } @@ -19605,20 +20553,6 @@ "type" : "string" } }, - "trialNames" : { - "type" : "array", - "description" : "The human readable name of a trial to search for", - "items" : { - "type" : "string" - } - }, - "md5checksums" : { - "type" : "array", - "description" : "If specified, return the references for which the `md5checksum` matches this string (case-sensitive, exact match).", - "items" : { - "type" : "string" - } - }, "studyNames" : { "type" : "array", "description" : "List of study names to filter search results", @@ -19626,25 +20560,19 @@ "type" : "string" } }, - "referenceDbIds" : { + "trialDbIds" : { "type" : "array", - "description" : "A list of IDs which uniquely identify `References` within the given database server", + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } }, - "accessions" : { + "trialNames" : { "type" : "array", - "description" : "If specified, return the references for which the `accession` matches this string (case-sensitive, exact match).", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } - }, - "maxLength" : { - "type" : "integer", - "description" : "The minimum length of this `References` sequence.", - "format" : "int32", - "example" : 90000 } }, "description" : "A `Reference` is a canonical assembled contig, intended to act as a reference coordinate space for other genomic annotations. A single `Reference` might represent the human chromosome 1, for instance. `References` are designed to be immutable." @@ -19711,16 +20639,16 @@ "description" : "Order-independent MD5 checksum which identifies this `ReferenceSet`.\n\nTo compute this checksum, make a list of `Reference.md5checksum` for all\n`Reference` s in this set. Then sort that list, and take the MD5 hash of\nall the strings concatenated together. Express the hash as a lower-case\nhexadecimal string.", "nullable" : true }, - "referenceDbId" : { - "type" : "string" - }, - "referenceName" : { - "type" : "string" - }, "referenceSetName" : { "type" : "string", "description" : "The human readable name of a ReferenceSet" }, + "referencesDbId" : { + "type" : "string" + }, + "referencesName" : { + "type" : "string" + }, "sourceAccessions" : { "type" : "array", "description" : "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`.", @@ -19869,88 +20797,116 @@ "ReferenceSetSearchRequest" : { "type" : "object", "properties" : { - "germplasmDbIds" : { + "accessions" : { "type" : "array", - "description" : "List of IDs which uniquely identify germplasm to search for", + "description" : "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match).", "nullable" : true, "items" : { "type" : "string" } }, - "germplasmNames" : { + "assemblyPUIs" : { "type" : "array", - "description" : "List of human readable names to identify germplasm to search for", + "description" : "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match).", "nullable" : true, "items" : { "type" : "string" } }, - "programNames" : { + "commonCropNames" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "commonCropNames" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "programDbIds" : { + "externalReferenceIds" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "trialDbIds" : { + "externalReferenceSources" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "referenceSetDbIds" : { + "germplasmDbIds" : { "type" : "array", - "description" : "The `ReferenceSets` to search.", + "description" : "List of IDs which uniquely identify germplasm to search for", "nullable" : true, "items" : { "type" : "string" } }, - "studyDbIds" : { + "germplasmNames" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "trialNames" : { + "md5checksums" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match).", + "nullable" : true, "items" : { "type" : "string" } }, - "md5checksums" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { "type" : "array", - "description" : "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match).", - "nullable" : true, + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "assemblyPUIs" : { + "programNames" : { "type" : "array", - "description" : "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match).", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "referenceSetDbIds" : { + "type" : "array", + "description" : "The `ReferenceSets` to search.", "nullable" : true, "items" : { "type" : "string" } }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, "studyNames" : { "type" : "array", "description" : "List of study names to filter search results", @@ -19958,10 +20914,16 @@ "type" : "string" } }, - "accessions" : { + "trialDbIds" : { "type" : "array", - "description" : "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match).", - "nullable" : true, + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } @@ -19996,14 +20958,6 @@ "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "callSetDbIds" : { - "type" : "array", - "description" : "", - "nullable" : true, - "items" : { - "type" : "string" - } - }, "column" : { "type" : "integer", "description" : "The Column identifier for this `Sample` location in the `Plate`", @@ -20013,32 +20967,15 @@ "externalReferences" : { "type" : "array", "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "nullable" : true, "items" : { - "$ref" : "#/components/schemas/ExternalReference" - } - }, - "germplasmDbId" : { - "type" : "string", - "nullable" : true - }, - "germplasmName" : { - "type" : "string", - "nullable" : true - }, - "germplasmPUI" : { - "type" : "string", - "nullable" : true - }, - "observationUnitDbId" : { - "type" : "string", - "nullable" : true + "$ref" : "#/components/schemas/ExternalReference" + } }, - "observationUnitName" : { + "germplasmDbId" : { "type" : "string", "nullable" : true }, - "observationUnitPUI" : { + "observationUnitDbId" : { "type" : "string", "nullable" : true }, @@ -20054,10 +20991,6 @@ "type" : "string", "nullable" : true }, - "programName" : { - "type" : "string", - "nullable" : true - }, "row" : { "type" : "string", "description" : "The Row identifier for this `Sample` location in the `Plate`", @@ -20073,7 +21006,7 @@ "description" : "Description of a `Sample`\n
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing.", "nullable" : true }, - "sampleGroupId" : { + "sampleGroupDbId" : { "type" : "string", "description" : "The ID which uniquely identifies a group of `Samples`", "nullable" : true @@ -20102,14 +21035,6 @@ "type" : "string", "nullable" : true }, - "studyName" : { - "type" : "string", - "nullable" : true - }, - "studyPUI" : { - "type" : "string", - "nullable" : true - }, "takenBy" : { "type" : "string", "description" : "The name or identifier of the entity which took the `Sample` from the field", @@ -20124,14 +21049,6 @@ "type" : "string", "nullable" : true }, - "trialName" : { - "type" : "string", - "nullable" : true - }, - "trialPUI" : { - "type" : "string", - "nullable" : true - }, "well" : { "type" : "string", "description" : "The Well identifier for this `Sample` location in the `Plate`. Usually a concatenation of Row and Column, or just a number if the `Samples` are not part of an ordered `Plate`.", @@ -20261,6 +21178,35 @@ "SampleSearchRequest" : { "type" : "object", "properties" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "externalReferenceIDs" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, + "items" : { + "type" : "string" + } + }, + "externalReferenceIds" : { + "type" : "array", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items" : { + "type" : "string" + } + }, + "externalReferenceSources" : { + "type" : "array", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "items" : { + "type" : "string" + } + }, "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", @@ -20285,24 +21231,30 @@ "type" : "string" } }, - "plateNames" : { - "type" : "array", - "description" : "The human readable name of a `Plate` of `Samples`", - "nullable" : true, - "items" : { - "type" : "string" - } + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 }, - "programNames" : { + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "plateDbIds" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The ID which uniquely identifies a `Plate` of `Samples`", + "nullable" : true, "items" : { "type" : "string" } }, - "commonCropNames" : { + "plateNames" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "The human readable name of a `Plate` of `Samples`", + "nullable" : true, "items" : { "type" : "string" } @@ -20314,9 +21266,9 @@ "type" : "string" } }, - "trialDbIds" : { + "programNames" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } @@ -20329,47 +21281,46 @@ "type" : "string" } }, - "plateDbIds" : { + "sampleGroupDbIds" : { "type" : "array", - "description" : "The ID which uniquely identifies a `Plate` of `Samples`", + "description" : "The unique identifier for a group of related `Samples`", "nullable" : true, "items" : { "type" : "string" } }, - "studyDbIds" : { + "sampleNames" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "The human readable name of the `Sample`", + "nullable" : true, "items" : { "type" : "string" } }, - "trialNames" : { + "studyDbIds" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } }, - "sampleGroupDbIds" : { + "studyNames" : { "type" : "array", - "description" : "The unique identifier for a group of related `Samples`", - "nullable" : true, + "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "studyNames" : { + "trialDbIds" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } }, - "sampleNames" : { + "trialNames" : { "type" : "array", - "description" : "The human readable name of the `Sample`", - "nullable" : true, + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } @@ -20462,7 +21413,14 @@ "nullable" : true }, "validValues" : { - "$ref" : "#/components/schemas/ValidValues" + "anyOf" : [ + { + "$ref" : "#/components/schemas/ValidValues" + }, + { + "type" : "null" + } + ] } }, "description" : "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"." @@ -20669,14 +21627,6 @@ "description" : "Description the storage location", "nullable" : true }, - "transactions" : { - "type" : "array", - "description" : "The complete history of transactions for this seed lot. This includes seed increases, seed usage (planting), and trading with other breeding programs.", - "nullable" : true, - "items" : { - "$ref" : "#/components/schemas/SeedLotTransaction" - } - }, "units" : { "type" : "string", "description" : "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)", @@ -20770,11 +21720,19 @@ "$ref" : "#/components/schemas/ExternalReference" } }, - "seedLotDbId" : { + "fromSeedLotDbId" : { "type" : "string", "nullable" : true }, - "seedLotName" : { + "fromSeedLotPUI" : { + "type" : "string", + "nullable" : true + }, + "toSeedLotDbId" : { + "type" : "string", + "nullable" : true + }, + "toSeedLotPUI" : { "type" : "string", "nullable" : true }, @@ -20813,19 +21771,35 @@ "studyType", "studyName", "studyLocation", - "programName" + "programName", + "germplasmDbId", + "observationVariableDbId" ] }, "SortOrder" : { "type" : "string", "description" : "Sort order direction. Ascending/Descending.", "enum" : [ - "asc", "ASC", - "desc", - "DESC" + "DESC", + "asc", + "desc" ] }, + "SourceGermplasm" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string", + "description" : "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, inventory lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below." + }, + "germplasmName" : { + "type" : "string", + "description" : "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space." + } + }, + "description" : "A reference to a Germplasm" + }, "StorageType" : { "type" : "object", "properties" : { @@ -20849,15 +21823,6 @@ "type" : "string", "description" : "A supplemental text description of the storage type", "nullable" : true - }, - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" } }, "description" : "The type of storage this germplasm is kept in at a genebank." @@ -20916,6 +21881,14 @@ "description" : "Common name for the crop associated with this study", "nullable" : true }, + "contacts" : { + "type" : "array", + "description" : "List of contact entities associated with this study", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/Contact" + } + }, "culturalPractices" : { "type" : "string", "description" : "MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study.", @@ -20992,6 +21965,13 @@ "description" : "MIAPPE V1.1 (DM-25) Observation unit description - General description of the observation units in the study.", "nullable" : true }, + "observationVariableDbIds" : { + "type" : "array", + "description" : "The list of Observation Variables being used in this study. \n\nThis list is intended to be the wishlist of variables to collect in this study. It may or may not match the set of variables used in the collected observation records. ", + "items" : { + "type" : "string" + } + }, "seasons" : { "type" : "array", "description" : "List of seasons over which this study was performed.", @@ -21013,8 +21993,7 @@ }, "studyDescription" : { "type" : "string", - "description" : "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study", - "nullable" : true + "description" : "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study" }, "studyName" : { "type" : "string", @@ -21036,9 +22015,6 @@ }, "trialName" : { "type" : "string" - }, - "trialPUI" : { - "type" : "string" } }, "description" : "A Study represents an experiment that has taken place at a single location. The Study contains metadata about the parameters and design of the experiment. It can also be used to group results and data sets generated from the experiment. A Trial can represent a collection of one or more Studies." @@ -21164,7 +22140,9 @@ "studyType", "studyName", "studyLocation", - "programName" + "programName", + "germplasmDbId", + "observationVariableDbId" ] }, "sortOrder" : { @@ -21172,10 +22150,10 @@ "description" : "Sort order direction. Ascending/Descending.", "nullable" : true, "enum" : [ - "asc", "ASC", - "desc", - "DESC" + "DESC", + "asc", + "desc" ] }, "studyCodes" : { @@ -21235,24 +22213,45 @@ "StudySearchRequest" : { "type" : "object", "properties" : { - "germplasmDbIds" : { - "type" : "array", - "description" : "List of IDs which uniquely identify germplasm to search for", + "active" : { + "type" : "boolean", + "description" : "A flag to indicate if a Study is currently active and ongoing", "nullable" : true, + "example" : true + }, + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "locationDbIds" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "The location ids to search for", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "locationNames" : { + "externalReferenceIds" : { "type" : "array", - "description" : "A human readable names to search for", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "items" : { + "type" : "string" + } + }, + "externalReferenceSources" : { + "type" : "array", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } @@ -21265,67 +22264,108 @@ "type" : "string" } }, - "programNames" : { + "locationDbIds" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The location ids to search for", "items" : { "type" : "string" } }, - "seasonDbIds" : { + "locationNames" : { "type" : "array", - "description" : "The ID which uniquely identifies a season", - "nullable" : true, + "description" : "A human readable names to search for", "items" : { "type" : "string" } }, - "active" : { - "type" : "boolean", - "description" : "A flag to indicate if a Study is currently active and ongoing", - "nullable" : true, - "example" : true + "observationVariableDbIds" : { + "type" : "array", + "description" : "The DbIds of Variables to search for", + "items" : { + "type" : "string" + } }, - "commonCropNames" : { + "observationVariableNames" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "The names of Variables to search for", "items" : { "type" : "string" } }, - "programDbIds" : { + "observationVariablePUIs" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", "items" : { "type" : "string" } }, - "studyCodes" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { "type" : "array", - "description" : "A short human readable code for a study", - "nullable" : true, + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "studyPUIs" : { + "programNames" : { "type" : "array", - "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", - "nullable" : true, + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "observationVariablePUIs" : { + "seasonDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "description" : "The ID which uniquely identifies a season", + "nullable" : true, "items" : { "type" : "string" } }, - "trialDbIds" : { + "sortBy" : { + "type" : "string", + "description" : "Name of the field to sort by.", + "nullable" : true, + "enum" : [ + "studyDbId", + "trialDbId", + "programDbId", + "locationDbId", + "seasonDbId", + "studyType", + "studyName", + "studyLocation", + "programName", + "germplasmDbId", + "observationVariableDbId" + ] + }, + "sortOrder" : { + "type" : "string", + "description" : "Sort order direction. Ascending/Descending.", + "nullable" : true, + "enum" : [ + "ASC", + "DESC", + "asc", + "desc" + ] + }, + "studyCodes" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "A short human readable code for a study", + "nullable" : true, "items" : { "type" : "string" } @@ -21337,65 +22377,39 @@ "type" : "string" } }, - "trialNames" : { + "studyNames" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "observationVariableNames" : { + "studyPUIs" : { "type" : "array", - "description" : "The names of Variables to search for", + "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", + "nullable" : true, "items" : { "type" : "string" } }, - "studyNames" : { + "studyTypes" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "The type of study being performed. ex. \"Yield Trial\", etc", + "nullable" : true, "items" : { "type" : "string" } }, - "observationVariableDbIds" : { + "trialDbIds" : { "type" : "array", - "description" : "The DbIds of Variables to search for", + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } }, - "sortOrder" : { - "type" : "string", - "description" : "Sort order direction. Ascending/Descending.", - "nullable" : true, - "enum" : [ - "asc", - "ASC", - "desc", - "DESC" - ] - }, - "sortBy" : { - "type" : "string", - "description" : "Name of the field to sort by.", - "nullable" : true, - "enum" : [ - "studyDbId", - "trialDbId", - "programDbId", - "locationDbId", - "seasonDbId", - "studyType", - "studyName", - "studyLocation", - "programName" - ] - }, - "studyTypes" : { + "trialNames" : { "type" : "array", - "description" : "The type of study being performed. ex. \"Yield Trial\", etc", - "nullable" : true, + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } @@ -21406,15 +22420,6 @@ "Synonym" : { "type" : "object", "properties" : { - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, "synonym" : { "type" : "string", "description" : "Alternative name or ID used to reference this germplasm", @@ -21435,15 +22440,6 @@ ], "type" : "object", "properties" : { - "germplasmDbId" : { - "type" : "string" - }, - "germplasmName" : { - "type" : "string" - }, - "germplasmPUI" : { - "type" : "string" - }, "sourceName" : { "type" : "string", "description" : "The human readable name of the taxonomy provider" @@ -21473,7 +22469,8 @@ "pageToken" : { "type" : "string", "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
Used to request a specific page of data to be returned.\n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. ", - "example" : "33c27874" + "example" : "33c27874", + "deprecated" : true } } }, @@ -21738,14 +22735,6 @@ "description" : "The date this trial started", "nullable" : true }, - "studyDbIds" : { - "type" : "array", - "description" : "", - "nullable" : true, - "items" : { - "type" : "string" - } - }, "trialDescription" : { "type" : "string", "description" : "The human readable description of a trial\n\nMIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail.", @@ -21882,44 +22871,73 @@ "TrialSearchRequest" : { "type" : "object", "properties" : { - "locationDbIds" : { + "active" : { + "type" : "boolean", + "description" : "A flag to indicate if a Trial is currently active and ongoing", + "example" : true + }, + "commonCropNames" : { "type" : "array", - "description" : "The location ids to search for", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "locationNames" : { + "contactDbIds" : { "type" : "array", - "description" : "A human readable names to search for", + "description" : "List of contact entities associated with this trial", "items" : { "type" : "string" } }, - "searchDateRangeEnd" : { - "type" : "string", - "description" : "The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", - "format" : "date" + "externalReferenceIDs" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, + "items" : { + "type" : "string" + } }, - "programNames" : { + "externalReferenceIds" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "active" : { - "type" : "boolean", - "description" : "A flag to indicate if a Trial is currently active and ongoing", - "example" : true + "externalReferenceSources" : { + "type" : "array", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", + "items" : { + "type" : "string" + } }, - "commonCropNames" : { + "locationDbIds" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "The location ids to search for", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "description" : "A human readable names to search for", "items" : { "type" : "string" } }, + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, "programDbIds" : { "type" : "array", "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", @@ -21927,13 +22945,23 @@ "type" : "string" } }, - "trialDbIds" : { + "programNames" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, + "searchDateRangeEnd" : { + "type" : "string", + "description" : "The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "format" : "date" + }, + "searchDateRangeStart" : { + "type" : "string", + "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "format" : "date" + }, "studyDbIds" : { "type" : "array", "description" : "List of study identifiers to search for", @@ -21941,38 +22969,33 @@ "type" : "string" } }, - "trialNames" : { + "studyNames" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "trialPUIs" : { + "trialDbIds" : { "type" : "array", - "description" : "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } }, - "studyNames" : { + "trialNames" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } }, - "contactDbIds" : { + "trialPUIs" : { "type" : "array", - "description" : "List of contact entities associated with this trial", + "description" : "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", "items" : { "type" : "string" } - }, - "searchDateRangeStart" : { - "type" : "string", - "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", - "format" : "date" } }, "description" : "A Trial represents a collection of Study objects, and the metadata associated with that collection. A Trial could represent a multi-location experiment, and could contain information related to publications and data licensing." @@ -22026,13 +23049,26 @@ }, "description" : "If the Scale is a categorical type, these objects define the valid options" }, + "Value" : { + "oneOf" : [ + { + "type" : "boolean", + "format" : "boolean" + }, + { + "type" : "number", + "format" : "double" + }, + { + "type" : "string" + } + ] + }, "Variable" : { "required" : [ - "methodDbId", - "methodName", - "scaleDbId", - "scaleName", - "traitName" + "method", + "scale", + "trait" ], "type" : "object", "properties" : { @@ -22086,26 +23122,14 @@ "description" : "2 letter ISO 639-1 code for the language of submission of the variable.", "nullable" : true }, - "methodDbId" : { - "type" : "string" - }, - "methodName" : { - "type" : "string" - }, - "methodPUI" : { - "type" : "string" + "method" : { + "$ref" : "#/components/schemas/Method" }, "ontologyReference" : { "$ref" : "#/components/schemas/OntologyReference" }, - "scaleDbId" : { - "type" : "string" - }, - "scaleName" : { - "type" : "string" - }, - "scalePUI" : { - "type" : "string" + "scale" : { + "$ref" : "#/components/schemas/Scale" }, "scientist" : { "type" : "string", @@ -22131,14 +23155,8 @@ "type" : "string" } }, - "traitDbId" : { - "type" : "string" - }, - "traitName" : { - "type" : "string" - }, - "traitPUI" : { - "type" : "string" + "trait" : { + "$ref" : "#/components/schemas/Trait" } }, "description" : "A unique combination of Trait, Method, and Scale to define a clear context for an Observation." @@ -22226,6 +23244,7 @@ "studyDbId" : { "type" : "array", "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "deprecated" : true, "items" : { "type" : "string" } @@ -22325,10 +23344,19 @@ "additionalInfo" : { "$ref" : "#/components/schemas/AdditionalInfo" }, - "analysis" : { + "alternateBases" : { "type" : "array", - "description" : "Set of Analysis descriptors for this VariantSet", + "description" : "The bases that appear instead of the reference bases. Multiple alternate alleles are possible.", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "alternate_bases" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `alternateBases`. Github issue number #549\n
The bases that appear instead of the reference bases. Multiple alternate alleles are possible.", "nullable" : true, + "deprecated" : true, "items" : { "type" : "string" } @@ -22366,7 +23394,6 @@ "externalReferences" : { "type" : "array", "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "nullable" : true, "items" : { "$ref" : "#/components/schemas/ExternalReference" } @@ -22435,7 +23462,15 @@ }, "variantNames" : { "type" : "array", - "description" : "A human readable name associated with a `Variant`", + "description" : "A human readable name associated with a `Variant`", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted.", "nullable" : true, "items" : { "type" : "string" @@ -22455,6 +23490,8 @@ "callSetDbIds" : { "type" : "array", "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", + "nullable" : true, + "deprecated" : true, "items" : { "type" : "string" } @@ -22489,11 +23526,14 @@ "referenceDbId" : { "type" : "string", "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", - "example" : "120a2d5c" + "nullable" : true, + "example" : "120a2d5c", + "deprecated" : true }, "referenceDbIds" : { "type" : "array", "description" : "The unique identifier representing a genotype `Reference`", + "nullable" : true, "items" : { "type" : "string" } @@ -22501,6 +23541,7 @@ "referenceSetDbIds" : { "type" : "array", "description" : "The unique identifier representing a genotype `ReferenceSet`", + "nullable" : true, "items" : { "type" : "string" } @@ -22542,6 +23583,7 @@ "variantDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Variants`", + "nullable" : true, "items" : { "type" : "string" } @@ -22549,6 +23591,7 @@ "variantSetDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `VariantSets`", + "nullable" : true, "items" : { "type" : "string" } @@ -22558,69 +23601,108 @@ "VariantSearchRequest" : { "type" : "object", "properties" : { - "referenceDbId" : { - "type" : "string", - "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", - "example" : "120a2d5c" + "callSetDbIds" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", + "nullable" : true, + "deprecated" : true, + "items" : { + "type" : "string" + } }, - "programNames" : { + "commonCropNames" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "start" : { + "end" : { "type" : "integer", - "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", + "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", "format" : "int32", - "example" : 100 + "example" : 1500 }, - "commonCropNames" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "programDbIds" : { + "externalReferenceIds" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "trialDbIds" : { + "externalReferenceSources" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "referenceSetDbIds" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { "type" : "array", - "description" : "The unique identifier representing a genotype `ReferenceSet`", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "studyDbIds" : { + "programNames" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "trialNames" : { + "referenceDbId" : { + "type" : "string", + "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", + "nullable" : true, + "example" : "120a2d5c", + "deprecated" : true + }, + "referenceDbIds" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "The unique identifier representing a genotype `Reference`", + "nullable" : true, "items" : { "type" : "string" } }, - "variantSetDbIds" : { + "referenceSetDbIds" : { "type" : "array", - "description" : "A list of IDs which uniquely identify `VariantSets`", + "description" : "The unique identifier representing a genotype `ReferenceSet`", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "start" : { + "type" : "integer", + "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", + "format" : "int32", + "example" : 100 + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } @@ -22632,9 +23714,16 @@ "type" : "string" } }, - "referenceDbIds" : { + "trialDbIds" : { "type" : "array", - "description" : "The unique identifier representing a genotype `Reference`", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } @@ -22642,19 +23731,15 @@ "variantDbIds" : { "type" : "array", "description" : "A list of IDs which uniquely identify `Variants`", + "nullable" : true, "items" : { "type" : "string" } }, - "end" : { - "type" : "integer", - "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", - "format" : "int32", - "example" : 1500 - }, - "callSetDbIds" : { + "variantSetDbIds" : { "type" : "array", - "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", + "description" : "A list of IDs which uniquely identify `VariantSets`", + "nullable" : true, "items" : { "type" : "string" } @@ -22688,7 +23773,6 @@ "externalReferences" : { "type" : "array", "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "nullable" : true, "items" : { "$ref" : "#/components/schemas/ExternalReference" } @@ -22709,18 +23793,6 @@ "type" : "string", "nullable" : true }, - "studyDbId" : { - "type" : "string", - "nullable" : true - }, - "studyName" : { - "type" : "string", - "nullable" : true - }, - "studyPUI" : { - "type" : "string", - "nullable" : true - }, "variantCount" : { "type" : "integer", "description" : "The number of Variants included in this VariantSet", @@ -22831,47 +23903,53 @@ "VariantSetSearchRequest" : { "type" : "object", "properties" : { - "variantSetDbIds" : { + "callSetDbIds" : { "type" : "array", - "description" : "The unique identifier representing a VariantSet", + "description" : "The unique identifier representing a CallSet", "items" : { "type" : "string" } }, - "studyNames" : { + "commonCropNames" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "items" : { "type" : "string" } }, - "referenceDbIds" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "The unique identifier representing a genotype Reference", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { "type" : "string" } }, - "programNames" : { + "externalReferenceIds" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "variantDbIds" : { + "externalReferenceSources" : { "type" : "array", - "description" : "The unique identifier representing a Variant", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "commonCropNames" : { - "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "items" : { - "type" : "string" - } + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 }, "programDbIds" : { "type" : "array", @@ -22880,16 +23958,16 @@ "type" : "string" } }, - "trialDbIds" : { + "programNames" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "callSetDbIds" : { + "referenceDbIds" : { "type" : "array", - "description" : "The unique identifier representing a CallSet", + "description" : "The unique identifier representing a genotype Reference", "items" : { "type" : "string" } @@ -22908,12 +23986,40 @@ "type" : "string" } }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, "trialNames" : { "type" : "array", "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } + }, + "variantDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a Variant", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "The unique identifier representing a VariantSet", + "items" : { + "type" : "string" + } } }, "description" : "A VariantSet is a collection of variants and variant calls intended to be analyzed together." @@ -23478,6 +24584,43 @@ } } }, + "SeedLotTransactionListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "SeedLotTransactionListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/SeedLotTransaction" + } + } + } + } + } + } + } + } + }, "CallSetListResponse" : { "description" : "OK", "content" : { @@ -23967,6 +25110,32 @@ } } }, + "AlleleMatrixSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "AlleleMatrixSingleResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/AlleleMatrix" + } + } + } + } + } + }, "PersonListResponse" : { "description" : "OK", "content" : { @@ -24952,9 +26121,34 @@ "properties" : { "data" : { "type" : "array", + "description" : "The `data` array is part of the BrAPI standard List Response JSON container. `data` will always contain the primary list of objects being returned by a BrAPI endpoint. `data` is also the only array impacted by the `metadata.pagination` details. When the pagination parameters change, the `data` array will reflect those changes in the JSON response.", "items" : { "$ref" : "#/components/schemas/Call" } + }, + "expandHomozygotes" : { + "type" : "boolean", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "nullable" : true, + "example" : true + }, + "sepPhased" : { + "type" : "string", + "description" : "The string used as a separator for phased allele calls.", + "nullable" : true, + "example" : "|" + }, + "sepUnphased" : { + "type" : "string", + "description" : "The string used as a separator for unphased allele calls.", + "nullable" : true, + "example" : "/" + }, + "unknownString" : { + "type" : "string", + "description" : "The string used as a representation for missing data.", + "nullable" : true, + "example" : "." } } } diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index 591a7ef3..a0b85407 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -305,7 +305,7 @@ }, "style" : "form" }, { - "description" : "\"dataMatrixNames\" is a comma seperated list of names (ie 'Genotype, Read Depth' etc). This list controls which data matrices are returned in the response.\n
This maps to a FORMAT field in the VCF file standard.", + "description" : "\"dataMatrixNames\" is a comma separated list of names (ie 'Genotype, Read Depth' etc). This list controls which data matrices are returned in the response.\n
This maps to a FORMAT field in the VCF file standard.", "explode" : true, "in" : "query", "name" : "dataMatrixNames", @@ -315,7 +315,7 @@ }, "style" : "form" }, { - "description" : "\"dataMatrixAbbreviations\" is a comma seperated list of abbreviations (ie 'GT, RD' etc). This list controls which data matrices are returned in the response.\n
This maps to a FORMAT field in the VCF file standard.", + "description" : "\"dataMatrixAbbreviations\" is a comma separated list of abbreviations (ie 'GT, RD' etc). This list controls which data matrices are returned in the response.\n
This maps to a FORMAT field in the VCF file standard.", "explode" : true, "in" : "query", "name" : "dataMatrixAbbreviations", @@ -15524,17 +15524,6 @@ "get" : { "description" : "Get the results of a `Observations` search request
\nClients should submit a search request using the corresponding `POST /search/observations` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", "parameters" : [ { - "description" : "A standard HTTP request header that is used to request a specific content type (JSON, CSV, etc) which is \"acceptable\" to the client and should be returned by the server", - "example" : "application/json", - "explode" : false, - "in" : "header", - "name" : "Accept", - "required" : true, - "schema" : { - "$ref" : "#/components/schemas/ContentTypes" - }, - "style" : "simple" - }, { "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", "example" : "Bearer XXXX", "explode" : false, @@ -19689,7 +19678,7 @@ "name" : "sortBy", "required" : false, "schema" : { - "enum" : [ "studyDbId", "trialDbId", "programDbId", "locationDbId", "seasonDbId", "studyType", "studyName", "studyLocation", "programName" ], + "enum" : [ "studyDbId", "trialDbId", "programDbId", "locationDbId", "seasonDbId", "studyType", "studyName", "studyLocation", "programName", "germplasmDbId", "observationVariableDbId" ], "type" : "string" }, "style" : "form" @@ -22209,6 +22198,17 @@ "type" : "string" }, "style" : "form" + }, { + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "explode" : true, + "in" : "query", + "name" : "externalReferenceID", + "required" : false, + "schema" : { + "type" : "string" + }, + "style" : "form" }, { "description" : "An identifier for the source system or database of an external reference (use with `externalReferenceId` parameter)", "explode" : true, @@ -23617,7 +23617,7 @@ "style" : "form" }, "dataMatrixAbbreviations" : { - "description" : "\"dataMatrixAbbreviations\" is a comma seperated list of abbreviations (ie 'GT, RD' etc). This list controls which data matrices are returned in the response.\n
This maps to a FORMAT field in the VCF file standard.", + "description" : "\"dataMatrixAbbreviations\" is a comma separated list of abbreviations (ie 'GT, RD' etc). This list controls which data matrices are returned in the response.\n
This maps to a FORMAT field in the VCF file standard.", "explode" : true, "in" : "query", "name" : "dataMatrixAbbreviations", @@ -23628,7 +23628,7 @@ "style" : "form" }, "dataMatrixNames" : { - "description" : "\"dataMatrixNames\" is a comma seperated list of names (ie 'Genotype, Read Depth' etc). This list controls which data matrices are returned in the response.\n
This maps to a FORMAT field in the VCF file standard.", + "description" : "\"dataMatrixNames\" is a comma separated list of names (ie 'Genotype, Read Depth' etc). This list controls which data matrices are returned in the response.\n
This maps to a FORMAT field in the VCF file standard.", "explode" : true, "in" : "query", "name" : "dataMatrixNames", @@ -25813,7 +25813,7 @@ }, "parentType" : { "description" : "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc.", - "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION" ], + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ], "example" : "MALE", "type" : "string" } @@ -35819,7 +35819,7 @@ }, "sortOrder" : { "description" : "Order results should be sorted. ex. \"ASC\" or \"DESC\"", - "enum" : [ "ASC", "DESC" ], + "enum" : [ "asc", "ASC", "desc", "DESC" ], "nullable" : true, "type" : "string" }, @@ -40908,7 +40908,7 @@ }, "parentType" : { "description" : "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc.", - "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION" ], + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ], "example" : "MALE", "type" : "string" } @@ -40964,7 +40964,7 @@ }, "parentType" : { "description" : "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc.", - "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION" ], + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ], "example" : "MALE", "type" : "string" } diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index 827a3253..29d857ad 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -1,9 +1,6 @@ #### What's Deleted --- -##### `GET` /allelematrix - - ##### `GET` /commoncropnames @@ -28,9 +25,6 @@ ##### `POST` /seedlots/transactions -##### `GET` /seedlots/{seedLotDbId}/transactions - - ##### `GET` /serverinfo @@ -55,32 +49,25 @@ #### What's Changed --- -##### `GET` /markerpositions - +##### `POST` /search/lists -###### Return Type: -Changed response : **200** +###### Request: * Changed content type : `application/json` - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): + * Changed property `listType` (string): + - Nullable changed: `true` -> `null` - Deleted properties: `variantName` +##### `GET` /allelematrix -##### `POST` /search/allelematrix +###### Return Type: -###### Request: +New response : **404** -* Changed content type : `application/json` +##### `GET` /germplasm/{germplasmDbId}/mcpd - * Changed property `preview` (boolean): - - Default changed: `false` -> `none` ###### Return Type: @@ -90,147 +77,124 @@ Changed response : **200** * Changed property `result` (object) - New properties: `data` - - Deleted properties: `callSetDbIds`, `dataMatrices`, `expandHomozygotes`, `pagination`, `sepPhased`, `sepUnphased`, `unknownString`, `variantDbIds`, `variantSetDbIds` - - New required properties: - - `data` + New properties: `germplasmName` - Removed required properties: - - `callSetDbIds` - - `variantSetDbIds` + Deleted properties: `germplasmPUI` -##### `GET` /search/allelematrix/{searchResultsDbId} +##### `PUT` /samples ###### Return Type: -Deleted response : **202** - Deleted response : **404** -Changed response : **200** +##### `POST` /search/allelematrix -* Changed content type : `application/json` - * Changed property `result` (object) +###### Request: - New properties: `data` +* Changed content type : `application/json` - Deleted properties: `callSetDbIds`, `dataMatrices`, `expandHomozygotes`, `pagination`, `sepPhased`, `sepUnphased`, `unknownString`, `variantDbIds`, `variantSetDbIds` + New properties: `dimensionCallSetPage`, `dimensionCallSetPageSize`, `dimensionVariantPage`, `dimensionVariantPageSize` - New required properties: - - `data` + * Changed property `dataMatrixAbbreviations` (array -> string): + - Type changed: `array` -> `string` - Removed required properties: - - `callSetDbIds` - - `variantSetDbIds` + * Changed property `dataMatrixNames` (array -> string): + - Type changed: `array` -> `string` -##### `POST` /search/attributes +##### `POST` /search/calls ###### Request: * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - - * Changed property `studyDbId` (array): + * Changed property `pageToken` (string): - Deprecated status changed -##### `GET` /search/attributes/{searchResultsDbId} - +##### `GET` /search/calls/{searchResultsDbId} -###### Return Type: -Deleted response : **202** +###### Parameters: -Deleted response : **404** +Deleted: `pageToken` in `query` -##### `POST` /search/attributevalues +##### `POST` /search/observations ###### Request: * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - -##### `GET` /search/attributevalues/{searchResultsDbId} - - -###### Return Type: + * Changed property `observationLevelRelationships` (array) -Deleted response : **202** + Changed items (array): -Deleted response : **404** + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` -##### `POST` /search/germplasm +##### `POST` /search/observationunits ###### Request: * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - -##### `GET` /search/germplasm/{searchResultsDbId} - - -###### Return Type: - -Deleted response : **202** - -Deleted response : **404** + * Changed property `observationLevelRelationships` (array) -##### `GET` /search/images/{searchResultsDbId} + Changed items (array): + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` -###### Return Type: +##### `POST` /search/variants -Deleted response : **202** -Deleted response : **404** +###### Request: -##### `POST` /search/lists +* Changed content type : `application/json` + Deleted properties: `pageToken` -###### Request: +##### `GET` /search/variants/{searchResultsDbId} -* Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` +###### Parameters: - * Changed property `listType` (string): - - Nullable changed: `true` -> `null` +Deleted: `pageToken` in `query` -##### `GET` /search/lists/{searchResultsDbId} +##### `POST` /search/variantsets ###### Return Type: -Deleted response : **202** +Changed response : **200** -Deleted response : **404** +* Changed content type : `application/json` -##### `GET` /search/locations/{searchResultsDbId} + * Changed property `result` (object) + * Changed property `data` (array) -###### Return Type: + Changed items (array): -Deleted response : **202** + New properties: `referenceSetName` -Deleted response : **404** + Deleted properties: `availableFormats`, `studyDbId` + + * Changed property `referenceSetDbId` (string): + - Nullable changed: `false` -> `true` -##### `POST` /search/markerpositions + * Changed property `analysis` (array) + Changed items (array): -###### Request: + New required properties: + - `analysisDbId` -* Changed content type : `application/json` +##### `GET` /search/variantsets/{searchResultsDbId} - Deleted properties: `page`, `pageSize` ###### Return Type: @@ -244,16 +208,30 @@ Changed response : **200** Changed items (array): - Deleted properties: `variantName` + New properties: `referenceSetName` + + Deleted properties: `availableFormats`, `studyDbId` -##### `GET` /search/markerpositions/{searchResultsDbId} + * Changed property `referenceSetDbId` (string): + - Nullable changed: `false` -> `true` + * Changed property `analysis` (array) -###### Return Type: + Changed items (array): -Deleted response : **202** + New required properties: + - `analysisDbId` -Deleted response : **404** +##### `GET` /seedlots/{seedLotDbId}/transactions + + +###### Parameters: + +Deleted: `transactionDbId` in `query` + +Deleted: `transactionDirection` in `query` + +###### Return Type: Changed response : **200** @@ -265,184 +243,197 @@ Changed response : **200** Changed items (array): - Deleted properties: `variantName` + New properties: `fromSeedLotPUI`, `toSeedLotPUI` -##### `GET` /search/observations/{searchResultsDbId} +##### `GET` /trials ###### Parameters: -Deleted: `Accept` in `header` - -###### Return Type: - -Deleted response : **202** +Deleted: `sortBy` in `query` -Deleted response : **404** +Deleted: `sortOrder` in `query` -##### `GET` /search/observationunits/{searchResultsDbId} +##### `GET` /variantsets ###### Return Type: -Deleted response : **202** +Changed response : **200** -Deleted response : **404** +* Changed content type : `application/json` -##### `POST` /search/people + * Changed property `result` (object) + * Changed property `data` (array) -###### Request: + Changed items (array): -* Changed content type : `application/json` + New properties: `referenceSetName` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + Deleted properties: `availableFormats`, `studyDbId` -##### `GET` /search/people/{searchResultsDbId} + * Changed property `referenceSetDbId` (string): + - Nullable changed: `false` -> `true` + * Changed property `analysis` (array) -###### Return Type: + Changed items (array): -Deleted response : **202** + New required properties: + - `analysisDbId` -Deleted response : **404** +##### `GET` /variantsets/{variantSetDbId} -##### `POST` /search/plates +###### Return Type: -###### Request: +Changed response : **200** * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + * Changed property `result` (object) -##### `GET` /search/plates/{searchResultsDbId} + New properties: `referenceSetName` + Deleted properties: `availableFormats`, `studyDbId` -###### Return Type: + * Changed property `referenceSetDbId` (string): + - Nullable changed: `false` -> `true` -Deleted response : **202** + * Changed property `analysis` (array) -Deleted response : **404** + Changed items (array): + + New required properties: + - `analysisDbId` -##### `POST` /search/programs +##### `POST` /attributes ###### Request: * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + Changed items (array): + + * Changed property `ontologyReference` (object): + - Nullable changed: `true` -> `false` -##### `GET` /search/programs/{searchResultsDbId} + New properties: `ontologyPUI`, `ontologyReferenceDbId` +##### `PUT` /attributes/{attributeDbId} -###### Return Type: -Deleted response : **202** +###### Request: -Deleted response : **404** +* Changed content type : `application/json` + + * Changed property `ontologyReference` (object): + - Nullable changed: `true` -> `false` + + New properties: `ontologyPUI`, `ontologyReferenceDbId` -##### `POST` /search/referencesets +##### `POST` /images ###### Request: * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + Changed items (array): -##### `GET` /search/referencesets/{searchResultsDbId} + New properties: `imageContent`, `observationUnitName` + Deleted properties: `observationDbIds` -###### Return Type: + * Changed property `mimeType` (string): + - Pattern changed: `image/.*` -> `null` -Deleted response : **202** + * Changed property `imageLocation` (object) -Deleted response : **404** + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` -##### `POST` /search/samples +##### `PUT` /images/{imageDbId} ###### Request: * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - -##### `GET` /search/samples/{searchResultsDbId} + New properties: `imageContent`, `observationUnitName` + Deleted properties: `observationDbIds` -###### Return Type: + * Changed property `mimeType` (string): + - Pattern changed: `image/.*` -> `null` -Deleted response : **202** + * Changed property `imageLocation` (object) -Deleted response : **404** + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` -##### `POST` /search/studies +##### `POST` /locations ###### Request: * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - - * Changed property `sortBy` (string): - - Removed enum values: [germplasmDbId, observationVariableDbId] - - * Changed property `sortOrder` (string): - - Added enum values: [asc, desc] - -##### `GET` /search/studies/{searchResultsDbId} - + Changed items (array): -###### Return Type: + New properties: `childLocationDbIds`, `parentLocationPUI` -Deleted response : **202** + * Changed property `coordinates` (object) -Deleted response : **404** + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` -##### `POST` /search/trials +##### `PUT` /locations/{locationDbId} ###### Request: * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + New properties: `childLocationDbIds`, `parentLocationPUI` -##### `GET` /search/trials/{searchResultsDbId} + * Changed property `coordinates` (object) + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` -###### Return Type: +##### `PUT` /observations -Deleted response : **202** + +###### Return Type: Deleted response : **404** -##### `POST` /search/variables +##### `POST` /observations ###### Request: * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` + Changed items (array): + + New properties: `observationVariablePUI`, `seasonDbId`, `seasonName`, `seasonPUI`, `studyName` - * Changed property `studyDbId` (array): - - Deprecated status changed + Deleted properties: `season` -##### `GET` /search/variables/{searchResultsDbId} + * Changed property `geoCoordinates` (object) + * Changed property `geometry` (object -> null): + - Type changed: `object` -> `null` ###### Return Type: -Deleted response : **202** - Deleted response : **404** -##### `POST` /attributevalues +##### `POST` /observationunits ###### Request: @@ -451,2029 +442,102 @@ Deleted response : **404** Changed items (array): - New properties: `attributePUI`, `germplasmPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `PUT` /attributevalues/{attributeValueDbId} + New properties: `crossPUI`, `locationPUI`, `programPUI`, `seedLotPUI` + * Changed property `observationUnitPosition` (object) -###### Request: + * Changed property `geoCoordinates` (object -> array): + - Type changed: `object` -> `array` -* Changed content type : `application/json` + * Changed property `positionCoordinateXType` (string): + - Nullable changed: `true` -> `null` - New properties: `attributePUI`, `germplasmPUI` + * Changed property `positionCoordinateYType` (string): + - Nullable changed: `true` -> `null` - * Changed property `externalReferences` (array) + * Changed property `observationLevelRelationships` (array) - Changed items (array): + Changed items (array): - * Changed property `referenceID` (string): - - Deprecated status changed + * Changed property `observationUnitDbId` (string): + - Nullable changed: `true` -> `null` -##### `GET` /calls +##### `GET` /pedigree ###### Return Type: +Deleted response : **404** + Changed response : **200** * Changed content type : `application/json` * Changed property `result` (object) - Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` - * Changed property `data` (array) Changed items (array): - Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - -##### `GET` /callsets + Deleted properties: `germplasmPUI` + * Changed property `parents` (array) -###### Return Type: + Changed items (array): -Changed response : **200** + New required properties: + - `germplasmName` -* Changed content type : `application/json` + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` - * Changed property `result` (object) +##### `POST` /pedigree - * Changed property `data` (array) - Changed items (array): +###### Request: - New properties: `sampleName`, `samplePUI`, `studyName`, `studyPUI` +* Changed content type : `application/json` - Deleted properties: `variantSetDbIds` + Changed items (array): - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` + Deleted properties: `germplasmPUI` - Changed items (array): + * Changed property `parents` (array) - * Changed property `referenceID` (string): - - Deprecated status changed + Changed items (array): -##### `GET` /callsets/{callSetDbId} + New required properties: + - `germplasmName` + * Changed property `germplasmName` (string): + - Nullable changed: `true` -> `null` ###### Return Type: +Deleted response : **404** + Changed response : **200** * Changed content type : `application/json` * Changed property `result` (object) - New properties: `sampleName`, `samplePUI`, `studyName`, `studyPUI` - - Deleted properties: `variantSetDbIds` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /callsets/{callSetDbId}/calls - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` - - * Changed property `data` (array) - - Changed items (array): - - Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - -##### `POST` /crosses - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - Deleted properties: `pollinationTimeStamp` - - * Changed property `crossType` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossAttributes` (array) - - Changed items (array): - - New properties: `crossDbId`, `crossName` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `parent1` (object): - - Nullable changed: `true` -> `null` - - New properties: `germplasmPUI`, `observationUnitPUI` - - * Changed property `pollinationEvents` (array) - - Changed items (array): - - New properties: `crossDbId`, `crossName` - -##### `POST` /crossingprojects - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `potentialParents` (array) - - Changed items (array): - - New properties: `germplasmPUI`, `observationUnitPUI` - -##### `PUT` /crossingprojects/{crossingProjectDbId} - - -###### Request: - -* Changed content type : `application/json` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `potentialParents` (array) - - Changed items (array): - - New properties: `germplasmPUI`, `observationUnitPUI` - -##### `GET` /events - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `studyPUI` - - Deleted properties: `date`, `observationUnitDbIds` - - * Changed property `studyDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `studyName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `eventDateRange` (object): - - Nullable changed: `true` -> `null` - - New properties: `eventDbId` - - * Changed property `eventParameters` (array) - - Changed items (array): - - New properties: `eventDbId` - - * Changed property `key` (string): - - Nullable changed: `true` -> `null` - - Deprecated status changed - - * Changed property `rdfValue` (string): - - Nullable changed: `true` -> `null` - - Deprecated status changed - -##### `GET` /germplasm/{germplasmDbId}/mcpd - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - New properties: `germplasmName` - - * Changed property `germplasmPUI` (string): - - Nullable changed: `true` -> `null` - -##### `POST` /lists - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `personDbId` - - Deleted properties: `listOwnerPersonDbId` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `PUT` /lists/{listDbId} - - -###### Request: - -* Changed content type : `application/json` - - New properties: `personDbId` - - Deleted properties: `listOwnerPersonDbId` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `POST` /people - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `PUT` /people/{personDbId} - - -###### Request: - -* Changed content type : `application/json` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /plannedcrosses - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - * Changed property `crossType` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `parent1` (object): - - Nullable changed: `true` -> `null` - - New properties: `germplasmPUI`, `observationUnitPUI` - -##### `PUT` /plannedcrosses - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - * Changed property `crossType` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `parent1` (object): - - Nullable changed: `true` -> `null` - - New properties: `germplasmPUI`, `observationUnitPUI` - -##### `POST` /plannedcrosses - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `plannedCrossDbId` - - New required properties: - - `plannedCrossDbId` - - * Changed property `crossType` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `parent1` (object): - - Nullable changed: `true` -> `null` - - New properties: `germplasmPUI`, `observationUnitPUI` - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - * Changed property `crossType` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `parent1` (object): - - Nullable changed: `true` -> `null` - - New properties: `germplasmPUI`, `observationUnitPUI` - -##### `POST` /plates - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `programName`, `studyName`, `studyPUI`, `trialName`, `trialPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /programs - - -###### Parameters: - -Changed: `programType` in `query`: - - Added enum values: [STANDARD] - - Removed enum values: [STANDARD] - -##### `POST` /programs - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `personDbId` - - Deleted properties: `leadPersonDbId`, `leadPersonName` - - * Changed property `programType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `PUT` /programs/{programDbId} - - -###### Request: - -* Changed content type : `application/json` - - New properties: `personDbId` - - Deleted properties: `leadPersonDbId`, `leadPersonName` - - * Changed property `programType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /references - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `sourceGermplasmDbIds`, `variantDbIds` - - Deleted properties: `sourceGermplasm` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /references/{referenceDbId} - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - New properties: `sourceGermplasmDbIds`, `variantDbIds` - - Deleted properties: `sourceGermplasm` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `PUT` /samples - - -###### Return Type: - -Deleted response : **404** - -##### `POST` /samples - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `callSetDbIds`, `germplasmName`, `germplasmPUI`, `observationUnitName`, `observationUnitPUI`, `programName`, `sampleGroupId`, `studyName`, `studyPUI`, `trialName`, `trialPUI` - - Deleted properties: `sampleGroupDbId` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `POST` /search/calls - - -###### Request: - -* Changed content type : `application/json` - - Deleted properties: `page`, `pageSize`, `pageToken` - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` - - * Changed property `data` (array) - - Changed items (array): - - Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - -##### `GET` /search/calls/{searchResultsDbId} - - -###### Parameters: - -Deleted: `pageToken` in `query` - -###### Return Type: - -Deleted response : **202** - -Deleted response : **404** - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` - - * Changed property `data` (array) - - Changed items (array): - - Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - -##### `POST` /search/callsets - - -###### Request: - -* Changed content type : `application/json` - - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `sampleName`, `samplePUI`, `studyName`, `studyPUI` - - Deleted properties: `variantSetDbIds` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /search/callsets/{searchResultsDbId} - - -###### Return Type: - -Deleted response : **202** - -Deleted response : **404** - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `sampleName`, `samplePUI`, `studyName`, `studyPUI` - - Deleted properties: `variantSetDbIds` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `POST` /search/observations - - -###### Request: - -* Changed content type : `application/json` - - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - - * Changed property `observationDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `observationTimeStampRangeEnd` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationTimeStampRangeStart` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `seasonDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `observationLevelRelationships` (array): - - Nullable changed: `true` -> `null` - - Changed items (array): - - New properties: `observationUnitName`, `observationUnitPUI` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationLevels` (array): - - Nullable changed: `true` -> `null` - -##### `POST` /search/observationunits - - -###### Request: - -* Changed content type : `application/json` - - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - - * Changed property `includeObservations` (boolean): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `observationUnitNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `seasonDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `observationLevelRelationships` (array): - - Nullable changed: `true` -> `null` - - Changed items (array): - - New properties: `observationUnitName`, `observationUnitPUI` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationLevels` (array): - - Nullable changed: `true` -> `null` - -##### `POST` /search/references - - -###### Request: - -* Changed content type : `application/json` - - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - - * Changed property `accessions` (array): - - Nullable changed: `true` -> `null` - - * Changed property `isDerived` (boolean): - - Nullable changed: `true` -> `null` - - * Changed property `md5checksums` (array): - - Nullable changed: `true` -> `null` - - * Changed property `referenceDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetDbIds` (array): - - Nullable changed: `true` -> `null` - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `sourceGermplasmDbIds`, `variantDbIds` - - Deleted properties: `sourceGermplasm` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /search/references/{searchResultsDbId} - - -###### Return Type: - -Deleted response : **202** - -Deleted response : **404** - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `sourceGermplasmDbIds`, `variantDbIds` - - Deleted properties: `sourceGermplasm` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `POST` /search/variants - - -###### Request: - -* Changed content type : `application/json` - - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize`, `pageToken` - - * Changed property `callSetDbIds` (array): - - Nullable changed: `true` -> `null` - - Deprecated status changed - - * Changed property `referenceDbId` (string): - - Nullable changed: `true` -> `null` - - Deprecated status changed - - * Changed property `referenceDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `referenceSetDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `variantDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `variantSetDbIds` (array): - - Nullable changed: `true` -> `null` - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `analysis` - - Deleted properties: `alternateBases`, `alternate_bases`, `variantSetDbIds` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /search/variants/{searchResultsDbId} - - -###### Parameters: - -Deleted: `pageToken` in `query` - -###### Return Type: - -Deleted response : **202** - -Deleted response : **404** - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `analysis` - - Deleted properties: `alternateBases`, `alternate_bases`, `variantSetDbIds` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `POST` /search/variantsets - - -###### Request: - -* Changed content type : `application/json` - - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `referenceSetName`, `studyName`, `studyPUI` - - Deleted properties: `availableFormats` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `true` - - * Changed property `analysis` (array) - - Changed items (array): - - New properties: `variantSetDbId`, `variantSetName` - - New required properties: - - `analysisDbId` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `metadataFields` (array) - - Changed items (array): - - New properties: `variantSetDbId`, `variantSetName` - - * Changed property `dataType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldAbbreviation` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldName` (string): - - Nullable changed: `null` -> `true` - -##### `GET` /search/variantsets/{searchResultsDbId} - - -###### Return Type: - -Deleted response : **202** - -Deleted response : **404** - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `referenceSetName`, `studyName`, `studyPUI` - - Deleted properties: `availableFormats` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `true` - - * Changed property `analysis` (array) - - Changed items (array): - - New properties: `variantSetDbId`, `variantSetName` - - New required properties: - - `analysisDbId` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `metadataFields` (array) - - Changed items (array): - - New properties: `variantSetDbId`, `variantSetName` - - * Changed property `dataType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldAbbreviation` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldName` (string): - - Nullable changed: `null` -> `true` - -##### `POST` /seedlots - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `transactions` - - * Changed property `contentMixture` (array) - - Changed items (array): - - New properties: `germplasmPUI`, `seedLotDbId`, `seedLotName` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `PUT` /seedlots/{seedLotDbId} - - -###### Request: - -* Changed content type : `application/json` - - New properties: `transactions` - - * Changed property `contentMixture` (array) - - Changed items (array): - - New properties: `germplasmPUI`, `seedLotDbId`, `seedLotName` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `POST` /studies - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `trialPUI` - - Deleted properties: `contacts`, `observationVariableDbIds` - - * Changed property `studyDescription` (string): - - Nullable changed: `null` -> `true` - - * Changed property `environmentParameters` (array) - - Changed items (array): - - New properties: `environmentParametersDbId`, `studyDbId`, `studyName`, `studyPUI` - - New required properties: - - `environmentParametersDbId` - - * Changed property `experimentalDesign` (object): - - Nullable changed: `true` -> `null` - - New properties: `studyDbId`, `studyName`, `studyPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `growthFacility` (object): - - Nullable changed: `true` -> `null` - - * Changed property `PUI` (string): - - Nullable changed: `null` -> `true` - - * Changed property `lastUpdate` (object): - - Nullable changed: `true` -> `null` - - New properties: `lastUpdateDbId`, `studyDbId`, `studyName`, `studyPUI` - - New required properties: - - `lastUpdateDbId` - -##### `PUT` /studies/{studyDbId} - - -###### Request: - -* Changed content type : `application/json` - - New properties: `trialPUI` - - Deleted properties: `contacts`, `observationVariableDbIds` - - * Changed property `studyDescription` (string): - - Nullable changed: `null` -> `true` - - * Changed property `environmentParameters` (array) - - Changed items (array): - - New properties: `environmentParametersDbId`, `studyDbId`, `studyName`, `studyPUI` - - New required properties: - - `environmentParametersDbId` - - * Changed property `experimentalDesign` (object): - - Nullable changed: `true` -> `null` - - New properties: `studyDbId`, `studyName`, `studyPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `growthFacility` (object): - - Nullable changed: `true` -> `null` - - * Changed property `PUI` (string): - - Nullable changed: `null` -> `true` - - * Changed property `lastUpdate` (object): - - Nullable changed: `true` -> `null` - - New properties: `lastUpdateDbId`, `studyDbId`, `studyName`, `studyPUI` - - New required properties: - - `lastUpdateDbId` - -##### `GET` /trials - - -###### Parameters: - -Deleted: `sortBy` in `query` - -Deleted: `sortOrder` in `query` - -##### `POST` /trials - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `studyDbIds` - - * Changed property `datasetAuthorships` (array) - - Changed items (array): - - New properties: `trialDbId`, `trialName`, `trialPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `publications` (array) - - Changed items (array): - - New properties: `trialDbId`, `trialName`, `trialPUI` - -##### `PUT` /trials/{trialDbId} - - -###### Request: - -* Changed content type : `application/json` - - New properties: `studyDbIds` - - * Changed property `datasetAuthorships` (array) - - Changed items (array): - - New properties: `trialDbId`, `trialName`, `trialPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `publications` (array) - - Changed items (array): - - New properties: `trialDbId`, `trialName`, `trialPUI` - -##### `GET` /variants - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `analysis` - - Deleted properties: `alternateBases`, `alternate_bases`, `variantSetDbIds` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /variants/{variantDbId} - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - New properties: `analysis` - - Deleted properties: `alternateBases`, `alternate_bases`, `variantSetDbIds` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /variants/{variantDbId}/calls - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` - - * Changed property `data` (array) - - Changed items (array): - - Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - -##### `GET` /variantsets - - -###### Parameters: - -Added: `externalReferenceID` in `query` - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `referenceSetName`, `studyName`, `studyPUI` - - Deleted properties: `availableFormats` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `true` - - * Changed property `analysis` (array) - - Changed items (array): - - New properties: `variantSetDbId`, `variantSetName` - - New required properties: - - `analysisDbId` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `metadataFields` (array) - - Changed items (array): - - New properties: `variantSetDbId`, `variantSetName` - - * Changed property `dataType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldAbbreviation` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldName` (string): - - Nullable changed: `null` -> `true` - -##### `GET` /variantsets/{variantSetDbId} - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - New properties: `referenceSetName`, `studyName`, `studyPUI` - - Deleted properties: `availableFormats` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `true` - - * Changed property `analysis` (array) - - Changed items (array): - - New properties: `variantSetDbId`, `variantSetName` - - New required properties: - - `analysisDbId` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `metadataFields` (array) - - Changed items (array): - - New properties: `variantSetDbId`, `variantSetName` - - * Changed property `dataType` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldAbbreviation` (string): - - Nullable changed: `null` -> `true` - - * Changed property `fieldName` (string): - - Nullable changed: `null` -> `true` - -##### `GET` /variantsets/{variantSetDbId}/calls - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - Deleted properties: `expandHomozygotes`, `sepPhased`, `sepUnphased`, `unknownString` - - * Changed property `data` (array) - - Changed items (array): - - Deleted properties: `genotype`, `genotype_likelihood`, `variantName` - -##### `GET` /variantsets/{variantSetDbId}/callsets - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `sampleName`, `samplePUI`, `studyName`, `studyPUI` - - Deleted properties: `variantSetDbIds` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `GET` /variantsets/{variantSetDbId}/variants - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `analysis` - - Deleted properties: `alternateBases`, `alternate_bases`, `variantSetDbIds` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - -##### `POST` /attributes - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `attributeValueDbIds`, `methodDbId`, `methodName`, `methodPUI`, `scaleDbId`, `scaleName`, `scalePUI`, `traitDbId`, `traitName`, `traitPUI` - - Deleted properties: `method`, `scale`, `trait` - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - Removed required properties: - - `method` - - `scale` - - `trait` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `ontologyReference` (object): - - Nullable changed: `true` -> `null` - - New properties: `ontologyReferenceDbId` - - * Changed property `documentationLinks` (array) - - Changed items (array): - - * Changed property `URL` (string): - - Nullable changed: `null` -> `true` - - * Changed property `type` (string): - - Nullable changed: `null` -> `true` - -##### `PUT` /attributes/{attributeDbId} - - -###### Request: - -* Changed content type : `application/json` - - New properties: `attributeValueDbIds`, `methodDbId`, `methodName`, `methodPUI`, `scaleDbId`, `scaleName`, `scalePUI`, `traitDbId`, `traitName`, `traitPUI` - - Deleted properties: `method`, `scale`, `trait` - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - Removed required properties: - - `method` - - `scale` - - `trait` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `ontologyReference` (object): - - Nullable changed: `true` -> `null` - - New properties: `ontologyReferenceDbId` - - * Changed property `documentationLinks` (array) - - Changed items (array): - - * Changed property `URL` (string): - - Nullable changed: `null` -> `true` - - * Changed property `type` (string): - - Nullable changed: `null` -> `true` - -##### `POST` /images - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `imageContent`, `observationUnitName`, `observationUnitPUI` - - Deleted properties: `observationDbIds` - - * Changed property `mimeType` (string): - - Pattern changed: `image/.*` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `imageLocation` (object): - - Nullable changed: `true` -> `null` - - * Changed property `type` (string): - - Default changed: `Feature` -> `none` - - * Changed property `geometry` (object -> null): - - Type changed: `object` -> `null` - -##### `PUT` /images/{imageDbId} - - -###### Request: - -* Changed content type : `application/json` - - New properties: `imageContent`, `observationUnitName`, `observationUnitPUI` - - Deleted properties: `observationDbIds` - - * Changed property `mimeType` (string): - - Pattern changed: `image/.*` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `imageLocation` (object): - - Nullable changed: `true` -> `null` - - * Changed property `type` (string): - - Default changed: `Feature` -> `none` - - * Changed property `geometry` (object -> null): - - Type changed: `object` -> `null` - -##### `POST` /locations - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `childLocationDbIds`, `locationDbId` - - Deleted properties: `parentLocationDbId`, `parentLocationName` - - * Changed property `locationName` (string): - - Nullable changed: `null` -> `true` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `coordinates` (object): - - Nullable changed: `true` -> `null` - - * Changed property `type` (string): - - Default changed: `Feature` -> `none` - - * Changed property `geometry` (object -> null): - - Type changed: `object` -> `null` - -##### `PUT` /locations/{locationDbId} - - -###### Request: - -* Changed content type : `application/json` - - New properties: `childLocationDbIds`, `locationDbId` - - Deleted properties: `parentLocationDbId`, `parentLocationName` - - * Changed property `locationName` (string): - - Nullable changed: `null` -> `true` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `coordinates` (object): - - Nullable changed: `true` -> `null` - - * Changed property `type` (string): - - Default changed: `Feature` -> `none` - - * Changed property `geometry` (object -> null): - - Type changed: `object` -> `null` - -##### `PUT` /observations - - -###### Return Type: - -Deleted response : **404** - -##### `POST` /observations - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `germplasmPUI`, `observationUnitPUI`, `observationVariablePUI`, `seasonDbId`, `seasonName`, `studyName`, `studyPUI` - - Deleted properties: `season` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `geoCoordinates` (object): - - Nullable changed: `true` -> `null` - - * Changed property `type` (string): - - Default changed: `Feature` -> `none` - - * Changed property `geometry` (object -> null): - - Type changed: `object` -> `null` - -###### Return Type: - -Deleted response : **404** - -##### `POST` /observationunits - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `germplasmPUI`, `studyPUI`, `trialPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `treatments` (array) - - Changed items (array): - - New properties: `observationUnitDbId`, `observationUnitName`, `observationUnitPUI` - - * Changed property `observationUnitPosition` (object): - - Nullable changed: `true` -> `null` - - New properties: `observationUnitDbId`, `observationUnitName`, `observationUnitPUI` - - * Changed property `geoCoordinates` (object -> array): - - Type changed: `object` -> `array` - - * Changed property `positionCoordinateXType` (string): - - Nullable changed: `true` -> `null` - - * Changed property `positionCoordinateYType` (string): - - Nullable changed: `true` -> `null` - - * Changed property `observationLevelRelationships` (array) - - Changed items (array): - - New properties: `observationUnitName`, `observationUnitPUI` - - * Changed property `observationUnitDbId` (string): - - Nullable changed: `true` -> `null` - -##### `GET` /pedigree - - -###### Return Type: - -Deleted response : **404** - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) + * Changed property `data` (array) Changed items (array): - New properties: `crossingProjectName`, `pedigreeNodeDbId`, `siblingDbIds` - - Deleted properties: `siblings` - - New required properties: - - `germplasmPUI` - - `pedigreeNodeDbId` - - * Changed property `breedingMethodDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `breedingMethodName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossingProjectDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmPUI` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `parents` (array) - - Changed items (array): - - New properties: `germplasmPUI`, `pedigreeNodeDbId` - - New required properties: - - `germplasmName` - - `germplasmPUI` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `parentType` (string): - - Removed enum values: [CLONAL] - -##### `POST` /pedigree - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - New properties: `crossingProjectName`, `pedigreeNodeDbId`, `siblingDbIds` - - Deleted properties: `siblings` - - New required properties: - - `germplasmPUI` - - `pedigreeNodeDbId` - - * Changed property `breedingMethodDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `breedingMethodName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossingProjectDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmPUI` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `parents` (array) - - Changed items (array): - - New properties: `germplasmPUI`, `pedigreeNodeDbId` - - New required properties: - - `germplasmName` - - `germplasmPUI` - - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `parentType` (string): - - Removed enum values: [CLONAL] - -###### Return Type: - -Deleted response : **404** - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `crossingProjectName`, `pedigreeNodeDbId`, `siblingDbIds` - - Deleted properties: `siblings` - - New required properties: - - `germplasmPUI` - - `pedigreeNodeDbId` - - * Changed property `breedingMethodDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `breedingMethodName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossingProjectDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmPUI` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed + Deleted properties: `germplasmPUI` * Changed property `parents` (array) Changed items (array): - New properties: `germplasmPUI`, `pedigreeNodeDbId` - New required properties: - `germplasmName` - - `germplasmPUI` * Changed property `germplasmName` (string): - Nullable changed: `true` -> `null` - * Changed property `parentType` (string): - - Removed enum values: [CLONAL] - ##### `POST` /search/images @@ -2481,14 +545,9 @@ Changed response : **200** * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - * Changed property `imageLocation` (object) - New properties: `germplasmOrigin`, `imageDbId`, `imageName`, `observationDbId`, `observationUnit` - - * Changed property `type` (string): - - Default changed: `Feature` -> `none` + New properties: `germplasmOrigin`, `imageDbId`, `imageName`, `imagePUI`, `observationDbId`, `observationName`, `observationPUI`, `observationUnit` * Changed property `geometry` (object -> null): - Type changed: `object` -> `null` @@ -2500,45 +559,10 @@ Changed response : **200** * Changed content type : `application/json` - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - - * Changed property `abbreviations` (array): - - Nullable changed: `true` -> `null` - - * Changed property `altitudeMax` (number): - - Nullable changed: `true` -> `null` - - * Changed property `altitudeMin` (number): - - Nullable changed: `true` -> `null` - - * Changed property `countryCodes` (array): - - Nullable changed: `true` -> `null` - - * Changed property `countryNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `instituteAddresses` (array): - - Nullable changed: `true` -> `null` - - * Changed property `instituteNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `locationTypes` (array): - - Nullable changed: `true` -> `null` - - * Changed property `parentLocationDbIds` (array): - - Nullable changed: `true` -> `null` - - * Changed property `parentLocationNames` (array): - - Nullable changed: `true` -> `null` - * Changed property `coordinates` (object): - Nullable changed: `true` -> `null` - New properties: `germplasmOrigin`, `imageDbId`, `imageName`, `observationDbId`, `observationUnit` - - * Changed property `type` (string): - - Default changed: `Feature` -> `none` + New properties: `germplasmOrigin`, `imageDbId`, `imageName`, `imagePUI`, `observationDbId`, `observationName`, `observationPUI`, `observationUnit` * Changed property `geometry` (object -> null): - Type changed: `object` -> `null` @@ -2546,51 +570,6 @@ Changed response : **200** ##### `POST` /search/pedigree -###### Request: - -* Changed content type : `application/json` - - Deleted properties: `externalReferenceIDs`, `externalReferenceIds`, `externalReferenceSources`, `page`, `pageSize` - - * Changed property `accessionNumbers` (array): - - Nullable changed: `true` -> `null` - - * Changed property `binomialNames` (array): - - Nullable changed: `true` -> `null` - - * Changed property `collections` (array): - - Nullable changed: `true` -> `null` - - * Changed property `familyCodes` (array): - - Nullable changed: `true` -> `null` - - * Changed property `genus` (array): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmPUIs` (array): - - Nullable changed: `true` -> `null` - - * Changed property `includeFullTree` (boolean): - - Nullable changed: `true` -> `null` - - * Changed property `includeParents` (boolean): - - Nullable changed: `true` -> `null` - - * Changed property `includeProgeny` (boolean): - - Nullable changed: `true` -> `null` - - * Changed property `includeSiblings` (boolean): - - Nullable changed: `true` -> `null` - - * Changed property `instituteCodes` (array): - - Nullable changed: `true` -> `null` - - * Changed property `species` (array): - - Nullable changed: `true` -> `null` - - * Changed property `synonyms` (array): - - Nullable changed: `true` -> `null` - ###### Return Type: Changed response : **200** @@ -2603,59 +582,23 @@ Changed response : **200** Changed items (array): - New properties: `crossingProjectName`, `pedigreeNodeDbId`, `siblingDbIds` - - Deleted properties: `siblings` - - New required properties: - - `germplasmPUI` - - `pedigreeNodeDbId` - - * Changed property `breedingMethodDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `breedingMethodName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossingProjectDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmPUI` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed + Deleted properties: `germplasmPUI` * Changed property `parents` (array) Changed items (array): - New properties: `germplasmPUI`, `pedigreeNodeDbId` - New required properties: - `germplasmName` - - `germplasmPUI` * Changed property `germplasmName` (string): - Nullable changed: `true` -> `null` - * Changed property `parentType` (string): - - Removed enum values: [CLONAL] - ##### `GET` /search/pedigree/{searchResultsDbId} ###### Return Type: -Deleted response : **202** - -Deleted response : **404** - Changed response : **200** * Changed content type : `application/json` @@ -2666,50 +609,18 @@ Changed response : **200** Changed items (array): - New properties: `crossingProjectName`, `pedigreeNodeDbId`, `siblingDbIds` - - Deleted properties: `siblings` - - New required properties: - - `germplasmPUI` - - `pedigreeNodeDbId` - - * Changed property `breedingMethodDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `breedingMethodName` (string): - - Nullable changed: `true` -> `null` - - * Changed property `crossingProjectDbId` (string): - - Nullable changed: `true` -> `null` - - * Changed property `germplasmPUI` (string): - - Nullable changed: `true` -> `null` - - * Changed property `externalReferences` (array): - - Nullable changed: `null` -> `true` - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed + Deleted properties: `germplasmPUI` * Changed property `parents` (array) Changed items (array): - New properties: `germplasmPUI`, `pedigreeNodeDbId` - New required properties: - `germplasmName` - - `germplasmPUI` * Changed property `germplasmName` (string): - Nullable changed: `true` -> `null` - * Changed property `parentType` (string): - - Removed enum values: [CLONAL] - ##### `POST` /variables @@ -2719,43 +630,10 @@ Changed response : **200** Changed items (array): - New properties: `methodDbId`, `methodName`, `methodPUI`, `scaleDbId`, `scaleName`, `scalePUI`, `traitDbId`, `traitName`, `traitPUI` - - Deleted properties: `method`, `scale`, `trait` - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - Removed required properties: - - `method` - - `scale` - - `trait` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - * Changed property `ontologyReference` (object): - - Nullable changed: `true` -> `null` - - New properties: `ontologyReferenceDbId` + - Nullable changed: `true` -> `false` - * Changed property `documentationLinks` (array) - - Changed items (array): - - * Changed property `URL` (string): - - Nullable changed: `null` -> `true` - - * Changed property `type` (string): - - Nullable changed: `null` -> `true` + New properties: `ontologyPUI`, `ontologyReferenceDbId` ##### `PUT` /variables/{observationVariableDbId} @@ -2764,43 +642,10 @@ Changed response : **200** * Changed content type : `application/json` - New properties: `methodDbId`, `methodName`, `methodPUI`, `scaleDbId`, `scaleName`, `scalePUI`, `traitDbId`, `traitName`, `traitPUI` - - Deleted properties: `method`, `scale`, `trait` - - New required properties: - - `methodDbId` - - `methodName` - - `scaleDbId` - - `scaleName` - - `traitName` - - Removed required properties: - - `method` - - `scale` - - `trait` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - * Changed property `ontologyReference` (object): - - Nullable changed: `true` -> `null` - - New properties: `ontologyReferenceDbId` - - * Changed property `documentationLinks` (array) - - Changed items (array): - - * Changed property `URL` (string): - - Nullable changed: `null` -> `true` + - Nullable changed: `true` -> `false` - * Changed property `type` (string): - - Nullable changed: `null` -> `true` + New properties: `ontologyPUI`, `ontologyReferenceDbId` ##### `POST` /germplasm @@ -2811,50 +656,13 @@ Changed response : **200** Changed items (array): - New properties: `sampleDbIds` - - * Changed property `donors` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `storageTypes` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `synonyms` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `taxonIds` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + New properties: `breedingMethodPUI` * Changed property `germplasmOrigin` (array) Changed items (array): - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `coordinates` (object): - - Nullable changed: `true` -> `null` - - * Changed property `type` (string): - - Default changed: `Feature` -> `none` + * Changed property `coordinates` (object) * Changed property `geometry` (object -> null): - Type changed: `object` -> `null` @@ -2866,50 +674,13 @@ Changed response : **200** * Changed content type : `application/json` - New properties: `sampleDbIds` - - * Changed property `donors` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `externalReferences` (array) - - Changed items (array): - - * Changed property `referenceID` (string): - - Deprecated status changed - - * Changed property `storageTypes` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `synonyms` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `taxonIds` (array) - - Changed items (array): - - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` + New properties: `breedingMethodPUI` * Changed property `germplasmOrigin` (array) Changed items (array): - New properties: `germplasmDbId`, `germplasmName`, `germplasmPUI` - - * Changed property `coordinates` (object): - - Nullable changed: `true` -> `null` - - * Changed property `type` (string): - - Default changed: `Feature` -> `none` + * Changed property `coordinates` (object) * Changed property `geometry` (object -> null): - Type changed: `object` -> `null` From 8a7264acd2c5913981751971e119d3c6ca487853 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Wed, 20 May 2026 12:31:21 +1200 Subject: [PATCH 47/62] Add script to check and fix nullable consistency between YAML and JSON schemas --- Scripts/checkNullableConsistency.py | 201 ++++++++++++++++++++++++++++ 1 file changed, 201 insertions(+) create mode 100644 Scripts/checkNullableConsistency.py diff --git a/Scripts/checkNullableConsistency.py b/Scripts/checkNullableConsistency.py new file mode 100644 index 00000000..82fb316b --- /dev/null +++ b/Scripts/checkNullableConsistency.py @@ -0,0 +1,201 @@ +#!/usr/bin/env python3 +""" +Check and fix nullable consistency between YAML NewRequest schemas and JSON entity schemas. + +For each *NewRequest.yaml, any property marked nullable: true must also be nullable +in the corresponding *.json entity schema in BrAPI-Schema. + +Usage: + python checkNullableConsistency.py [--fix] [--root ] + +Options: + --fix Apply fixes to JSON files (default: dry run / report only) + --root Root of the BrAPI workspace (default: current directory) +""" + +import yaml +import json +import glob +import os +import sys +import copy + + +def find_json_entity_file(entity_name, schema_root): + """Find the JSON schema file for an entity name in BrAPI-Schema.""" + matches = glob.glob(os.path.join(schema_root, "**", f"{entity_name}.json"), recursive=True) + # Exclude files in Requests/ subfolder + matches = [m for m in matches if "Requests" not in m.replace("\\", "/")] + return matches[0] if matches else None + + +def collect_nullable_yaml_properties(schema_def, prefix=""): + """ + Recursively collect all property names (top-level only) that are nullable: true + from an OpenAPI schema definition. Returns dict of {prop_name: prop_def}. + """ + nullable = {} + for prop_name, prop_def in schema_def.get("properties", {}).items(): + if prop_def.get("nullable", False): + nullable[prefix + prop_name] = prop_def + return nullable + + +def derive_json_rel_name(yaml_prop_name): + """ + Given a YAML flat property name like 'programDbId' or 'programName', + derive the likely JSON relationship field name (e.g. 'program'). + Returns the candidate name, or None if the pattern doesn't apply. + """ + for suffix in ("DbId", "Name", "PUI"): + if yaml_prop_name.endswith(suffix) and len(yaml_prop_name) > len(suffix): + return yaml_prop_name[: -len(suffix)] + return None + + +def is_nullable_in_json(json_prop): + """Return True if a JSON Schema property is already nullable.""" + prop_type = json_prop.get("type", "") + if isinstance(prop_type, list) and "null" in prop_type: + return True + if "anyOf" in json_prop: + for item in json_prop["anyOf"]: + if item.get("type") == "null": + return True + return False + + +def make_nullable_in_json(json_prop): + """ + Return a copy of json_prop that is nullable. + - If the property has a $ref (and no anyOf yet), wrap $ref in anyOf with null. + - If the property has a simple type, change to ["null", type]. + """ + prop = copy.deepcopy(json_prop) + + if "$ref" in prop: + ref = prop.pop("$ref") + anyof_entry = {"$ref": ref} + prop["anyOf"] = [anyof_entry, {"type": "null"}] + return prop + + prop_type = prop.get("type") + if isinstance(prop_type, str): + prop["type"] = ["null", prop_type] + elif isinstance(prop_type, list) and "null" not in prop_type: + prop["type"] = ["null"] + prop_type + + # Also ensure null is in enum if present + if "enum" in prop and None not in prop["enum"]: + prop["enum"] = prop["enum"] + [None] + + return prop + + +def get_entity_name_from_yaml(yaml_path): + """Derive entity name from a *NewRequest.yaml path.""" + basename = os.path.basename(yaml_path) + return basename.replace("NewRequest.yaml", "") + + +def main(): + fix_mode = "--fix" in sys.argv + root = "." + if "--root" in sys.argv: + idx = sys.argv.index("--root") + root = sys.argv[idx + 1] + + yaml_root = os.path.join(root, "Specification") + schema_root = os.path.join(root, "Specification", "BrAPI-Schema") + + yaml_files = sorted(glob.glob( + os.path.join(yaml_root, "**", "*NewRequest.yaml"), recursive=True + )) + + total_issues = 0 + total_fixed = 0 + + for yaml_file in yaml_files: + entity_name = get_entity_name_from_yaml(yaml_file) + + json_file = find_json_entity_file(entity_name, schema_root) + if not json_file: + print(f"[SKIP] No JSON file found for '{entity_name}' (from {os.path.basename(yaml_file)})") + continue + + with open(yaml_file, "r", encoding="utf-8") as f: + try: + yaml_obj = yaml.safe_load(f) + except yaml.YAMLError as e: + print(f"[ERROR] Failed to parse {yaml_file}: {e}") + continue + + with open(json_file, "r", encoding="utf-8") as f: + try: + json_obj = json.load(f) + except json.JSONDecodeError as e: + print(f"[ERROR] Failed to parse {json_file}: {e}") + continue + + # Get schemas from YAML (look for entity name or NewRequest name) + yaml_schemas = yaml_obj.get("components", {}).get("schemas", {}) + yaml_schema_def = ( + yaml_schemas.get(f"{entity_name}NewRequest") + or yaml_schemas.get(entity_name) + or {} + ) + + nullable_yaml_props = collect_nullable_yaml_properties(yaml_schema_def) + if not nullable_yaml_props: + continue + + # Get properties from JSON entity + json_entity_def = json_obj.get("$defs", {}).get(entity_name, {}) + json_props = json_entity_def.get("properties", {}) + + issues = [] # list of (json_prop_name, yaml_prop_name) + seen_json_props = set() + for prop_name, yaml_prop_def in nullable_yaml_props.items(): + # Check direct name match + if prop_name in json_props: + if prop_name not in seen_json_props and not is_nullable_in_json(json_props[prop_name]): + issues.append((prop_name, prop_name)) + seen_json_props.add(prop_name) + continue + + # Check derived relationship name (e.g. programDbId -> program) + rel_name = derive_json_rel_name(prop_name) + if rel_name and rel_name in json_props: + if rel_name not in seen_json_props and not is_nullable_in_json(json_props[rel_name]): + issues.append((rel_name, prop_name)) + seen_json_props.add(rel_name) + + if issues: + total_issues += len(issues) + print(f"\n[{entity_name}] YAML: {os.path.relpath(yaml_file, root)} | JSON: {os.path.relpath(json_file, root)}") + for json_prop_name, yaml_prop_name in issues: + yaml_type = yaml_schema_def["properties"][yaml_prop_name].get("type", "object/$ref") + json_type = json_props[json_prop_name].get("type", "$ref") + label = json_prop_name if json_prop_name == yaml_prop_name else f"{json_prop_name} (from yaml:{yaml_prop_name})" + print(f" MISMATCH '{label}' yaml_type={yaml_type} json_type={json_type}") + + if fix_mode: + for json_prop_name, yaml_prop_name in issues: + json_props[json_prop_name] = make_nullable_in_json(json_props[json_prop_name]) + print(f" FIXED '{json_prop_name}'") + total_fixed += 1 + + with open(json_file, "w", encoding="utf-8") as f: + json.dump(json_obj, f, indent=4, ensure_ascii=False) + f.write("\n") + + print(f"\n{'='*60}") + print(f"Total mismatches found: {total_issues}") + if fix_mode: + print(f"Total fixes applied: {total_fixed}") + else: + print("Run with --fix to apply corrections.") + + +if __name__ == "__main__": + main() From 7c9a6f1d211b0073252c77b85c727b7b0b64bc3f Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Wed, 20 May 2026 19:47:05 +1200 Subject: [PATCH 48/62] changed schema tool version to 0.69 --- generator/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/generator/build.gradle b/generator/build.gradle index f694fb39..afbb3101 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.68.0' + brapiSchemaToolsVersion = '0.69.0' } repositories { From fe79bbe94b8eba3719180b45c6ed096168364cf3 Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Wed, 20 May 2026 07:50:10 +0000 Subject: [PATCH 49/62] Generate specifications (manually triggered) --- Specification/Generated/BrAPI-Germplasm.yaml | 2 -- Specification/Generated/brapi_generated.json | 3 --- Specification/Generated/brapi_openapi_comparison.md | 2 -- 3 files changed, 7 deletions(-) diff --git a/Specification/Generated/BrAPI-Germplasm.yaml b/Specification/Generated/BrAPI-Germplasm.yaml index 3200cf83..15a1e21b 100644 --- a/Specification/Generated/BrAPI-Germplasm.yaml +++ b/Specification/Generated/BrAPI-Germplasm.yaml @@ -4249,8 +4249,6 @@ components: example: Aspergillus germplasmDbId: type: string - germplasmName: - type: string instituteCode: type: string description: "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute\ diff --git a/Specification/Generated/brapi_generated.json b/Specification/Generated/brapi_generated.json index 56c257bf..3450d31d 100644 --- a/Specification/Generated/brapi_generated.json +++ b/Specification/Generated/brapi_generated.json @@ -14343,9 +14343,6 @@ "germplasmDbId" : { "type" : "string" }, - "germplasmName" : { - "type" : "string" - }, "instituteCode" : { "type" : "string", "description" : "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index 29d857ad..c3acbbc5 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -77,8 +77,6 @@ Changed response : **200** * Changed property `result` (object) - New properties: `germplasmName` - Deleted properties: `germplasmPUI` ##### `PUT` /samples From 3e3406fc071bd18ab71c74a1fd4d9ab9b735efd9 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Thu, 21 May 2026 19:49:12 +1200 Subject: [PATCH 50/62] changed schema tool version to 0.72, fixed other issues. --- .../Schemas/AlleleMatrixSearchRequest.yaml | 2 +- .../VariantSets/Schemas/VariantSet.yaml | 2 +- .../Germplasm/Schemas/GermplasmMCPD.yaml | 1 - .../Pedigree/Schemas/PedigreeNode.yaml | 2 - .../BrAPI-Genotyping/VariantSet.json | 3 -- .../BrAPI-Schema/BrAPI-Phenotyping/Image.json | 14 +------ .../Requests/AlleleMatrixRequest.json | 20 +++++++--- .../BrAPI-Schema/Requests/CallRequest.json | 3 +- .../Requests/SeedLotTransactionRequest.json | 37 +++++++++++++++++++ .../BrAPI-Schema/Requests/TrialRequest.json | 23 ++++++++++++ .../BrAPI-Schema/Requests/VarientRequest.json | 5 +++ generator/build.gradle | 2 +- 12 files changed, 85 insertions(+), 29 deletions(-) create mode 100644 Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json diff --git a/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixSearchRequest.yaml b/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixSearchRequest.yaml index fae4c380..d84fb3ff 100644 --- a/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixSearchRequest.yaml +++ b/Specification/BrAPI-Genotyping/AlleleMatrix/Schemas/AlleleMatrixSearchRequest.yaml @@ -60,7 +60,7 @@ components: example: ['Genotype', 'Read Depth'] dataMatrixAbbreviations: description: |- - `dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response. + `dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response. type: array nullable: true items: diff --git a/Specification/BrAPI-Genotyping/VariantSets/Schemas/VariantSet.yaml b/Specification/BrAPI-Genotyping/VariantSets/Schemas/VariantSet.yaml index a9244dae..5c2fdc0e 100644 --- a/Specification/BrAPI-Genotyping/VariantSets/Schemas/VariantSet.yaml +++ b/Specification/BrAPI-Genotyping/VariantSets/Schemas/VariantSet.yaml @@ -97,6 +97,6 @@ components: referenceSetDbId: description: The ID of the reference set that describes the sequences used by the variants in this set. type: string - nullable: tru + nullable: true example: 57eae639 diff --git a/Specification/BrAPI-Germplasm/Germplasm/Schemas/GermplasmMCPD.yaml b/Specification/BrAPI-Germplasm/Germplasm/Schemas/GermplasmMCPD.yaml index 81a97069..258b2228 100644 --- a/Specification/BrAPI-Germplasm/Germplasm/Schemas/GermplasmMCPD.yaml +++ b/Specification/BrAPI-Germplasm/Germplasm/Schemas/GermplasmMCPD.yaml @@ -275,7 +275,6 @@ components: germplasmPUI: description: MCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties. type: string - nullable: true example: http://pui.per/accession/A0403652 instituteCode: description: MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with "obsolete" codes, see "Common formatting rules (v)". diff --git a/Specification/BrAPI-Germplasm/Pedigree/Schemas/PedigreeNode.yaml b/Specification/BrAPI-Germplasm/Pedigree/Schemas/PedigreeNode.yaml index 07905dd8..a6022908 100644 --- a/Specification/BrAPI-Germplasm/Pedigree/Schemas/PedigreeNode.yaml +++ b/Specification/BrAPI-Germplasm/Pedigree/Schemas/PedigreeNode.yaml @@ -43,7 +43,6 @@ components: MCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties. type: string - nullable: true example: http://pui.per/accession/A0000003 defaultDisplayName: description: Human readable name used for display purposes @@ -100,7 +99,6 @@ components: germplasmName: description: A human readable name for a germplasm type: string - nullable: true example: A0000592 parentType: $ref: '#/components/schemas/ParentType' diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json index 91a1095c..cc9889ea 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json @@ -236,9 +236,6 @@ "referencedAttribute": "analysis" } }, - "required": [ - "analysisDbId" - ], "title": "Analysis", "description": "An analysis contains an interpretation of one or several experiments. (e.g. SNVs, copy number variations, methylation status) together with information about the methodology used.", "type": "object", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json index f735551e..868f5a33 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json @@ -41,11 +41,6 @@ "title": "ExternalReferences", "type": "array" }, - "imageContent": { - "description": "The content of the image", - "type": "string", - "format": "binary" - }, "imageDbId": { "description": "The unique identifier of an image", "type": "string" @@ -75,14 +70,7 @@ "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", "relationshipType": "one-to-one", "referencedAttribute": "image", - "anyOf": [ - { - "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON" - }, - { - "type": "null" - } - ] + "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON" }, "imageName": { "description": "The human readable name of an image. Might be the same as 'imageFileName', but could be different.", diff --git a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json index d0080959..ccffe5ef 100644 --- a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json +++ b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json @@ -67,17 +67,25 @@ "type": ["null", "integer"] }, "dataMatrixNames": { - "description": "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", - "type": ["null", "string"], + "description": "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "type": ["null", "array"], + "items": { + "type": "string" + }, "example": [ - "Genotype,Read Depth" + "Genotype", + "Read Depth" ] }, "dataMatrixAbbreviations": { - "description": "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", - "type": ["null", "string"], + "description": "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "type": ["null", "array"], + "items": { + "type": "string" + }, "example": [ - "GT,RD" + "GT", + "RD" ] }, "positionRanges": { diff --git a/Specification/BrAPI-Schema/Requests/CallRequest.json b/Specification/BrAPI-Schema/Requests/CallRequest.json index 2dbb870f..bb52ddba 100644 --- a/Specification/BrAPI-Schema/Requests/CallRequest.json +++ b/Specification/BrAPI-Schema/Requests/CallRequest.json @@ -58,7 +58,8 @@ }, "pageToken": { "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response.", - "type": "string" + "type": "string", + "deprecated": true } }, "brapi-metadata": { diff --git a/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json b/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json new file mode 100644 index 00000000..aa7d660b --- /dev/null +++ b/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json @@ -0,0 +1,37 @@ +{ + "$defs": { + "SeedLotTransactionRequest": { + "type": "object", + "properties": { + "transactionDbIs": { + "description": "Unique id for a Transaction that has occurred", + "type": "array", + "items": { + "type": "string" + } + }, + "transactionDirection": { + "description": "Filter results to only include transactions directed to the specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The default value for this parameter is BOTH", + "enum": [ + "TO", + "FROM", + "BOTH" + ], + "type": [ + "null", + "string" + ] + } + }, + "brapi-metadata": { + "request": true, + "subQueryProperties" : [ + "transactionDbIds", + "transactionDirection" + ] + } + } + }, + "$id": "https://brapi.org/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json", + "$schema": "http://json-schema.org/draft/2020-12/schema" +} \ No newline at end of file diff --git a/Specification/BrAPI-Schema/Requests/TrialRequest.json b/Specification/BrAPI-Schema/Requests/TrialRequest.json index ec662643..f7a8e2e3 100644 --- a/Specification/BrAPI-Schema/Requests/TrialRequest.json +++ b/Specification/BrAPI-Schema/Requests/TrialRequest.json @@ -56,6 +56,29 @@ "https://doi.org/01093190", "https://doi.org/11192409" ] + }, + "sortBy": { + "description": "Name of the field to sort by.", + "enum": [ + "trialDbId", + "trialName", + "programDbId", + "programName", + "locationDbId", + "startDate", + "endDate" + ], + "type": ["null", "string"] + }, + "sortOrder": { + "description": "Sort order direction. Ascending/Descending.", + "enum": [ + "ASC", + "DESC", + "asc", + "desc" + ], + "type": ["null", "string"] } } } diff --git a/Specification/BrAPI-Schema/Requests/VarientRequest.json b/Specification/BrAPI-Schema/Requests/VarientRequest.json index 46da2f1d..565d813c 100644 --- a/Specification/BrAPI-Schema/Requests/VarientRequest.json +++ b/Specification/BrAPI-Schema/Requests/VarientRequest.json @@ -88,6 +88,11 @@ "ba63d810", "434d1760" ] + }, + "pageToken": { + "description": "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response.", + "type": "string", + "deprecated": true } } } diff --git a/generator/build.gradle b/generator/build.gradle index afbb3101..9fc4f032 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.69.0' + brapiSchemaToolsVersion = '0.72.0' } repositories { From 53c1217cc34f6b628970eeb22ca72f6d4f86ca80 Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Thu, 21 May 2026 07:59:32 +0000 Subject: [PATCH 51/62] Generate specifications (manually triggered) --- Specification/Generated/BrAPI-Core.yaml | 133 +++++-- Specification/Generated/BrAPI-Genotyping.yaml | 198 ++++++---- Specification/Generated/BrAPI-Germplasm.yaml | 132 +++++-- .../Generated/BrAPI-Phenotyping.yaml | 170 ++++----- .../Generated/brapi_generated.graphqls | 31 +- Specification/Generated/brapi_generated.json | 355 +++++++++--------- Specification/Generated/brapi_openapi.json | 27 +- .../Generated/brapi_openapi_comparison.md | 316 +++++----------- 8 files changed, 700 insertions(+), 662 deletions(-) diff --git a/Specification/Generated/BrAPI-Core.yaml b/Specification/Generated/BrAPI-Core.yaml index 9695bd1f..55788e37 100644 --- a/Specification/Generated/BrAPI-Core.yaml +++ b/Specification/Generated/BrAPI-Core.yaml @@ -790,6 +790,33 @@ paths: required: false schema: type: string + - name: sortBy + in: query + description: Name of the field to sort by. + required: false + schema: + type: string + description: Name of the field to sort by. + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + - name: sortOrder + in: query + description: Sort order direction. Ascending/Descending. + required: false + schema: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - ASC + - DESC + - asc + - desc - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" @@ -1838,19 +1865,21 @@ components: items: type: string dataMatrixAbbreviations: - type: string - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." nullable: true - example: "GT,RD" + items: + type: string dataMatrixNames: - type: string - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." nullable: true - example: "Genotype,Read Depth" + items: + type: string dimensionCallSetPage: type: integer description: The requested page number for the CallSet dimension of the @@ -2101,6 +2130,7 @@ components: The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `next_page_token` from the previous response. + deprecated: true sepPhased: type: string description: The string used as a separator for phased allele calls. @@ -2819,22 +2849,6 @@ components: properties: geometry: $ref: "#/components/schemas/GeoJSONGeometry" - germplasmOrigin: - $ref: "#/components/schemas/GermplasmOrigin" - imageDbId: - type: string - imageName: - type: string - imagePUI: - type: string - observationDbId: - type: string - observationName: - type: string - observationPUI: - type: string - observationUnit: - $ref: "#/components/schemas/ObservationUnitPosition" type: type: string description: The literal string "Feature" @@ -6288,21 +6302,35 @@ components: description: Unique id for a seed lot on this server items: type: string + SeedLotTransactionRequest: + type: object + properties: + transactionDbIs: + type: array + description: Unique id for a Transaction that has occurred + items: + type: string + transactionDirection: + type: string + description: "Filter results to only include transactions directed to the\ + \ specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both\ + \ (BOTH). The default value for this parameter is BOTH" + nullable: true + enum: + - TO + - FROM + - BOTH SortBy: type: string description: Name of the field to sort by. enum: - - studyDbId - trialDbId + - trialName - programDbId - - locationDbId - - seasonDbId - - studyType - - studyName - - studyLocation - programName - - germplasmDbId - - observationVariableDbId + - locationDbId + - startDate + - endDate SortOrder: type: string description: Sort order direction. Ascending/Descending. @@ -6915,6 +6943,15 @@ components: description: The unique identifier for a trait. items: type: string + TransactionDirection: + type: string + description: "Filter results to only include transactions directed to the specific\ + \ Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The\ + \ default value for this parameter is BOTH" + enum: + - TO + - FROM + - BOTH Trial: allOf: - $ref: "#/components/schemas/TrialNewRequest" @@ -7102,6 +7139,27 @@ components: \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ \ is before `trial.endDate`" format: date + sortBy: + type: string + description: Name of the field to sort by. + nullable: true + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + nullable: true + enum: + - ASC + - DESC + - asc + - desc studyDbIds: type: array description: List of study identifiers to search for @@ -7531,6 +7589,13 @@ components: \ variants should be returned." format: int32 example: 1500 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + deprecated: true programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ diff --git a/Specification/Generated/BrAPI-Genotyping.yaml b/Specification/Generated/BrAPI-Genotyping.yaml index fccd0df3..a154ce91 100644 --- a/Specification/Generated/BrAPI-Genotyping.yaml +++ b/Specification/Generated/BrAPI-Genotyping.yaml @@ -49,19 +49,18 @@ paths: schema: type: integer format: int32 - - name: dataMatrixNames + - name: dataMatrixName in: query - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth'\ + \ etc). This list controls which data matrices are returned in the response." required: false schema: type: string - - name: dataMatrixAbbreviations + - name: dataMatrixAbbreviation in: query - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." required: false schema: type: string @@ -913,6 +912,15 @@ paths: required: false schema: type: string + - name: pageToken + in: query + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + required: false + schema: + type: string - $ref: "#/components/parameters/externalReferenceId" - $ref: "#/components/parameters/externalReferenceID" - $ref: "#/components/parameters/externalReferenceSource" @@ -2360,19 +2368,21 @@ components: items: type: string dataMatrixAbbreviations: - type: string - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." nullable: true - example: "GT,RD" + items: + type: string dataMatrixNames: - type: string - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." nullable: true - example: "Genotype,Read Depth" + items: + type: string dimensionCallSetPage: type: integer description: The requested page number for the CallSet dimension of the @@ -2510,41 +2520,21 @@ components: items: type: string dataMatrixAbbreviations: - type: string - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." nullable: true - example: "GT,RD" + items: + type: string dataMatrixNames: - type: string - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." - nullable: true - example: "Genotype,Read Depth" - dimensionCallSetPage: - type: integer - description: The requested page number for the CallSet dimension of the - matrix - format: int32 - nullable: true - dimensionCallSetPageSize: - type: integer - description: The requested page size for the CallSet dimension of the matrix - format: int32 - nullable: true - dimensionVariantPage: - type: integer - description: The requested page number for the Variant dimension of the - matrix - format: int32 - nullable: true - dimensionVariantPageSize: - type: integer - description: The requested page size for the Variant dimension of the matrix - format: int32 + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." nullable: true + items: + type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single @@ -2655,8 +2645,6 @@ components: \ for larger datasets, when compared to the Calls endpoints. This makes genotype\ \ data retrieval faster and easier." Analysis: - required: - - analysisDbId type: object properties: analysisDbId: @@ -2928,6 +2916,7 @@ components: The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `next_page_token` from the previous response. + deprecated: true sepPhased: type: string description: The string used as a separator for phased allele calls. @@ -2990,6 +2979,7 @@ components: The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `next_page_token` from the previous response. + deprecated: true sepPhased: type: string description: The string used as a separator for phased allele calls. @@ -3857,22 +3847,6 @@ components: properties: geometry: $ref: "#/components/schemas/GeoJSONGeometry" - germplasmOrigin: - $ref: "#/components/schemas/GermplasmOrigin" - imageDbId: - type: string - imageName: - type: string - imagePUI: - type: string - observationDbId: - type: string - observationName: - type: string - observationPUI: - type: string - observationUnit: - $ref: "#/components/schemas/ObservationUnitPosition" type: type: string description: The literal string "Feature" @@ -7553,21 +7527,35 @@ components: description: Unique id for a seed lot on this server items: type: string + SeedLotTransactionRequest: + type: object + properties: + transactionDbIs: + type: array + description: Unique id for a Transaction that has occurred + items: + type: string + transactionDirection: + type: string + description: "Filter results to only include transactions directed to the\ + \ specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both\ + \ (BOTH). The default value for this parameter is BOTH" + nullable: true + enum: + - TO + - FROM + - BOTH SortBy: type: string description: Name of the field to sort by. enum: - - studyDbId - trialDbId + - trialName - programDbId - - locationDbId - - seasonDbId - - studyType - - studyName - - studyLocation - programName - - germplasmDbId - - observationVariableDbId + - locationDbId + - startDate + - endDate SortOrder: type: string description: Sort order direction. Ascending/Descending. @@ -7846,6 +7834,15 @@ components: description: The unique identifier for a trait. items: type: string + TransactionDirection: + type: string + description: "Filter results to only include transactions directed to the specific\ + \ Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The\ + \ default value for this parameter is BOTH" + enum: + - TO + - FROM + - BOTH TrialParameters: type: object properties: @@ -7932,6 +7929,27 @@ components: \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ \ is before `trial.endDate`" format: date + sortBy: + type: string + description: Name of the field to sort by. + nullable: true + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + nullable: true + enum: + - ASC + - DESC + - asc + - desc studyDbIds: type: array description: List of study identifiers to search for @@ -8380,6 +8398,13 @@ components: \ variants should be returned." format: int32 example: 1500 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + deprecated: true programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -8521,6 +8546,13 @@ components: description: The size of the pages to be returned. Default is `1000`. format: int32 example: 1000 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + deprecated: true programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -8616,6 +8648,18 @@ components: nullable: true items: $ref: "#/components/schemas/Analysis" + availableFormats: + type: array + description: "When the data for a VariantSet is retrieved, it can be retrieved\ + \ in a variety of data formats and file formats. \n
'dataFormat' defines\ + \ the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular,\ + \ etc)\n
'fileFormat' defines the MIME type of the file (ie text/csv,\ + \ application/excel, application/zip). This should also be reflected in\ + \ the Accept and ContentType HTTP headers for every relevant request and\ + \ response." + nullable: true + items: + $ref: "#/components/schemas/AvailableFormat" callSetCount: type: integer description: The number of CallSets included in this VariantSet @@ -8639,7 +8683,7 @@ components: referenceSetDbId: type: string nullable: true - referenceSetName: + studyDbId: type: string nullable: true variantCount: diff --git a/Specification/Generated/BrAPI-Germplasm.yaml b/Specification/Generated/BrAPI-Germplasm.yaml index 15a1e21b..90285372 100644 --- a/Specification/Generated/BrAPI-Germplasm.yaml +++ b/Specification/Generated/BrAPI-Germplasm.yaml @@ -1424,6 +1424,21 @@ paths: required: true schema: type: string + - name: transactionDirection + in: query + description: "Filter results to only include transactions directed to the\ + \ specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both\ + \ (BOTH). The default value for this parameter is BOTH" + required: false + schema: + type: string + description: "Filter results to only include transactions directed to the\ + \ specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both\ + \ (BOTH). The default value for this parameter is BOTH" + enum: + - TO + - FROM + - BOTH - $ref: "#/components/parameters/page" - $ref: "#/components/parameters/pageSize" - $ref: "#/components/parameters/authorizationHeader" @@ -1811,19 +1826,21 @@ components: items: type: string dataMatrixAbbreviations: - type: string - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." nullable: true - example: "GT,RD" + items: + type: string dataMatrixNames: - type: string - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." nullable: true - example: "Genotype,Read Depth" + items: + type: string dimensionCallSetPage: type: integer description: The requested page number for the CallSet dimension of the @@ -2133,6 +2150,7 @@ components: The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `next_page_token` from the previous response. + deprecated: true sepPhased: type: string description: The string used as a separator for phased allele calls. @@ -3068,22 +3086,6 @@ components: properties: geometry: $ref: "#/components/schemas/GeoJSONGeometry" - germplasmOrigin: - $ref: "#/components/schemas/GermplasmOrigin" - imageDbId: - type: string - imageName: - type: string - imagePUI: - type: string - observationDbId: - type: string - observationName: - type: string - observationPUI: - type: string - observationUnit: - $ref: "#/components/schemas/ObservationUnitPosition" type: type: string description: The literal string "Feature" @@ -4249,6 +4251,8 @@ components: example: Aspergillus germplasmDbId: type: string + germplasmPUI: + type: string instituteCode: type: string description: "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute\ @@ -6133,6 +6137,7 @@ components: required: - germplasmDbId - germplasmName + - germplasmPUI type: object properties: additionalInfo: @@ -6170,6 +6175,8 @@ components: type: string germplasmName: type: string + germplasmPUI: + type: string parents: type: array description: "A list of parent germplasm references in the pedigree tree\ @@ -7591,15 +7598,9 @@ components: fromSeedLotDbId: type: string nullable: true - fromSeedLotPUI: - type: string - nullable: true toSeedLotDbId: type: string nullable: true - toSeedLotPUI: - type: string - nullable: true transactionDbId: type: string description: Unique DbId for the Seed Lot Transaction @@ -7619,21 +7620,35 @@ components: nullable: true description: The record of an event where material was moved in or out of a particular SeedLot + SeedLotTransactionRequest: + type: object + properties: + transactionDbIs: + type: array + description: Unique id for a Transaction that has occurred + items: + type: string + transactionDirection: + type: string + description: "Filter results to only include transactions directed to the\ + \ specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both\ + \ (BOTH). The default value for this parameter is BOTH" + nullable: true + enum: + - TO + - FROM + - BOTH SortBy: type: string description: Name of the field to sort by. enum: - - studyDbId - trialDbId + - trialName - programDbId - - locationDbId - - seasonDbId - - studyType - - studyName - - studyLocation - programName - - germplasmDbId - - observationVariableDbId + - locationDbId + - startDate + - endDate SortOrder: type: string description: Sort order direction. Ascending/Descending. @@ -7972,6 +7987,15 @@ components: description: The unique identifier for a trait. items: type: string + TransactionDirection: + type: string + description: "Filter results to only include transactions directed to the specific\ + \ Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The\ + \ default value for this parameter is BOTH" + enum: + - TO + - FROM + - BOTH TrialParameters: type: object properties: @@ -8058,6 +8082,27 @@ components: \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ \ is before `trial.endDate`" format: date + sortBy: + type: string + description: Name of the field to sort by. + nullable: true + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + nullable: true + enum: + - ASC + - DESC + - asc + - desc studyDbIds: type: array description: List of study identifiers to search for @@ -8352,6 +8397,13 @@ components: \ variants should be returned." format: int32 example: 1500 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + deprecated: true programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ diff --git a/Specification/Generated/BrAPI-Phenotyping.yaml b/Specification/Generated/BrAPI-Phenotyping.yaml index f2638c46..03ceab37 100644 --- a/Specification/Generated/BrAPI-Phenotyping.yaml +++ b/Specification/Generated/BrAPI-Phenotyping.yaml @@ -1176,37 +1176,6 @@ paths: $ref: "#/components/responses/403Forbidden" "404": $ref: "#/components/responses/404NotFound" - /images/{imageDbId}/imagecontent: - put: - tags: - - Images - summary: Update the details for an existing string - description: Update the details for an existing string - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: imageDbId - in: path - description: The unique identifier of an image - required: true - schema: - type: string - requestBody: - content: - image/*: - schema: - type: string - format: binary - responses: - "200": - $ref: "#/components/responses/ImageSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" /methods/{methodDbId}: get: tags: @@ -1873,19 +1842,21 @@ components: items: type: string dataMatrixAbbreviations: - type: string - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." nullable: true - example: "GT,RD" + items: + type: string dataMatrixNames: - type: string - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." nullable: true - example: "Genotype,Read Depth" + items: + type: string dimensionCallSetPage: type: integer description: The requested page number for the CallSet dimension of the @@ -2136,6 +2107,7 @@ components: The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `next_page_token` from the previous response. + deprecated: true sepPhased: type: string description: The string used as a separator for phased allele calls. @@ -2883,22 +2855,6 @@ components: properties: geometry: $ref: "#/components/schemas/GeoJSONGeometry" - germplasmOrigin: - $ref: "#/components/schemas/GermplasmOrigin" - imageDbId: - type: string - imageName: - type: string - imagePUI: - type: string - observationDbId: - type: string - observationName: - type: string - observationPUI: - type: string - observationUnit: - $ref: "#/components/schemas/ObservationUnitPosition" type: type: string description: The literal string "Feature" @@ -3401,10 +3357,6 @@ components: a URI. items: $ref: "#/components/schemas/ExternalReference" - imageContent: - type: string - description: The content of the image - format: binary imageFileName: type: string description: "The name of the image file. Might be the same as 'imageName',\ @@ -3450,9 +3402,6 @@ components: observationUnitDbId: type: string nullable: true - observationUnitName: - type: string - nullable: true description: The metadata for an image file that is connected to some phenotypic observation data. ImageRequest: @@ -4133,24 +4082,12 @@ components: observationVariableName: type: string nullable: true - observationVariablePUI: - type: string - nullable: true seasonDbId: type: string nullable: true - seasonName: - type: string - nullable: true - seasonPUI: - type: string - nullable: true studyDbId: type: string nullable: true - studyName: - type: string - nullable: true uploadedBy: type: string description: The name or id of the user who uploaded the observation to @@ -4701,9 +4638,6 @@ components: crossName: type: string nullable: true - crossPUI: - type: string - nullable: true externalReferences: type: array description: An array of external reference ids. These are references to @@ -4724,9 +4658,6 @@ components: locationName: type: string nullable: true - locationPUI: - type: string - nullable: true observationUnitName: type: string description: A human readable name for an observation unit @@ -4746,18 +4677,12 @@ components: programName: type: string nullable: true - programPUI: - type: string - nullable: true seedLotDbId: type: string nullable: true seedLotName: type: string nullable: true - seedLotPUI: - type: string - nullable: true studyDbId: type: string nullable: true @@ -5786,8 +5711,6 @@ components: type: string ontologyName: type: string - ontologyPUI: - type: string ontologyReferenceDbId: type: string description: The ID which uniquely identifies a ontology reference @@ -6930,21 +6853,35 @@ components: description: Unique id for a seed lot on this server items: type: string + SeedLotTransactionRequest: + type: object + properties: + transactionDbIs: + type: array + description: Unique id for a Transaction that has occurred + items: + type: string + transactionDirection: + type: string + description: "Filter results to only include transactions directed to the\ + \ specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both\ + \ (BOTH). The default value for this parameter is BOTH" + nullable: true + enum: + - TO + - FROM + - BOTH SortBy: type: string description: Name of the field to sort by. enum: - - studyDbId - trialDbId + - trialName - programDbId - - locationDbId - - seasonDbId - - studyType - - studyName - - studyLocation - programName - - germplasmDbId - - observationVariableDbId + - locationDbId + - startDate + - endDate SortOrder: type: string description: Sort order direction. Ascending/Descending. @@ -7308,6 +7245,15 @@ components: description: The unique identifier for a trait. items: type: string + TransactionDirection: + type: string + description: "Filter results to only include transactions directed to the specific\ + \ Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The\ + \ default value for this parameter is BOTH" + enum: + - TO + - FROM + - BOTH TrialParameters: type: object properties: @@ -7394,6 +7340,27 @@ components: \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ \ is before `trial.endDate`" format: date + sortBy: + type: string + description: Name of the field to sort by. + nullable: true + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + nullable: true + enum: + - ASC + - DESC + - asc + - desc studyDbIds: type: array description: List of study identifiers to search for @@ -7727,6 +7694,13 @@ components: \ variants should be returned." format: int32 example: 1500 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + deprecated: true programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ diff --git a/Specification/Generated/brapi_generated.graphqls b/Specification/Generated/brapi_generated.graphqls index 94c89da9..a94e42a9 100644 --- a/Specification/Generated/brapi_generated.graphqls +++ b/Specification/Generated/brapi_generated.graphqls @@ -1415,8 +1415,6 @@ type Image { descriptiveOntologyTerms: [String] "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] - "The content of the image" - imageContent: String "The unique identifier of an image" imageDbId: String "The name of the image file. Might be the same as 'imageName', but could be different." @@ -3696,17 +3694,13 @@ enum SampleType { "Name of the field to sort by." enum SortBy { - germplasmDbId + endDate locationDbId - observationVariableDbId programDbId programName - seasonDbId - studyDbId - studyLocation - studyName - studyType + startDate trialDbId + trialName } "Sort order direction. Ascending/Descending." @@ -3749,6 +3743,13 @@ enum TraitDataType { Text } +"Filter results to only include transactions directed to the specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The default value for this parameter is BOTH" +enum TransactionDirection { + BOTH + FROM + TO +} + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." scalar AdditionalInfoInput @@ -5263,8 +5264,6 @@ input ImageInput { descriptiveOntologyTerms: [String] "Filter by External References" externalReferences: [ExternalReferenceInput] - "The content of the image" - imageContent: String "The unique identifier of an image" imageDbId: String "The name of the image file. Might be the same as 'imageName', but could be different." @@ -7840,6 +7839,10 @@ input TrialsInput { - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate` """ searchDateRangeStart: String + "Name of the field to sort by." + sortBy: SortBy + "Sort order direction. Ascending/Descending." + sortOrder: SortOrder "List of study identifiers to search for" studyDbIds: [String] "List of study names to filter search results" @@ -8054,6 +8057,12 @@ input VariantsInput { "The end of the window (0-based, exclusive) for which overlapping variants should be returned." end: Int """ + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + """ + pageToken: String + """ A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. Use this parameter to only return results associated with the given programs. diff --git a/Specification/Generated/brapi_generated.json b/Specification/Generated/brapi_generated.json index 3450d31d..722acf40 100644 --- a/Specification/Generated/brapi_generated.json +++ b/Specification/Generated/brapi_generated.json @@ -63,18 +63,18 @@ } }, { - "name" : "dataMatrixNames", + "name" : "dataMatrixName", "in" : "query", - "description" : "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "dataMatrixAbbreviations", + "name" : "dataMatrixAbbreviation", "in" : "query", - "description" : "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "description" : "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", "required" : false, "schema" : { "type" : "string" @@ -5260,6 +5260,41 @@ "type" : "string" } }, + { + "name" : "sortBy", + "in" : "query", + "description" : "Name of the field to sort by.", + "required" : false, + "schema" : { + "type" : "string", + "description" : "Name of the field to sort by.", + "enum" : [ + "trialDbId", + "trialName", + "programDbId", + "programName", + "locationDbId", + "startDate", + "endDate" + ] + } + }, + { + "name" : "sortOrder", + "in" : "query", + "description" : "Sort order direction. Ascending/Descending.", + "required" : false, + "schema" : { + "type" : "string", + "description" : "Sort order direction. Ascending/Descending.", + "enum" : [ + "ASC", + "DESC", + "asc", + "desc" + ] + } + }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -5377,6 +5412,15 @@ "type" : "string" } }, + { + "name" : "pageToken", + "in" : "query", + "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -6324,56 +6368,6 @@ } } }, - "/images/{imageDbId}/imagecontent" : { - "put" : { - "tags" : [ - "Images" - ], - "summary" : "Update the details for an existing string", - "description" : "Update the details for an existing string", - "parameters" : [ - { - "$ref" : "#/components/parameters/authorizationHeader" - }, - { - "name" : "imageDbId", - "in" : "path", - "description" : "The unique identifier of an image", - "required" : true, - "schema" : { - "type" : "string" - } - } - ], - "requestBody" : { - "content" : { - "image/*" : { - "schema" : { - "type" : "string", - "format" : "binary" - } - } - } - }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ImageSingleResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - } - } - } - }, "/lists/{listDbId}" : { "get" : { "tags" : [ @@ -7619,6 +7613,21 @@ "type" : "string" } }, + { + "name" : "transactionDirection", + "in" : "query", + "description" : "Filter results to only include transactions directed to the specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The default value for this parameter is BOTH", + "required" : false, + "schema" : { + "type" : "string", + "description" : "Filter results to only include transactions directed to the specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The default value for this parameter is BOTH", + "enum" : [ + "TO", + "FROM", + "BOTH" + ] + } + }, { "$ref" : "#/components/parameters/page" }, @@ -10555,16 +10564,20 @@ } }, "dataMatrixAbbreviations" : { - "type" : "string", - "description" : "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "type" : "array", + "description" : "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", "nullable" : true, - "example" : "GT,RD" + "items" : { + "type" : "string" + } }, "dataMatrixNames" : { - "type" : "string", - "description" : "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "type" : "array", + "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", "nullable" : true, - "example" : "Genotype,Read Depth" + "items" : { + "type" : "string" + } }, "dimensionCallSetPage" : { "type" : "integer", @@ -10720,40 +10733,20 @@ } }, "dataMatrixAbbreviations" : { - "type" : "string", - "description" : "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "type" : "array", + "description" : "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", "nullable" : true, - "example" : "GT,RD" + "items" : { + "type" : "string" + } }, "dataMatrixNames" : { - "type" : "string", - "description" : "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "type" : "array", + "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", "nullable" : true, - "example" : "Genotype,Read Depth" - }, - "dimensionCallSetPage" : { - "type" : "integer", - "description" : "The requested page number for the CallSet dimension of the matrix", - "format" : "int32", - "nullable" : true - }, - "dimensionCallSetPageSize" : { - "type" : "integer", - "description" : "The requested page size for the CallSet dimension of the matrix", - "format" : "int32", - "nullable" : true - }, - "dimensionVariantPage" : { - "type" : "integer", - "description" : "The requested page number for the Variant dimension of the matrix", - "format" : "int32", - "nullable" : true - }, - "dimensionVariantPageSize" : { - "type" : "integer", - "description" : "The requested page size for the Variant dimension of the matrix", - "format" : "int32", - "nullable" : true + "items" : { + "type" : "string" + } }, "expandHomozygotes" : { "type" : "boolean", @@ -10876,9 +10869,6 @@ "description" : "The AlleleMatrix object is used to describe a matrix of genotyping results. This 2d array of data reduces the overall size of the response for larger datasets, when compared to the Calls endpoints. This makes genotype data retrieval faster and easier." }, "Analysis" : { - "required" : [ - "analysisDbId" - ], "type" : "object", "properties" : { "analysisDbId" : { @@ -11239,7 +11229,8 @@ }, "pageToken" : { "type" : "string", - "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response." + "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response.", + "deprecated" : true }, "sepPhased" : { "type" : "string", @@ -11308,7 +11299,8 @@ }, "pageToken" : { "type" : "string", - "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response." + "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response.", + "deprecated" : true }, "sepPhased" : { "type" : "string", @@ -13082,30 +13074,6 @@ "geometry" : { "$ref" : "#/components/schemas/GeoJSONGeometry" }, - "germplasmOrigin" : { - "$ref" : "#/components/schemas/GermplasmOrigin" - }, - "imageDbId" : { - "type" : "string" - }, - "imageName" : { - "type" : "string" - }, - "imagePUI" : { - "type" : "string" - }, - "observationDbId" : { - "type" : "string" - }, - "observationName" : { - "type" : "string" - }, - "observationPUI" : { - "type" : "string" - }, - "observationUnit" : { - "$ref" : "#/components/schemas/ObservationUnitPosition" - }, "type" : { "type" : "string", "description" : "The literal string \"Feature\"", @@ -14343,6 +14311,9 @@ "germplasmDbId" : { "type" : "string" }, + "germplasmPUI" : { + "type" : "string" + }, "instituteCode" : { "type" : "string", "description" : "MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", @@ -15099,11 +15070,6 @@ "$ref" : "#/components/schemas/ExternalReference" } }, - "imageContent" : { - "type" : "string", - "description" : "The content of the image", - "format" : "binary" - }, "imageFileName" : { "type" : "string", "description" : "The name of the image file. Might be the same as 'imageName', but could be different.", @@ -15154,10 +15120,6 @@ "observationUnitDbId" : { "type" : "string", "nullable" : true - }, - "observationUnitName" : { - "type" : "string", - "nullable" : true } }, "description" : "The metadata for an image file that is connected to some phenotypic observation data." @@ -16662,30 +16624,14 @@ "type" : "string", "nullable" : true }, - "observationVariablePUI" : { - "type" : "string", - "nullable" : true - }, "seasonDbId" : { "type" : "string", "nullable" : true }, - "seasonName" : { - "type" : "string", - "nullable" : true - }, - "seasonPUI" : { - "type" : "string", - "nullable" : true - }, "studyDbId" : { "type" : "string", "nullable" : true }, - "studyName" : { - "type" : "string", - "nullable" : true - }, "uploadedBy" : { "type" : "string", "description" : "The name or id of the user who uploaded the observation to the database system", @@ -17214,10 +17160,6 @@ "type" : "string", "nullable" : true }, - "crossPUI" : { - "type" : "string", - "nullable" : true - }, "externalReferences" : { "type" : "array", "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", @@ -17242,10 +17184,6 @@ "type" : "string", "nullable" : true }, - "locationPUI" : { - "type" : "string", - "nullable" : true - }, "observationUnitName" : { "type" : "string", "description" : "A human readable name for an observation unit", @@ -17267,10 +17205,6 @@ "type" : "string", "nullable" : true }, - "programPUI" : { - "type" : "string", - "nullable" : true - }, "seedLotDbId" : { "type" : "string", "nullable" : true @@ -17279,10 +17213,6 @@ "type" : "string", "nullable" : true }, - "seedLotPUI" : { - "type" : "string", - "nullable" : true - }, "studyDbId" : { "type" : "string", "nullable" : true @@ -18425,9 +18355,6 @@ "ontologyName" : { "type" : "string" }, - "ontologyPUI" : { - "type" : "string" - }, "ontologyReferenceDbId" : { "type" : "string", "description" : "The ID which uniquely identifies a ontology reference", @@ -18547,7 +18474,8 @@ "PedigreeNode" : { "required" : [ "germplasmDbId", - "germplasmName" + "germplasmName", + "germplasmPUI" ], "type" : "object", "properties" : { @@ -18595,6 +18523,9 @@ "germplasmName" : { "type" : "string" }, + "germplasmPUI" : { + "type" : "string" + }, "parents" : { "type" : "array", "description" : "A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. \n
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response.", @@ -21721,18 +21652,10 @@ "type" : "string", "nullable" : true }, - "fromSeedLotPUI" : { - "type" : "string", - "nullable" : true - }, "toSeedLotDbId" : { "type" : "string", "nullable" : true }, - "toSeedLotPUI" : { - "type" : "string", - "nullable" : true - }, "transactionDbId" : { "type" : "string", "description" : "Unique DbId for the Seed Lot Transaction" @@ -21756,21 +21679,39 @@ }, "description" : "The record of an event where material was moved in or out of a particular SeedLot" }, + "SeedLotTransactionRequest" : { + "type" : "object", + "properties" : { + "transactionDbIs" : { + "type" : "array", + "description" : "Unique id for a Transaction that has occurred", + "items" : { + "type" : "string" + } + }, + "transactionDirection" : { + "type" : "string", + "description" : "Filter results to only include transactions directed to the specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The default value for this parameter is BOTH", + "nullable" : true, + "enum" : [ + "TO", + "FROM", + "BOTH" + ] + } + } + }, "SortBy" : { "type" : "string", "description" : "Name of the field to sort by.", "enum" : [ - "studyDbId", "trialDbId", + "trialName", "programDbId", - "locationDbId", - "seasonDbId", - "studyType", - "studyName", - "studyLocation", "programName", - "germplasmDbId", - "observationVariableDbId" + "locationDbId", + "startDate", + "endDate" ] }, "SortOrder" : { @@ -22637,6 +22578,15 @@ } } }, + "TransactionDirection" : { + "type" : "string", + "description" : "Filter results to only include transactions directed to the specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The default value for this parameter is BOTH", + "enum" : [ + "TO", + "FROM", + "BOTH" + ] + }, "Trial" : { "allOf" : [ { @@ -22828,6 +22778,31 @@ "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", "format" : "date" }, + "sortBy" : { + "type" : "string", + "description" : "Name of the field to sort by.", + "nullable" : true, + "enum" : [ + "trialDbId", + "trialName", + "programDbId", + "programName", + "locationDbId", + "startDate", + "endDate" + ] + }, + "sortOrder" : { + "type" : "string", + "description" : "Sort order direction. Ascending/Descending.", + "nullable" : true, + "enum" : [ + "ASC", + "DESC", + "asc", + "desc" + ] + }, "studyDbIds" : { "type" : "array", "description" : "List of study identifiers to search for", @@ -23506,6 +23481,11 @@ "format" : "int32", "example" : 1500 }, + "pageToken" : { + "type" : "string", + "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response.", + "deprecated" : true + }, "programDbIds" : { "type" : "array", "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", @@ -23654,6 +23634,11 @@ "format" : "int32", "example" : 1000 }, + "pageToken" : { + "type" : "string", + "description" : "The continuation token, which is used to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`next_page_token` from the previous response.", + "deprecated" : true + }, "programDbIds" : { "type" : "array", "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", @@ -23761,6 +23746,14 @@ "$ref" : "#/components/schemas/Analysis" } }, + "availableFormats" : { + "type" : "array", + "description" : "When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. \n
'dataFormat' defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)\n
'fileFormat' defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response.", + "nullable" : true, + "items" : { + "$ref" : "#/components/schemas/AvailableFormat" + } + }, "callSetCount" : { "type" : "integer", "description" : "The number of CallSets included in this VariantSet", @@ -23786,7 +23779,7 @@ "type" : "string", "nullable" : true }, - "referenceSetName" : { + "studyDbId" : { "type" : "string", "nullable" : true }, diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index a0b85407..e8524ad5 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -24888,7 +24888,7 @@ "type" : "array" }, "dataMatrixAbbreviations" : { - "description" : "`dataMatrixAbbreviations` is a comma seperated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "description" : "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", "example" : [ "GT", "RD" ], "items" : { "type" : "string" @@ -27477,7 +27477,6 @@ "germplasmPUI" : { "description" : "MCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties.", "example" : "http://pui.per/accession/A0403652", - "nullable" : true, "type" : "string" }, "instituteCode" : { @@ -31654,7 +31653,6 @@ "germplasmPUI" : { "description" : "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties.", "example" : "http://pui.per/accession/A0000003", - "nullable" : true, "type" : "string" }, "parents" : { @@ -31696,7 +31694,7 @@ "parentType" : "FEMALE" } ], "items" : { - "$ref" : "#/components/schemas/PedigreeNode_parents_inner" + "$ref" : "#/components/schemas/PedigreeNode_progeny_inner" }, "nullable" : true, "type" : "array" @@ -36859,7 +36857,7 @@ "referenceSetDbId" : { "description" : "The ID of the reference set that describes the sequences used by the variants in this set.", "example" : "57eae639", - "nullable" : false, + "nullable" : true, "type" : "string" }, "studyDbId" : { @@ -42087,6 +42085,25 @@ "type" : "object" }, "PedigreeNode_parents_inner" : { + "properties" : { + "germplasmDbId" : { + "description" : "The ID which uniquely identifies a germplasm", + "example" : "a55847ed", + "type" : "string" + }, + "germplasmName" : { + "description" : "A human readable name for a germplasm", + "example" : "A0000592", + "type" : "string" + }, + "parentType" : { + "$ref" : "#/components/schemas/ParentType" + } + }, + "required" : [ "germplasmDbId", "parentType" ], + "type" : "object" + }, + "PedigreeNode_progeny_inner" : { "properties" : { "germplasmDbId" : { "description" : "The ID which uniquely identifies a germplasm", diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index c3acbbc5..b312a2bc 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -10,6 +10,9 @@ ##### `POST` /delete/observations +##### `PUT` /images/{imageDbId}/imagecontent + + ##### `GET` /observationlevels @@ -62,22 +65,19 @@ ##### `GET` /allelematrix -###### Return Type: +###### Parameters: -New response : **404** +Deleted: `dataMatrixNames` in `query` -##### `GET` /germplasm/{germplasmDbId}/mcpd +Deleted: `dataMatrixAbbreviations` in `query` +Added: `dataMatrixName` in `query` -###### Return Type: +Added: `dataMatrixAbbreviation` in `query` -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) +###### Return Type: - Deleted properties: `germplasmPUI` +New response : **404** ##### `PUT` /samples @@ -86,31 +86,6 @@ Changed response : **200** Deleted response : **404** -##### `POST` /search/allelematrix - - -###### Request: - -* Changed content type : `application/json` - - New properties: `dimensionCallSetPage`, `dimensionCallSetPageSize`, `dimensionVariantPage`, `dimensionVariantPageSize` - - * Changed property `dataMatrixAbbreviations` (array -> string): - - Type changed: `array` -> `string` - - * Changed property `dataMatrixNames` (array -> string): - - Type changed: `array` -> `string` - -##### `POST` /search/calls - - -###### Request: - -* Changed content type : `application/json` - - * Changed property `pageToken` (string): - - Deprecated status changed - ##### `GET` /search/calls/{searchResultsDbId} @@ -146,15 +121,6 @@ Deleted: `pageToken` in `query` * Changed property `observationUnitDbId` (string): - Nullable changed: `true` -> `null` -##### `POST` /search/variants - - -###### Request: - -* Changed content type : `application/json` - - Deleted properties: `pageToken` - ##### `GET` /search/variants/{searchResultsDbId} @@ -162,64 +128,6 @@ Deleted: `pageToken` in `query` Deleted: `pageToken` in `query` -##### `POST` /search/variantsets - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `referenceSetName` - - Deleted properties: `availableFormats`, `studyDbId` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `true` - - * Changed property `analysis` (array) - - Changed items (array): - - New required properties: - - `analysisDbId` - -##### `GET` /search/variantsets/{searchResultsDbId} - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `referenceSetName` - - Deleted properties: `availableFormats`, `studyDbId` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `true` - - * Changed property `analysis` (array) - - Changed items (array): - - New required properties: - - `analysisDbId` - ##### `GET` /seedlots/{seedLotDbId}/transactions @@ -227,85 +135,6 @@ Changed response : **200** Deleted: `transactionDbId` in `query` -Deleted: `transactionDirection` in `query` - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `fromSeedLotPUI`, `toSeedLotPUI` - -##### `GET` /trials - - -###### Parameters: - -Deleted: `sortBy` in `query` - -Deleted: `sortOrder` in `query` - -##### `GET` /variantsets - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - * Changed property `data` (array) - - Changed items (array): - - New properties: `referenceSetName` - - Deleted properties: `availableFormats`, `studyDbId` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `true` - - * Changed property `analysis` (array) - - Changed items (array): - - New required properties: - - `analysisDbId` - -##### `GET` /variantsets/{variantSetDbId} - - -###### Return Type: - -Changed response : **200** - -* Changed content type : `application/json` - - * Changed property `result` (object) - - New properties: `referenceSetName` - - Deleted properties: `availableFormats`, `studyDbId` - - * Changed property `referenceSetDbId` (string): - - Nullable changed: `false` -> `true` - - * Changed property `analysis` (array) - - Changed items (array): - - New required properties: - - `analysisDbId` - ##### `POST` /attributes @@ -318,7 +147,7 @@ Changed response : **200** * Changed property `ontologyReference` (object): - Nullable changed: `true` -> `false` - New properties: `ontologyPUI`, `ontologyReferenceDbId` + New properties: `ontologyReferenceDbId` ##### `PUT` /attributes/{attributeDbId} @@ -330,7 +159,7 @@ Changed response : **200** * Changed property `ontologyReference` (object): - Nullable changed: `true` -> `false` - New properties: `ontologyPUI`, `ontologyReferenceDbId` + New properties: `ontologyReferenceDbId` ##### `POST` /images @@ -341,8 +170,6 @@ Changed response : **200** Changed items (array): - New properties: `imageContent`, `observationUnitName` - Deleted properties: `observationDbIds` * Changed property `mimeType` (string): @@ -360,8 +187,6 @@ Changed response : **200** * Changed content type : `application/json` - New properties: `imageContent`, `observationUnitName` - Deleted properties: `observationDbIds` * Changed property `mimeType` (string): @@ -418,7 +243,7 @@ Deleted response : **404** Changed items (array): - New properties: `observationVariablePUI`, `seasonDbId`, `seasonName`, `seasonPUI`, `studyName` + New properties: `seasonDbId` Deleted properties: `season` @@ -440,8 +265,6 @@ Deleted response : **404** Changed items (array): - New properties: `crossPUI`, `locationPUI`, `programPUI`, `seedLotPUI` - * Changed property `observationUnitPosition` (object) * Changed property `geoCoordinates` (object -> array): @@ -477,7 +300,23 @@ Changed response : **200** Changed items (array): - Deleted properties: `germplasmPUI` + New required properties: + - `germplasmPUI` + + * Changed property `progeny` (array) + + Changed items (array): + + New properties: `childGermplasmDbId`, `childGermplasmName`, `pedigreeNodeDbId`, `pedigreeNodeName`, `pedigreeNodePUI` + + Deleted properties: `germplasmDbId`, `germplasmName` + + New required properties: + - `childGermplasmDbId` + - `childGermplasmName` + + Removed required properties: + - `germplasmDbId` * Changed property `parents` (array) @@ -486,9 +325,6 @@ Changed response : **200** New required properties: - `germplasmName` - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - ##### `POST` /pedigree @@ -498,7 +334,23 @@ Changed response : **200** Changed items (array): - Deleted properties: `germplasmPUI` + New required properties: + - `germplasmPUI` + + * Changed property `progeny` (array) + + Changed items (array): + + New properties: `childGermplasmDbId`, `childGermplasmName`, `pedigreeNodeDbId`, `pedigreeNodeName`, `pedigreeNodePUI` + + Deleted properties: `germplasmDbId`, `germplasmName` + + New required properties: + - `childGermplasmDbId` + - `childGermplasmName` + + Removed required properties: + - `germplasmDbId` * Changed property `parents` (array) @@ -507,9 +359,6 @@ Changed response : **200** New required properties: - `germplasmName` - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - ###### Return Type: Deleted response : **404** @@ -524,7 +373,23 @@ Changed response : **200** Changed items (array): - Deleted properties: `germplasmPUI` + New required properties: + - `germplasmPUI` + + * Changed property `progeny` (array) + + Changed items (array): + + New properties: `childGermplasmDbId`, `childGermplasmName`, `pedigreeNodeDbId`, `pedigreeNodeName`, `pedigreeNodePUI` + + Deleted properties: `germplasmDbId`, `germplasmName` + + New required properties: + - `childGermplasmDbId` + - `childGermplasmName` + + Removed required properties: + - `germplasmDbId` * Changed property `parents` (array) @@ -533,9 +398,6 @@ Changed response : **200** New required properties: - `germplasmName` - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - ##### `POST` /search/images @@ -545,8 +407,6 @@ Changed response : **200** * Changed property `imageLocation` (object) - New properties: `germplasmOrigin`, `imageDbId`, `imageName`, `imagePUI`, `observationDbId`, `observationName`, `observationPUI`, `observationUnit` - * Changed property `geometry` (object -> null): - Type changed: `object` -> `null` @@ -560,8 +420,6 @@ Changed response : **200** * Changed property `coordinates` (object): - Nullable changed: `true` -> `null` - New properties: `germplasmOrigin`, `imageDbId`, `imageName`, `imagePUI`, `observationDbId`, `observationName`, `observationPUI`, `observationUnit` - * Changed property `geometry` (object -> null): - Type changed: `object` -> `null` @@ -580,7 +438,23 @@ Changed response : **200** Changed items (array): - Deleted properties: `germplasmPUI` + New required properties: + - `germplasmPUI` + + * Changed property `progeny` (array) + + Changed items (array): + + New properties: `childGermplasmDbId`, `childGermplasmName`, `pedigreeNodeDbId`, `pedigreeNodeName`, `pedigreeNodePUI` + + Deleted properties: `germplasmDbId`, `germplasmName` + + New required properties: + - `childGermplasmDbId` + - `childGermplasmName` + + Removed required properties: + - `germplasmDbId` * Changed property `parents` (array) @@ -589,9 +463,6 @@ Changed response : **200** New required properties: - `germplasmName` - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - ##### `GET` /search/pedigree/{searchResultsDbId} @@ -607,7 +478,23 @@ Changed response : **200** Changed items (array): - Deleted properties: `germplasmPUI` + New required properties: + - `germplasmPUI` + + * Changed property `progeny` (array) + + Changed items (array): + + New properties: `childGermplasmDbId`, `childGermplasmName`, `pedigreeNodeDbId`, `pedigreeNodeName`, `pedigreeNodePUI` + + Deleted properties: `germplasmDbId`, `germplasmName` + + New required properties: + - `childGermplasmDbId` + - `childGermplasmName` + + Removed required properties: + - `germplasmDbId` * Changed property `parents` (array) @@ -616,9 +503,6 @@ Changed response : **200** New required properties: - `germplasmName` - * Changed property `germplasmName` (string): - - Nullable changed: `true` -> `null` - ##### `POST` /variables @@ -631,7 +515,7 @@ Changed response : **200** * Changed property `ontologyReference` (object): - Nullable changed: `true` -> `false` - New properties: `ontologyPUI`, `ontologyReferenceDbId` + New properties: `ontologyReferenceDbId` ##### `PUT` /variables/{observationVariableDbId} @@ -643,7 +527,7 @@ Changed response : **200** * Changed property `ontologyReference` (object): - Nullable changed: `true` -> `false` - New properties: `ontologyPUI`, `ontologyReferenceDbId` + New properties: `ontologyReferenceDbId` ##### `POST` /germplasm From 3c6e348fc2b51a875e7512a6a17b3b6090d76848 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Sat, 23 May 2026 20:00:15 +1200 Subject: [PATCH 52/62] changed schema tool version to 0.73, fixed other issues. --- .../Lists/Schemas/ListSearchRequest.yaml | 5 +++-- .../BrAPI-Common/GeoJSONGeometry.json | 3 ++- .../BrAPI-Schema/BrAPI-Common/Variable.json | 9 ++++++++- .../BrAPI-Schema/BrAPI-Core/List.json | 3 ++- .../BrAPI-Germplasm/PedigreeNode.json | 4 ++-- .../BrAPI-Phenotyping/ObservationUnit.json | 18 +++++++++++++++-- .../Requests/AlleleMatrixRequest.json | 20 ++++++------------- .../BrAPI-Schema/Requests/ListRequest.json | 5 ++++- .../Requests/LocationRequest.json | 9 ++++++++- Specification/Generated/brapi_openapi.json | 3 +-- generator/build.gradle | 2 +- 11 files changed, 53 insertions(+), 28 deletions(-) diff --git a/Specification/BrAPI-Core/Lists/Schemas/ListSearchRequest.yaml b/Specification/BrAPI-Core/Lists/Schemas/ListSearchRequest.yaml index bfefd920..e0ea910c 100644 --- a/Specification/BrAPI-Core/Lists/Schemas/ListSearchRequest.yaml +++ b/Specification/BrAPI-Core/Lists/Schemas/ListSearchRequest.yaml @@ -69,6 +69,7 @@ components: type: string example: ['USER', 'SYSTEM', 'EXTERNAL'] listType: - $ref: '#/components/schemas/ListTypes' - nullable: true + anyOf: + - $ref: "#/components/schemas/ListTypes" + - type: "null" diff --git a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json index 6261c3d9..28beb3e3 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json @@ -60,7 +60,8 @@ ], "type": "object" } - ] + ], + "type": "object" } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/Components/Common/AdditionalInfo.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json index 59e0a822..5e2dc3ed 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json @@ -81,7 +81,14 @@ "ontologyReference": { "description": "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology).", "relationshipType": "one-to-one", - "$ref": "../BrAPI-Phenotyping/OntologyReference.json#/$defs/OntologyReference" + "anyOf": [ + { + "$ref": "../BrAPI-Phenotyping/OntologyReference.json#/$defs/OntologyReference" + }, + { + "type": "null" + } + ] }, "scale": { "description": "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\".", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/List.json b/Specification/BrAPI-Schema/BrAPI-Core/List.json index 3bec2ab1..be9e1364 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/List.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/List.json @@ -91,7 +91,8 @@ }, "listType": { "description": "A flag to indicate the type of objects that are referenced in a List", - "$ref": "ListType.json#/$defs/ListType" + "$ref": "ListType.json#/$defs/ListType", + "nullable": false } }, "required": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json index 250c92a1..2ff61df7 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json @@ -160,7 +160,7 @@ }, "GermplasmChild": { "properties": { - "childGermplasm": { + "germplasm": { "$ref": "Germplasm.json#/$defs/Germplasm", "description": "The child germplasm", "referencedAttribute": "parentPedigreeNodes", @@ -178,7 +178,7 @@ } }, "required": [ - "childGermplasm", + "germplasm", "parentType" ], "title": "GermplasmChild", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json index dbf3e225..9905e5c6 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json @@ -272,7 +272,14 @@ }, "positionCoordinateXType": { "description": "The type of positional coordinate used for the X coordinate of the position.", - "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/PositionCoordinateType" + "anyOf": [ + { + "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/PositionCoordinateType" + }, + { + "type": "null" + } + ] }, "positionCoordinateY": { "description": "The Y position coordinate for an observation unit. Different systems may use different coordinate systems.", @@ -283,7 +290,14 @@ }, "positionCoordinateYType": { "description": "The type of positional coordinate used for the Y coordinate of the position.", - "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/PositionCoordinateType" + "anyOf": [ + { + "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/PositionCoordinateType" + }, + { + "type": "null" + } + ] }, "observationUnit": { "description": "associated observation Unit", diff --git a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json index ccffe5ef..d0080959 100644 --- a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json +++ b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json @@ -67,25 +67,17 @@ "type": ["null", "integer"] }, "dataMatrixNames": { - "description": "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", - "type": ["null", "array"], - "items": { - "type": "string" - }, + "description": "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "type": ["null", "string"], "example": [ - "Genotype", - "Read Depth" + "Genotype,Read Depth" ] }, "dataMatrixAbbreviations": { - "description": "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", - "type": ["null", "array"], - "items": { - "type": "string" - }, + "description": "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "type": ["null", "string"], "example": [ - "GT", - "RD" + "GT,RD" ] }, "positionRanges": { diff --git a/Specification/BrAPI-Schema/Requests/ListRequest.json b/Specification/BrAPI-Schema/Requests/ListRequest.json index ff26a1c1..561f4cd1 100644 --- a/Specification/BrAPI-Schema/Requests/ListRequest.json +++ b/Specification/BrAPI-Schema/Requests/ListRequest.json @@ -89,7 +89,10 @@ ] }, "listType": { - "$ref": "../BrAPI-Core/ListType.json#/$defs/ListType" + "anyOf": [ + {"$ref": "../BrAPI-Core/ListType.json#/$defs/ListType"}, + {"type": "string"} + ] } } } diff --git a/Specification/BrAPI-Schema/Requests/LocationRequest.json b/Specification/BrAPI-Schema/Requests/LocationRequest.json index 43eeef93..2e50d4f5 100644 --- a/Specification/BrAPI-Schema/Requests/LocationRequest.json +++ b/Specification/BrAPI-Schema/Requests/LocationRequest.json @@ -58,7 +58,14 @@ ] }, "coordinates": { - "$ref": "Schemas/GeoJSONSearchArea.json#/$defs/GeoJSONSearchArea" + "anyOf": [ + { + "$ref": "Schemas/GeoJSONSearchArea.json#/$defs/GeoJSONSearchArea" + }, + { + "type": "null" + } + ] }, "instituteAddresses": { "description": "The street address of the institute to search for", diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index e8524ad5..18bb21be 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -41812,8 +41812,7 @@ "type" : "string" } }, - "title" : "GeoJSONSearchArea", - "type" : "object" + "title" : "GeoJSONSearchArea" }, "Observation_season" : { "nullable" : true, diff --git a/generator/build.gradle b/generator/build.gradle index 9fc4f032..5f3e4a47 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.72.0' + brapiSchemaToolsVersion = '0.73.0' } repositories { From 56d5263e8e857c4a419c55002acd42794963b75b Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Tue, 2 Jun 2026 11:58:50 +1200 Subject: [PATCH 53/62] changed schema tool version to 0.75 --- generator/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/generator/build.gradle b/generator/build.gradle index 5f3e4a47..3252eff2 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.73.0' + brapiSchemaToolsVersion = '0.75.0' } repositories { From 7c1b33c60f8a3ddd08578d4fb686509d75dbc9ea Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Thu, 4 Jun 2026 16:23:19 +1200 Subject: [PATCH 54/62] add commonCropName as CV on Program.json --- Specification/BrAPI-Schema/BrAPI-Core/Program.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Program.json b/Specification/BrAPI-Schema/BrAPI-Core/Program.json index f7990981..0f8f6f15 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Program.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Program.json @@ -179,7 +179,10 @@ "description": "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. A Program can contain multiple Trials. A Trial can contain multiple Studies.", "type": "object", "brapi-metadata": { - "primaryModel": true + "primaryModel": true, + "controlledVocabularyProperties": [ + "commonCropName" + ] } } }, From e25dc6b4e15061167775185347d995e1067165e2 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 5 Jun 2026 09:25:38 +1200 Subject: [PATCH 55/62] various changes to get the comparison working --- .../BrAPI-Common/GeoJSONGeometry.json | 4 +++- .../BrAPI-Schema/BrAPI-Phenotyping/Image.json | 4 ++-- .../BrAPI-Phenotyping/ObservationUnit.json | 12 +--------- .../Requests/AlleleMatrixRequest.json | 23 +++++++++++++------ .../Requests/SeedLotTransactionRequest.json | 2 +- 5 files changed, 23 insertions(+), 22 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json index 28beb3e3..14c95c26 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSONGeometry.json @@ -1,7 +1,9 @@ { "$defs": { "GeoJSONGeometry": { - "nullable": true, + "brapi-metadata": { + "discriminatorPropertyName": "type" + }, "oneOf": [ { "description": "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json index 868f5a33..4198242e 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json @@ -128,8 +128,8 @@ "$ref": "Observation.json#/$defs/Observation" }, "referencedAttribute": "images", - "relationshipType": "many-to-many", - "type": "array" + "relationshipType": "one-to-many", + "type": ["null", "array"] } }, "required": [ diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json index 9905e5c6..1916c380 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json @@ -235,17 +235,7 @@ }, "geoCoordinates": { "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", - "relationshipType": "one-to-many", - "referencedAttribute": "observationUnit", - "items": { - "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON", - "description": "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed." - }, - "title": "GeoJSON", - "type": [ - "null", - "array" - ] + "$ref": "../BrAPI-Common/GeoJSON.json#/$defs/GeoJSON" }, "observationLevel": { "$ref": "../BrAPI-Phenotyping/ObservationUnitLevel.json#/$defs/ObservationUnitLevel", diff --git a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json index d0080959..cb9fb84a 100644 --- a/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json +++ b/Specification/BrAPI-Schema/Requests/AlleleMatrixRequest.json @@ -67,17 +67,25 @@ "type": ["null", "integer"] }, "dataMatrixNames": { - "description": "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", - "type": ["null", "string"], + "description": "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "type": ["null", "array"], + "items": { + "type": "string" + }, "example": [ - "Genotype,Read Depth" + "Genotype", + "Read Depth" ] }, "dataMatrixAbbreviations": { - "description": "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", - "type": ["null", "string"], + "description": "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "type": ["null", "array"], + "items": { + "type": "string" + }, "example": [ - "GT,RD" + "GT", + "RD" ] }, "positionRanges": { @@ -190,7 +198,8 @@ } }, "brapi-metadata": { - "request": true + "request": true, + "noSingularizeProperties": ["dataMatrixNames", "dataMatrixAbbreviations"] } } }, diff --git a/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json b/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json index aa7d660b..8e514620 100644 --- a/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json +++ b/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json @@ -3,7 +3,7 @@ "SeedLotTransactionRequest": { "type": "object", "properties": { - "transactionDbIs": { + "transactionDbIds": { "description": "Unique id for a Transaction that has occurred", "type": "array", "items": { From 70e8bbb53d0be31d031a597d6f58c9bcf942b6ba Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Sat, 6 Jun 2026 17:10:13 +1200 Subject: [PATCH 56/62] added table schemas, image content, seed lot transaction request --- .../Observations/Observations_Table_GET.yaml | 6 - .../BrAPI-Germplasm/SeedLotTransaction.json | 2 +- .../BrAPI-Schema/BrAPI-Phenotyping/Image.json | 5 + .../BrAPI-Phenotyping/Observation.json | 294 ++++++++++++++++++ .../BrAPI-Phenotyping/ObservationUnit.json | 188 +++++++++++ .../Requests/SeedLotTransactionRequest.json | 74 +++-- generator/openapi-single-file-options.yaml | 3 +- 7 files changed, 543 insertions(+), 29 deletions(-) diff --git a/Specification/BrAPI-Phenotyping/Observations/Observations_Table_GET.yaml b/Specification/BrAPI-Phenotyping/Observations/Observations_Table_GET.yaml index 2969b2e7..57dcbea7 100644 --- a/Specification/BrAPI-Phenotyping/Observations/Observations_Table_GET.yaml +++ b/Specification/BrAPI-Phenotyping/Observations/Observations_Table_GET.yaml @@ -79,12 +79,6 @@ paths: schema: type: string deprecated: true - - description: Permanent unique identifier which references the search results - in: query - name: searchResultsDbId - required: false - schema: - type: string - description: Timestamp range start in: query name: observationTimeStampRangeStart diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json index c124d11d..c159070d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLotTransaction.json @@ -85,7 +85,7 @@ "description": "The record of an event where material was moved in or out of a particular SeedLot", "type": "object", "brapi-metadata": { - "primaryModel": false + "primaryModel": true } } }, diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json index 4198242e..dbd5f4a4 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Image.json @@ -41,6 +41,11 @@ "title": "ExternalReferences", "type": "array" }, + "imageContent": { + "description": "The unique identifier of an image", + "type": "string", + "format": "binary" + }, "imageDbId": { "description": "The unique identifier of an image", "type": "string" diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json index f877913a..71eabc18 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json @@ -154,6 +154,300 @@ "brapi-metadata": { "primaryModel": true } + }, + "ObservationTable": { + "type": "object", + "properties": { + "data": { + "description": "The 2D matrix of observation data. ObservationVariables and other metadata are the columns, ObservationUnits are the rows.", + "type": "array", + "items": { + "type": "array", + "items": { + "type": "string" + } + }, + "example": [ + [ + "2019-09-10T18:13:27.223Z", + "f3a8a3db", + "Plant Alpha", + "0fe3e48b", + "2017 Plant Study", + "06307ec0", + "A0043001", + "76.50106681", + "42.44409301", + "2017", + "Field_1", + "Plot_11", + "SubPlot_111", + "Plant_1111", + "Pot_1111", + "Block_11", + "Entry_11", + "Rep_11", + "25.3", + "", + "", + "" + ], + [ + "2019-09-10T18:14:27.223Z", + "f3a8a3db", + "Plant Alpha", + "0fe3e48b", + "2017 Plant Study", + "06307ec0", + "A0043001", + "76.50106681", + "42.44409301", + "2017", + "Field_1", + "Plot_11", + "SubPlot_111", + "Plant_1111", + "Pot_1111", + "Block_11", + "Entry_11", + "Rep_11", + "", + "3", + "", + "" + ], + [ + "2019-09-10T18:15:54.868Z", + "05d1b011", + "Plant Beta", + "0fe3e48b", + "2017 Plant Study", + "59d435cd", + "A0043002", + "76.50106683", + "42.44409301", + "2017", + "Field_1", + "Plot_11", + "SubPlot_112", + "Plant_1122", + "Pot_1122", + "Block_11", + "Entry_11", + "Rep_12", + "27.9", + "", + "", + "" + ], + [ + "2019-09-10T18:16:54.868Z", + "05d1b011", + "Plant Beta", + "0fe3e48b", + "2017 Plant Study", + "59d435cd", + "A0043002", + "76.50106683", + "42.44409301", + "2017", + "Field_1", + "Plot_11", + "SubPlot_112", + "Plant_1122", + "Pot_1122", + "Block_11", + "Entry_11", + "Rep_12", + "", + "1", + "", + "" + ], + [ + "2019-09-10T18:17:34.433Z", + "67e2d87c", + "Plant Gamma", + "0fe3e48b", + "2017 Plant Study", + "06307ec0", + "A0043001", + "76.50106681", + "42.44409356", + "2017", + "Field_1", + "Plot_12", + "SubPlot_123", + "Plant_1233", + "Pot_1233", + "Block_12", + "Entry_12", + "Rep_11", + "", + "3", + "", + "" + ], + [ + "2019-09-10T18:18:34.433Z", + "67e2d87c", + "Plant Gamma", + "0fe3e48b", + "2017 Plant Study", + "06307ec0", + "A0043001", + "76.50106681", + "42.44409356", + "2017", + "Field_1", + "Plot_12", + "SubPlot_123", + "Plant_1233", + "Pot_1233", + "Block_12", + "Entry_12", + "Rep_11", + "25.5", + "", + "", + "" + ], + [ + "2019-09-10T18:19:15.629Z", + "d98d0d4c", + "Plant Epsilon", + "0fe3e48b", + "2017 Plant Study", + "59d435cd", + "A0043002", + "76.50106683", + "42.44409356", + "2017", + "Field_1", + "Plot_12", + "SubPlot_124", + "Plant_1244", + "Pot_1244", + "Block_12", + "Entry_12", + "Rep_12", + "28.9", + "", + "", + "" + ], + [ + "2019-09-10T18:20:15.629Z", + "d98d0d4c", + "Plant Epsilon", + "0fe3e48b", + "2017 Plant Study", + "59d435cd", + "A0043002", + "76.50106683", + "42.44409356", + "2017", + "Field_1", + "Plot_12", + "SubPlot_124", + "Plant_1244", + "Pot_1244", + "Block_12", + "Entry_12", + "Rep_12", + "", + "0", + "", + "" + ] + ] + }, + "headerRow": { + "description": "

The table is REQUIRED to have the following columns

\n
    \n
  • observationUnitDbId - Each row is related to one Observation Unit
    • \n
  • observationTimeStamp - Each row is has a time stamp for when the observation was taken
    • \n
  • At least one column with an observationVariableDbId
    • \n
\n

The table may have any or all of the following OPTIONAL columns. Included columns are decided by the server developer

\n
    \n
  • observationUnitName
    • \n
  • studyDbId
    • \n
  • studyName
    • \n
  • germplasmDbId
    • \n
  • germplasmName
    • \n
  • positionCoordinateX
    • \n
  • positionCoordinateY
    • \n
  • year
    • \n
\n

The table also may have any number of Observation Unit Hierarchy Level columns. For example:

\n
    \n
  • field
    • \n
  • plot
    • \n
  • sub-plot
    • \n
  • plant
    • \n
  • pot
    • \n
  • block
    • \n
  • entry
    • \n
  • rep
    • \n
\n

The JSON representation provides a pair of extra arrays for defining the headers of the table. \nThe first array \"headerRow\" will always contain \"observationUnitDbId\" and any or all of the OPTIONAL column header names. \nThe second array \"observationVariables\" contains the names and DbIds for the Observation Variables represented in the table. \nBy appending the two arrays, you can construct the complete header row of the table.

", + "items": { + "description": "valid header fields", + "enum": [ + "observationTimeStamp", + "observationUnitDbId", + "observationUnitName", + "studyDbId", + "studyName", + "germplasmDbId", + "germplasmName", + "positionCoordinateX", + "positionCoordinateY", + "year", + "field", + "plot", + "sub-plot", + "plant", + "pot", + "block", + "entry", + "rep" + ], + "type": "string" + }, + "type": "array", + "example": [ + "observationTimeStamp", + "observationUnitDbId", + "observationUnitName", + "studyDbId", + "studyName", + "germplasmDbId", + "germplasmName", + "positionCoordinateX", + "positionCoordinateY", + "year", + "field", + "plot", + "sub-plot", + "plant", + "pot", + "block", + "entry", + "rep" + ] + }, + "observationVariables": { + "description": "The list of observation variables which have values recorded for them in the data matrix. Append to the 'headerRow' for complete header row of the table.", + "type": "array", + "items": { + "type": "object", + "properties": { + "observationVariableDbId": { + "description": "Variable unique identifier", + "type": "string", + "example": "367aa1a9" + }, + "observationVariableName": { + "description": "Variable name (usually a short name)", + "type": "string", + "example": "Plant height" + } + } + }, + "example": [ + { + "observationVariableDbId": "367aa1a9", + "observationVariableName": "Plant height" + }, + { + "observationVariableDbId": "2acb934c", + "observationVariableName": "Carotenoid" + }, + { + "observationVariableDbId": "85a21ce1", + "observationVariableName": "Root color" + }, + { + "observationVariableDbId": "46f590e5", + "observationVariableName": "Virus severity" + } + ] + } + } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json index 1916c380..8a3392e4 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json @@ -356,6 +356,194 @@ "null", "string" ] + }, + "ObservationUnitTable": { + "type": "object", + "properties": { + "data": { + "description": "The 2D matrix of observation data. ObservationVariables and other metadata are the columns, ObservationUnits are the rows.", + "type": "array", + "items": { + "type": "array", + "items": { + "type": "string" + } + }, + "example": [ + [ + "f3a8a3db", + "Plant Alpha", + "0fe3e48b", + "2017 Plant Study", + "06307ec0", + "A0043001", + "76.50106681", + "42.44409301", + "2017", + "Field_1", + "Plot_11", + "SubPlot_111", + "Plant_1111", + "Pot_1111", + "Block_11", + "Entry_11", + "Rep_11", + "25.3", + "3", + "50.75" + ], + [ + "05d1b011", + "Plant Beta", + "0fe3e48b", + "2017 Plant Study", + "59d435cd", + "A0043002", + "76.50106683", + "42.44409301", + "2017", + "Field_1", + "Plot_11", + "SubPlot_112", + "Plant_1122", + "Pot_1122", + "Block_11", + "Entry_11", + "Rep_12", + "27.9", + "1", + "45.345" + ], + [ + "67e2d87c", + "Plant Gamma", + "0fe3e48b", + "2017 Plant Study", + "06307ec0", + "A0043001", + "76.50106681", + "42.44409356", + "2017", + "Field_1", + "Plot_12", + "SubPlot_123", + "Plant_1233", + "Pot_1233", + "Block_12", + "Entry_12", + "Rep_11", + "25.5", + "3", + "50.76" + ], + [ + "d98d0d4c", + "Plant Epsilon", + "0fe3e48b", + "2017 Plant Study", + "59d435cd", + "A0043002", + "76.50106683", + "42.44409356", + "2017", + "Field_1", + "Plot_12", + "SubPlot_124", + "Plant_1244", + "Pot_1244", + "Block_12", + "Entry_12", + "Rep_12", + "28.9", + "0", + "46.5" + ] + ] + }, + "headerRow": { + "description": "

The table is REQUIRED to have the following columns

\n
    \n
  • observationUnitDbId - Each row is related to one Observation Unit
    • \n
  • At least one column with an observationVariableDbId
    • \n
\n

The table may have any or all of the following OPTIONAL columns. Included columns are decided by the server developer

\n
    \n
  • observationUnitName
    • \n
  • studyDbId
    • \n
  • studyName
    • \n
  • germplasmDbId
    • \n
  • germplasmName
    • \n
  • positionCoordinateX
    • \n
  • positionCoordinateY
    • \n
  • year
    • \n
\n

The table also may have any number of Observation Unit Hierarchy Level columns. For example:

\n
    \n
  • field
    • \n
  • plot
    • \n
  • sub-plot
    • \n
  • plant
    • \n
  • pot
    • \n
  • block
    • \n
  • entry
    • \n
  • rep
    • \n
\n

The JSON representation provides a pair of extra arrays for defining the headers of the table. \nThe first array \"headerRow\" will always contain \"observationUnitDbId\" and any or all of the OPTIONAL column header names. \nThe second array \"observationVariables\" contains the names and DbIds for the Observation Variables represented in the table. \nBy appending the two arrays, you can construct the complete header row of the table.

", + "type": "array", + "items": { + "description": "valid header fields", + "type": "string", + "enum": [ + "observationUnitDbId", + "observationUnitName", + "studyDbId", + "studyName", + "germplasmDbId", + "germplasmName", + "positionCoordinateX", + "positionCoordinateY", + "year", + "field", + "plot", + "sub-plot", + "plant", + "pot", + "block", + "entry", + "rep" + ] + }, + "example": [ + "observationUnitDbId", + "observationUnitName", + "studyDbId", + "studyName", + "germplasmDbId", + "germplasmName", + "positionCoordinateX", + "positionCoordinateY", + "year", + "field", + "plot", + "sub-plot", + "plant", + "pot", + "block", + "entry", + "rep" + ] + }, + "observationVariables": { + "description": "The list of observation variables which have values recorded for them in the data matrix. Append to the 'headerRow' for complete header row of the table.", + "type": "array", + "items": { + "type": "object", + "properties": { + "observationVariableDbId": { + "description": "Variable unique identifier", + "type": "string", + "example": "367aa1a9" + }, + "observationVariableName": { + "description": "Variable name (usually a short name)", + "type": "string", + "example": "Plant height" + } + } + }, + "example": [ + { + "observationVariableDbId": "367aa1a9", + "observationVariableName": "Plant height" + }, + { + "observationVariableDbId": "2acb934c", + "observationVariableName": "Carotenoid" + }, + { + "observationVariableDbId": "85a21ce1", + "observationVariableName": "Root color" + }, + { + "observationVariableDbId": "46f590e5", + "observationVariableName": "Virus severity" + } + ] + } + } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json", diff --git a/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json b/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json index 8e514620..b9304327 100644 --- a/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json +++ b/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json @@ -1,28 +1,62 @@ { "$defs": { "SeedLotTransactionRequest": { - "type": "object", - "properties": { - "transactionDbIds": { - "description": "Unique id for a Transaction that has occurred", - "type": "array", - "items": { - "type": "string" - } + "allOf": [ + { + "$ref": "Parameters/CommonCropNamesParameters.json#/$defs/CommonCropNamesParameters" + }, + { + "$ref": "Parameters/GermplasmParameters.json#/$defs/GermplasmParameters" }, - "transactionDirection": { - "description": "Filter results to only include transactions directed to the specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The default value for this parameter is BOTH", - "enum": [ - "TO", - "FROM", - "BOTH" - ], - "type": [ - "null", - "string" - ] + { + "$ref": "Parameters/ProgramParameters.json#/$defs/ProgramParameters" + }, + { + "type": "object", + "properties": { + "seedLotDbIds": { + "description": "Unique id for a seed lot on this server", + "type": "array", + "items": { + "type": "string" + } + }, + "crossDbIds": { + "description": "Search for Cross with this unique id", + "type": "array", + "items": { + "type": "string" + } + }, + "crossNames": { + "description": "Search for Cross with this human readable name", + "type": "array", + "items": { + "type": "string" + } + }, + "transactionDbIds": { + "description": "Unique id for a Transaction that has occurred", + "type": "array", + "items": { + "type": "string" + } + }, + "transactionDirection": { + "description": "Filter results to only include transactions directed to the specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The default value for this parameter is BOTH", + "enum": [ + "TO", + "FROM", + "BOTH" + ], + "type": [ + "null", + "string" + ] + } + } } - }, + ], "brapi-metadata": { "request": true, "subQueryProperties" : [ diff --git a/generator/openapi-single-file-options.yaml b/generator/openapi-single-file-options.yaml index 04e17b3a..fbaa7706 100644 --- a/generator/openapi-single-file-options.yaml +++ b/generator/openapi-single-file-options.yaml @@ -1,3 +1,2 @@ separateByModule: false -supplementalSpecificationFor: - BrAPI-Core: generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml \ No newline at end of file +supplementalSpecification: generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml \ No newline at end of file From ad1a1193f85d7446e9dbfd6e116a559b9a8d665f Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Sat, 6 Jun 2026 19:16:03 +1200 Subject: [PATCH 57/62] added observationLevels as control vocabulary on study --- .../BrAPI-Schema/BrAPI-Core/Study.json | 1 + .../ObservationUnitHierarchyLevelRequest.json | 22 +++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 Specification/BrAPI-Schema/Requests/ObservationUnitHierarchyLevelRequest.json diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index e7b716d2..dec28497 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -347,6 +347,7 @@ "brapi-metadata": { "primaryModel": true, "controlledVocabularyProperties": [ + "observationLevels", "studyType" ] } diff --git a/Specification/BrAPI-Schema/Requests/ObservationUnitHierarchyLevelRequest.json b/Specification/BrAPI-Schema/Requests/ObservationUnitHierarchyLevelRequest.json new file mode 100644 index 00000000..60fa61ba --- /dev/null +++ b/Specification/BrAPI-Schema/Requests/ObservationUnitHierarchyLevelRequest.json @@ -0,0 +1,22 @@ +{ + "$defs": { + "ObservationUnitHierarchyLevelRequest": { + "allOf": [ + { + "$ref": "Parameters/StudyParameters.json#/$defs/StudyParameters" + }, + { + "$ref": "Parameters/ProgramParameters.json#/$defs/ProgramParameters" + }, + { + "$ref": "Parameters/TrialParameters.json#/$defs/TrialParameters" + } + ], + "brapi-metadata": { + "request": true + } + } + }, + "$id": "https://brapi.org/Specification/BrAPI-Schema/Requests/ObservationUnitHierarchyLevelRequest.json", + "$schema": "http://json-schema.org/draft/2020-12/schema" +} \ No newline at end of file From 0e2094349c82bdd31010f6ecc1bda86982cd6c2c Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Sat, 6 Jun 2026 20:35:01 +1200 Subject: [PATCH 58/62] added extract to VariantSet as an action --- .../BrAPI-Genotyping/VariantSet.json | 9 +- .../Requests/VariantSetsExtractRequest.json | 90 +++++++++++++++++++ generator/build.gradle | 2 +- 3 files changed, 99 insertions(+), 2 deletions(-) create mode 100644 Specification/BrAPI-Schema/Requests/VariantSetsExtractRequest.json diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json index cc9889ea..f35ae40d 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json @@ -161,6 +161,10 @@ "null", "array" ] + }, + "extract": { + "description": "Will perform a search for `Calls` which match the search criteria in `variantSetsExtractRequest`. The results of the search will be used to create a new `VariantSet` on the server. The new `VariantSet` will be returned.", + "$ref": "VariantSet.json#/$defs/VariantSet" } }, "required": [ @@ -170,7 +174,10 @@ "description": "A VariantSet is a collection of variants and variant calls intended to be analyzed together.", "type": "object", "brapi-metadata": { - "primaryModel": true + "primaryModel": true, + "actionProperties": [ + "extract" + ] } }, "Analysis": { diff --git a/Specification/BrAPI-Schema/Requests/VariantSetsExtractRequest.json b/Specification/BrAPI-Schema/Requests/VariantSetsExtractRequest.json new file mode 100644 index 00000000..9f190ef4 --- /dev/null +++ b/Specification/BrAPI-Schema/Requests/VariantSetsExtractRequest.json @@ -0,0 +1,90 @@ +{ + "$defs": { + "VariantSetsExtractRequest": { + "description": "Request object for extracting data subsets as new Variant Sets", + "type": "object", + "properties": { + "callSetDbIds": { + "description": "The CallSet to search.", + "type": "array", + "items": { + "type": "string" + }, + "example": [ + "9569cfc4", + "da1e888c" + ] + }, + "expandHomozygotes": { + "description": "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "type": "boolean", + "example": true + }, + "sepPhased": { + "description": "The string used as a separator for phased allele calls.", + "type": "string", + "example": "~" + }, + "sepUnphased": { + "description": "The string used as a separator for unphased allele calls.", + "type": "string", + "example": "|" + }, + "studyDbIds": { + "description": "List of study identifiers to search for", + "type": "array", + "items": { + "type": "string" + }, + "example": [ + "cf6c4bd4", + "691e69d6" + ] + }, + "studyNames": { + "description": "List of study names to filter search results", + "type": "array", + "items": { + "type": "string" + }, + "example": [ + "The First Bob Study 2017", + "Wheat Yield Trial 246" + ] + }, + "unknownString": { + "description": "The string used as a representation for missing data.", + "type": "string", + "example": "-" + }, + "variantDbIds": { + "description": "The Variant to search.", + "type": "array", + "items": { + "type": "string" + }, + "example": [ + "c80f068b", + "eb7c5f50" + ] + }, + "variantSetDbIds": { + "description": "The VariantSet to search.", + "type": "array", + "items": { + "type": "string" + }, + "example": [ + "b2903842", + "dcbb8558" + ] + } + }, + "brapi-metadata": { + "request": true + } + } + }, + "$id": "https://brapi.org/Specification/BrAPI-Schema/Requests/VariantSetsExtractRequest.json", + "$schema": "http://json-schema.org/draft/2020-12/schema" +} diff --git a/generator/build.gradle b/generator/build.gradle index 3252eff2..6af3cebb 100644 --- a/generator/build.gradle +++ b/generator/build.gradle @@ -4,7 +4,7 @@ plugins { ext { javaMainClass = 'org.brapi.schematools.cli.BrAPICommand' - brapiSchemaToolsVersion = '0.75.0' + brapiSchemaToolsVersion = '0.77.0' } repositories { From 81a44176d9c51c55f6827f7f684baab6ac88475d Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Sun, 7 Jun 2026 00:43:52 +0000 Subject: [PATCH 59/62] Generate specifications (manually triggered) --- Specification/Generated/BrAPI-Genotyping.yaml | 408 +- Specification/Generated/BrAPI-Germplasm.yaml | 420 +- .../Generated/BrAPI-Phenotyping.yaml | 2094 ++-- Specification/Generated/BrAPI.yaml | 8708 +++++++++++++++++ .../Generated/brapi_generated.graphqls | 340 +- Specification/Generated/brapi_generated.json | 3775 ++++--- Specification/Generated/brapi_openapi.json | 418 +- .../Generated/brapi_openapi_comparison.md | 286 +- 8 files changed, 13197 insertions(+), 3252 deletions(-) create mode 100644 Specification/Generated/BrAPI.yaml diff --git a/Specification/Generated/BrAPI-Genotyping.yaml b/Specification/Generated/BrAPI-Genotyping.yaml index 5be65abe..fd1ae90e 100644 --- a/Specification/Generated/BrAPI-Genotyping.yaml +++ b/Specification/Generated/BrAPI-Genotyping.yaml @@ -51,17 +51,16 @@ paths: format: int32 - name: dataMatrixNames in: query - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth'\ + \ etc). This list controls which data matrices are returned in the response." required: false schema: type: string - name: dataMatrixAbbreviations in: query - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." required: false schema: type: string @@ -148,8 +147,6 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" /calls: get: tags: @@ -225,6 +222,29 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + put: + tags: + - Calls + summary: Update the details for an existing Call + description: Update the details for an existing Call + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/Call" + responses: + "200": + $ref: "#/components/responses/CallListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" /callsets: get: tags: @@ -509,6 +529,37 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + put: + tags: + - Plates + summary: Update the details for an existing Plate + description: Update the details for an existing Plate + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: object + additionalProperties: + $ref: "#/components/schemas/PlateNewRequest" + example: "{_1={additionalInfo={}, externalReferences=[{}],\ + \ plateBarcode=4eacf0b7, plateDbId=71ea8b72, plateFormat={}, plateName=72778960,\ + \ program={}, sampleType={}, study={}, trial={}, samples=[{}]}, _2={additionalInfo={},\ + \ externalReferences=[{}], plateBarcode=4eacf0b8, plateDbId=71ea8b73,\ + \ plateFormat={}, plateName=72778961, program={}, sampleType={}, study={},\ + \ trial={}, samples=[{}]}}" + responses: + "200": + $ref: "#/components/responses/PlateListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" post: tags: - Plates @@ -857,6 +908,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" post: tags: - Samples @@ -1090,14 +1143,14 @@ paths: responses: "200": $ref: "#/components/responses/CallListResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /maps/{mapDbId}: get: tags: @@ -1142,14 +1195,14 @@ paths: responses: "200": $ref: "#/components/responses/LinkageGroupListResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /plates/{plateDbId}: get: tags: @@ -1375,14 +1428,14 @@ paths: responses: "200": $ref: "#/components/responses/CallListResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /variantsets/{variantSetDbId}: get: tags: @@ -1453,14 +1506,14 @@ paths: responses: "200": $ref: "#/components/responses/CallListResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /variantsets/{variantSetDbId}/callsets: get: tags: @@ -1493,14 +1546,14 @@ paths: responses: "200": $ref: "#/components/responses/CallSetListResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /variantsets/{variantSetDbId}/variants: get: tags: @@ -1527,14 +1580,14 @@ paths: responses: "200": $ref: "#/components/responses/VariantListResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/allelematrix: post: tags: @@ -1872,14 +1925,14 @@ paths: $ref: "#/components/responses/AlleleMatrixSingleResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/calls/{searchResultsDbId}: get: tags: @@ -1915,14 +1968,14 @@ paths: $ref: "#/components/responses/CallListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/callsets/{searchResultsDbId}: get: tags: @@ -1957,14 +2010,14 @@ paths: $ref: "#/components/responses/CallSetListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/markerpositions/{searchResultsDbId}: get: tags: @@ -2000,14 +2053,14 @@ paths: $ref: "#/components/responses/MarkerPositionListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/plates/{searchResultsDbId}: get: tags: @@ -2042,14 +2095,14 @@ paths: $ref: "#/components/responses/PlateListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/references/{searchResultsDbId}: get: tags: @@ -2084,14 +2137,14 @@ paths: $ref: "#/components/responses/ReferenceListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/referencesets/{searchResultsDbId}: get: tags: @@ -2126,14 +2179,14 @@ paths: $ref: "#/components/responses/ReferenceSetListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/samples/{searchResultsDbId}: get: tags: @@ -2168,14 +2221,14 @@ paths: $ref: "#/components/responses/SampleListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/variants/{searchResultsDbId}: get: tags: @@ -2211,14 +2264,14 @@ paths: $ref: "#/components/responses/VariantListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/variantsets/{searchResultsDbId}: get: tags: @@ -2253,14 +2306,38 @@ paths: $ref: "#/components/responses/VariantSetListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" "404": $ref: "#/components/responses/404NotFound" + /variantsets/extract: + post: + tags: + - VariantSets + summary: Perform `extract` on `VariantSet` + description: Perform the `extract` action on `VariantSet`. + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/VariantSetsExtractRequest" + responses: + "200": + $ref: "#/components/responses/VariantSetSingleResponse" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" components: schemas: AdditionalInfo: @@ -2371,19 +2448,21 @@ components: items: type: string dataMatrixAbbreviations: - type: string - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." nullable: true - example: "GT,RD" + items: + type: string dataMatrixNames: - type: string - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." nullable: true - example: "Genotype,Read Depth" + items: + type: string dimensionCallSetPage: type: integer description: The requested page number for the CallSet dimension of the @@ -2521,19 +2600,21 @@ components: items: type: string dataMatrixAbbreviations: - type: string - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." nullable: true - example: "GT,RD" + items: + type: string dataMatrixNames: - type: string - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." nullable: true - example: "Genotype,Read Depth" + items: + type: string expandHomozygotes: type: boolean description: Should homozygotes be expanded (true) or collapsed into a single @@ -2758,9 +2839,9 @@ components: method: $ref: "#/components/schemas/Method" ontologyReference: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/OntologyReference" - - type: "null" scale: $ref: "#/components/schemas/Scale" scientist: @@ -3765,7 +3846,8 @@ components: nullable: true GeoJSONGeometry: type: object - nullable: true + discriminator: + propertyName: type oneOf: - required: - coordinates @@ -4529,7 +4611,9 @@ components: items: type: string listType: - $ref: "#/components/schemas/ListType" + nullable: true + allOf: + - $ref: "#/components/schemas/ListType" programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -5119,6 +5203,47 @@ components: \ associated observed variable (see observed variables). \nAlternatively,\ \ it is possible to use samples for more detailed tracing of sub-plant units,\ \ attaching the observations to them instead.\" " + ObservationUnitHierarchyLevelRequest: + type: object + properties: + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string ObservationUnitRequest: type: object properties: @@ -7543,7 +7668,64 @@ components: SeedLotTransactionRequest: type: object properties: - transactionDbIs: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seedLotDbIds: + type: array + description: Unique id for a seed lot on this server + items: + type: string + transactionDbIds: type: array description: Unique id for a Transaction that has occurred items: @@ -8050,9 +8232,9 @@ components: method: $ref: "#/components/schemas/Method" ontologyReference: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/OntologyReference" - - type: "null" scale: $ref: "#/components/schemas/Scale" scientist: @@ -8903,6 +9085,52 @@ components: type: string description: A VariantSet is a collection of variants and variant calls intended to be analyzed together. + VariantSetsExtractRequest: + type: object + properties: + callSetDbIds: + type: array + description: The CallSet to search. + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + example: "~" + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + example: '|' + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + unknownString: + type: string + description: The string used as a representation for missing data. + example: "-" + variantDbIds: + type: array + description: The Variant to search. + items: + type: string + variantSetDbIds: + type: array + description: The VariantSet to search. + items: + type: string + description: Request object for extracting data subsets as new Variant Sets basePagination: required: - currentPage @@ -9265,6 +9493,32 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/Sample" + StudyObservationLevelsListResponse: + description: OK + content: + application/json: + schema: + title: StudyObservationLevelsListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: array + items: + $ref: "#/components/schemas/ObservationUnitHierarchyLevel" ReferenceSetListResponse: description: OK content: @@ -9647,6 +9901,30 @@ components: type: array items: $ref: "#/components/schemas/Reference" + ProgramCommonCropNameListResponse: + description: OK + content: + application/json: + schema: + title: ProgramCommonCropNameListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: string AlleleMatrixListResponse: description: OK content: diff --git a/Specification/Generated/BrAPI-Germplasm.yaml b/Specification/Generated/BrAPI-Germplasm.yaml index 7c3850c6..cc0926e5 100644 --- a/Specification/Generated/BrAPI-Germplasm.yaml +++ b/Specification/Generated/BrAPI-Germplasm.yaml @@ -800,6 +800,40 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + put: + tags: + - PedigreeNodes + summary: Update the details for an existing PedigreeNode + description: Update the details for an existing PedigreeNode + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: object + additionalProperties: + $ref: "#/components/schemas/PedigreeNode" + example: "{_1={additionalInfo={}, breedingMethod={}, crossingProject={},\ + \ crossingYear=10, defaultDisplayName=5761c815, externalReferences=[{}],\ + \ familyCode=42f142b0, germplasm={}, parents=[{}], pedigreeString=5e286b4b,\ + \ progeny=[{}], siblings=[{}]}, _2={additionalInfo={}, breedingMethod={},\ + \ crossingProject={}, crossingYear=20, defaultDisplayName=5761c816,\ + \ externalReferences=[{}], familyCode=42f142b1, germplasm={}, parents=[{}],\ + \ pedigreeString=5e286b4c, progeny=[{}], siblings=[{}]}}" + responses: + "200": + $ref: "#/components/responses/PedigreeNodeListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" post: tags: - PedigreeNodes @@ -823,6 +857,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /plannedcrosses: get: tags: @@ -1053,6 +1089,110 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + /seedlots/transactions: + get: + tags: + - Seed Lots + summary: Get a filtered list of SeedLotTransaction + description: Get a list of SeedLotTransaction + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: germplasmName + in: query + description: List of human readable names to identify germplasm to search + for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: seedLotDbId + in: query + description: Unique id for a seed lot on this server + required: false + schema: + type: string + - name: crossDbId + in: query + description: Search for Cross with this unique id + required: false + schema: + type: string + - name: crossName + in: query + description: Search for Cross with this human readable name + required: false + schema: + type: string + - name: transactionDbId + in: query + description: Unique id for a Transaction that has occurred + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/SeedLotTransactionListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Seed Lots + summary: Create new SeedLotTransaction + description: Add new SeedLotTransaction to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/SeedLotTransactionNewRequest" + responses: + "200": + $ref: "#/components/responses/SeedLotTransactionListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" /attributes/categories: get: tags: @@ -1424,6 +1564,12 @@ paths: required: true schema: type: string + - name: transactionDbId + in: query + description: Unique id for a Transaction that has occurred + required: false + schema: + type: string - name: transactionDirection in: query description: "Filter results to only include transactions directed to the\ @@ -1445,14 +1591,14 @@ paths: responses: "200": $ref: "#/components/responses/SeedLotTransactionListResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/germplasm: post: tags: @@ -1611,14 +1757,14 @@ paths: $ref: "#/components/responses/GermplasmListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/attributes/{searchResultsDbId}: get: tags: @@ -1654,14 +1800,14 @@ paths: $ref: "#/components/responses/GermplasmAttributeListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/attributevalues/{searchResultsDbId}: get: tags: @@ -1698,14 +1844,14 @@ paths: $ref: "#/components/responses/GermplasmAttributeValueListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/pedigree/{searchResultsDbId}: get: tags: @@ -1740,14 +1886,14 @@ paths: $ref: "#/components/responses/PedigreeNodeListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" components: schemas: AcquisitionSourceCode: @@ -1826,19 +1972,21 @@ components: items: type: string dataMatrixAbbreviations: - type: string - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." nullable: true - example: "GT,RD" + items: + type: string dataMatrixNames: - type: string - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." nullable: true - example: "Genotype,Read Depth" + items: + type: string dimensionCallSetPage: type: integer description: The requested page number for the CallSet dimension of the @@ -2042,9 +2190,9 @@ components: method: $ref: "#/components/schemas/Method" ontologyReference: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/OntologyReference" - - type: "null" scale: $ref: "#/components/schemas/Scale" scientist: @@ -3000,7 +3148,8 @@ components: nullable: true GeoJSONGeometry: type: object - nullable: true + discriminator: + propertyName: type oneOf: - required: - coordinates @@ -3206,9 +3355,9 @@ components: method: $ref: "#/components/schemas/Method" ontologyReference: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/OntologyReference" - - type: "null" scale: $ref: "#/components/schemas/Scale" scientist: @@ -5190,7 +5339,9 @@ components: items: type: string listType: - $ref: "#/components/schemas/ListType" + nullable: true + allOf: + - $ref: "#/components/schemas/ListType" programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -5667,6 +5818,47 @@ components: \ associated observed variable (see observed variables). \nAlternatively,\ \ it is possible to use samples for more detailed tracing of sub-plant units,\ \ attaching the observations to them instead.\" " + ObservationUnitHierarchyLevelRequest: + type: object + properties: + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string ObservationUnitRequest: type: object properties: @@ -7576,8 +7768,18 @@ components: items: type: string SeedLotTransaction: - required: - - transactionDbId + allOf: + - $ref: "#/components/schemas/SeedLotTransactionNewRequest" + - required: + - transactionDbId + type: object + properties: + transactionDbId: + type: string + description: Unique DbId for the Seed Lot Transaction + description: The record of an event where material was moved in or out of + a particular SeedLot + SeedLotTransactionNewRequest: type: object properties: additionalInfo: @@ -7601,9 +7803,6 @@ components: toSeedLotDbId: type: string nullable: true - transactionDbId: - type: string - description: Unique DbId for the Seed Lot Transaction transactionDescription: type: string description: A general description of this Seed Lot Transaction @@ -7623,7 +7822,64 @@ components: SeedLotTransactionRequest: type: object properties: - transactionDbIs: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seedLotDbIds: + type: array + description: Unique id for a seed lot on this server + items: + type: string + transactionDbIds: type: array description: Unique id for a Transaction that has occurred items: @@ -8183,9 +8439,9 @@ components: method: $ref: "#/components/schemas/Method" ontologyReference: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/OntologyReference" - - type: "null" scale: $ref: "#/components/schemas/Scale" scientist: @@ -8562,6 +8818,52 @@ components: description: The unique identifier representing a VariantSet items: type: string + VariantSetsExtractRequest: + type: object + properties: + callSetDbIds: + type: array + description: The CallSet to search. + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + example: "~" + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + example: '|' + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + unknownString: + type: string + description: The string used as a representation for missing data. + example: "-" + variantDbIds: + type: array + description: The Variant to search. + items: + type: string + variantSetDbIds: + type: array + description: The VariantSet to search. + items: + type: string + description: Request object for extracting data subsets as new Variant Sets basePagination: required: - currentPage @@ -9498,6 +9800,32 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/GermplasmMCPD" + StudyObservationLevelsListResponse: + description: OK + content: + application/json: + schema: + title: StudyObservationLevelsListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: array + items: + $ref: "#/components/schemas/ObservationUnitHierarchyLevel" ReferenceSetListResponse: description: OK content: @@ -9750,6 +10078,30 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/Person" + ProgramCommonCropNameListResponse: + description: OK + content: + application/json: + schema: + title: ProgramCommonCropNameListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: string VariantListResponse: description: OK content: diff --git a/Specification/Generated/BrAPI-Phenotyping.yaml b/Specification/Generated/BrAPI-Phenotyping.yaml index 9b87a58a..aaa14ec5 100644 --- a/Specification/Generated/BrAPI-Phenotyping.yaml +++ b/Specification/Generated/BrAPI-Phenotyping.yaml @@ -465,6 +465,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" post: tags: - Observations @@ -488,6 +490,8 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /observationunits: get: tags: @@ -718,180 +722,6 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - /variables: - get: - tags: - - ObservationVariables - summary: Get a filtered list of ObservationVariable - description: Get a list of ObservationVariable - parameters: - - name: observationVariableDbId - in: query - description: The DbIds of Variables to search for - required: false - schema: - type: string - - name: observationVariableName - in: query - description: The names of Variables to search for - required: false - schema: - type: string - - name: observationVariablePUI - in: query - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - required: false - schema: - type: string - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: trialDbId - in: query - description: The ID which uniquely identifies a trial to search for - required: false - schema: - type: string - - name: studyDbId - in: query - description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ - \ number #483 \n
The unique ID of a studies to filter on" - required: false - schema: - type: string - - name: ontologyDbId - in: query - description: List of ontology IDs to search for - required: false - schema: - type: string - - name: methodDbId - in: query - description: List of methods to filter search results - required: false - schema: - type: string - - name: methodName - in: query - description: |- - Human readable name for the method -
MIAPPE V1.1 (DM-88) Method Name of the method of observation - required: false - schema: - type: string - - name: methodPUI - in: query - description: "The Permanent Unique Identifier of a Method, usually in the\ - \ form of a URI" - required: false - schema: - type: string - - name: scaleDbId - in: query - description: The unique identifier for a Scale - required: false - schema: - type: string - - name: scaleName - in: query - description: |- - Name of the scale -
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable - required: false - schema: - type: string - - name: scalePUI - in: query - description: "The Permanent Unique Identifier of a Scale, usually in the form\ - \ of a URI" - required: false - schema: - type: string - - name: traitClass - in: query - description: List of trait classes to filter search results - required: false - schema: - type: string - - name: traitDbId - in: query - description: The unique identifier for a Trait - required: false - schema: - type: string - - name: traitName - in: query - description: |- - The human readable name of a trait -
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation - required: false - schema: - type: string - - name: traitPUI - in: query - description: "The Permanent Unique Identifier of a Trait, usually in the form\ - \ of a URI" - required: false - schema: - type: string - - $ref: "#/components/parameters/externalReferenceId" - - $ref: "#/components/parameters/externalReferenceID" - - $ref: "#/components/parameters/externalReferenceSource" - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/ObservationVariableListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - post: - tags: - - ObservationVariables - summary: Create new ObservationVariable - description: Add new ObservationVariable to database - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - type: array - items: - $ref: "#/components/schemas/ObservationVariableNewRequest" - responses: - "200": - $ref: "#/components/responses/ObservationVariableListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" /ontologies: get: tags: @@ -1176,6 +1006,37 @@ paths: $ref: "#/components/responses/403Forbidden" "404": $ref: "#/components/responses/404NotFound" + /images/{imageDbId}/imagecontent: + put: + tags: + - Images + summary: Update the details for an existing string + description: Update the details for an existing string + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: imageDbId + in: path + description: The unique identifier of an image + required: true + schema: + type: string + requestBody: + content: + image/*: + schema: + type: string + format: binary + responses: + "200": + $ref: "#/components/responses/ImageSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /methods/{methodDbId}: get: tags: @@ -1255,26 +1116,27 @@ paths: $ref: "#/components/responses/403Forbidden" "404": $ref: "#/components/responses/404NotFound" - /observationunits/{observationUnitDbId}: - get: + put: tags: - - ObservationUnits - summary: Get the details of a specific ObservationUnit - description: Get details for a ObservationUnit + - Observations + summary: Update the details for an existing Observation + description: Update the details for an existing Observation parameters: - $ref: "#/components/parameters/authorizationHeader" - - name: observationUnitDbId + - name: observationDbId in: path - description: "The ID which uniquely identifies an observation unit\n\nMIAPPE\ - \ V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation\ - \ unit in data files containing the values observed or measured on that\ - \ unit. Must be locally unique. " + description: The ID which uniquely identifies an observation required: true schema: type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationNewRequest" responses: "200": - $ref: "#/components/responses/ObservationUnitSingleResponse" + $ref: "#/components/responses/ObservationSingleResponse" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1283,26 +1145,26 @@ paths: $ref: "#/components/responses/403Forbidden" "404": $ref: "#/components/responses/404NotFound" - /variables/{observationVariableDbId}: + /observationunits/{observationUnitDbId}: get: tags: - - ObservationVariables - summary: Get the details of a specific ObservationVariable - description: Get details for a ObservationVariable + - ObservationUnits + summary: Get the details of a specific ObservationUnit + description: Get details for a ObservationUnit parameters: - $ref: "#/components/parameters/authorizationHeader" - - name: observationVariableDbId + - name: observationUnitDbId in: path - description: |- - Variable unique identifier - - MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. + description: "The ID which uniquely identifies an observation unit\n\nMIAPPE\ + \ V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation\ + \ unit in data files containing the values observed or measured on that\ + \ unit. Must be locally unique. " required: true schema: type: string responses: "200": - $ref: "#/components/responses/ObservationVariableSingleResponse" + $ref: "#/components/responses/ObservationUnitSingleResponse" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1313,17 +1175,17 @@ paths: $ref: "#/components/responses/404NotFound" put: tags: - - ObservationVariables - summary: Update the details for an existing ObservationVariable - description: Update the details for an existing ObservationVariable + - ObservationUnits + summary: Update the details for an existing ObservationUnit + description: Update the details for an existing ObservationUnit parameters: - $ref: "#/components/parameters/authorizationHeader" - - name: observationVariableDbId + - name: observationUnitDbId in: path - description: |- - Variable unique identifier - - MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. + description: "The ID which uniquely identifies an observation unit\n\nMIAPPE\ + \ V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation\ + \ unit in data files containing the values observed or measured on that\ + \ unit. Must be locally unique. " required: true schema: type: string @@ -1331,10 +1193,10 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ObservationVariableNewRequest" + $ref: "#/components/schemas/ObservationUnitNewRequest" responses: "200": - $ref: "#/components/responses/ObservationVariableSingleResponse" + $ref: "#/components/responses/ObservationUnitSingleResponse" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1507,18 +1369,12 @@ paths: $ref: "#/components/responses/403Forbidden" "404": $ref: "#/components/responses/404NotFound" - /search/images: + /delete/images: post: tags: - Images - summary: Submit a search request for `Image` - description: "Submit a search request for `Image`
\nSearch requests allow\ - \ a client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.\ - \
\nReview the Search Services documentation for additional implementation details." + summary: Submit a delete request for `Images` + description: Submit a delete request for `Images` parameters: - $ref: "#/components/parameters/authorizationHeader" requestBody: @@ -1528,28 +1384,19 @@ paths: $ref: "#/components/schemas/ImageSearchRequest" responses: "200": - $ref: "#/components/responses/ImageListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" + $ref: "#/components/responses/ImageDeleteResponse" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - /search/observations: + /delete/observations: post: tags: - Observations - summary: Submit a search request for `Observation` - description: "Submit a search request for `Observation`
\nSearch requests\ - \ allow a client to send a complex query for data. However, the server may\ - \ not respond with the search results immediately. \nIf a server needs more\ - \ time to process the request, it might respond with a `searchResultsDbId`.\ - \ \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to\ - \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + summary: Submit a delete request for `Observations` + description: Submit a delete request for `Observations` parameters: - $ref: "#/components/parameters/authorizationHeader" requestBody: @@ -1559,38 +1406,393 @@ paths: $ref: "#/components/schemas/ObservationSearchRequest" responses: "200": - $ref: "#/components/responses/ObservationListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" + $ref: "#/components/responses/ObservationDeleteResponse" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - /search/observationunits: - post: + /observations/table: + get: tags: - - ObservationUnits - summary: Submit a search request for `ObservationUnit` - description: "Submit a search request for `ObservationUnit`
\nSearch requests\ - \ allow a client to send a complex query for data. However, the server may\ - \ not respond with the search results immediately. \nIf a server needs more\ - \ time to process the request, it might respond with a `searchResultsDbId`.\ - \ \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}`\ - \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + - Observations + summary: Get a table of `Observation` records as a CSV file. + description: Get a table of `Observation` records returned directly as CSV text. parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ObservationUnitSearchRequest" - responses: - "200": - $ref: "#/components/responses/ObservationUnitListResponse" + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: locationDbId + in: query + description: The location ids to search for + required: false + schema: + type: string + - name: observationVariableDbId + in: query + description: The DbIds of Variables to search for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: observationUnitDbId + in: query + description: The unique id of an Observation Unit + required: false + schema: + type: string + - name: observationLevel + in: query + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + required: false + schema: + type: string + - name: observationUnitLevelName + in: query + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on Observation\ + \ Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationUnitLevelOrder + in: query + description: "The Observation Unit Level Order Number. Returns only the observation\ + \ unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationUnitLevelCode + in: query + description: "The Observation Unit Level Code. This parameter should be used\ + \ together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationUnitLevelRelationshipName + in: query + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a relationship\ + \ level. \n
**Standard Level Names: study, field, entry, rep, block,\ + \ sub-block, plot, sub-plot, plant, pot, sample** \n
For more information\ + \ on Observation Levels, please review the Observation Levels\ + \ documentation. " + required: false + schema: + type: string + - name: observationUnitLevelRelationshipOrder + in: query + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationUnitLevelRelationshipCode + in: query + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationUnitLevelRelationshipDbId + in: query + description: "The observationUnitDbId associated with a particular level and\ + \ code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationTimeStampRangeEnd + in: query + description: Timestamp range end + required: false + schema: + type: string + format: date-time + - name: observationTimeStampRangeStart + in: query + description: Timestamp range start + required: false + schema: + type: string + format: date-time + - name: seasonDbId + in: query + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + required: false + schema: + type: string + - $ref: "#/components/parameters/acceptHeader" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ObservationTableResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /observationunits/table: + get: + tags: + - ObservationUnits + summary: Get a table of `ObservationUnit` records as a CSV file. + description: Get a table of `ObservationUnit` records returned directly as CSV + text. + parameters: + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: locationDbId + in: query + description: The location ids to search for + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: observationVariableDbId + in: query + description: The DbIds of Variables to search for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: observationUnitDbId + in: query + description: The unique id of an observation unit + required: false + schema: + type: string + - name: observationLevel + in: query + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + required: false + schema: + type: string + - name: observationUnitLevelName + in: query + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on Observation\ + \ Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationUnitLevelOrder + in: query + description: "The Observation Unit Level Order Number. Returns only the observation\ + \ unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationUnitLevelCode + in: query + description: "The Observation Unit Level Code. This parameter should be used\ + \ together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationUnitLevelRelationshipName + in: query + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a relationship\ + \ level. \n
**Standard Level Names: study, field, entry, rep, block,\ + \ sub-block, plot, sub-plot, plant, pot, sample** \n
For more information\ + \ on Observation Levels, please review the Observation Levels\ + \ documentation. " + required: false + schema: + type: string + - name: observationUnitLevelRelationshipOrder + in: query + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationUnitLevelRelationshipCode + in: query + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: observationUnitLevelRelationshipDbId + in: query + description: "The observationUnitDbId associated with a particular level and\ + \ code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the Observation Levels documentation. " + required: false + schema: + type: string + - name: seasonDbId + in: query + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + required: false + schema: + type: string + - $ref: "#/components/parameters/acceptHeader" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ObservationUnitTableResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/images: + post: + tags: + - Images + summary: Submit a search request for `Image` + description: "Submit a search request for `Image`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ImageSearchRequest" + responses: + "200": + $ref: "#/components/responses/ImageListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/observations: + post: + tags: + - Observations + summary: Submit a search request for `Observation` + description: "Submit a search request for `Observation`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to\ + \ retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ObservationSearchRequest" + responses: + "200": + $ref: "#/components/responses/ObservationListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" "400": @@ -1599,16 +1801,16 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - /search/variables: + /search/observationunits: post: tags: - - ObservationVariables - summary: Submit a search request for `ObservationVariable` - description: "Submit a search request for `ObservationVariable`
\nSearch\ - \ requests allow a client to send a complex query for data. However, the server\ - \ may not respond with the search results immediately. \nIf a server needs\ - \ more time to process the request, it might respond with a `searchResultsDbId`.\ - \ \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}`\ + - ObservationUnits + summary: Submit a search request for `ObservationUnit` + description: "Submit a search request for `ObservationUnit`
\nSearch requests\ + \ allow a client to send a complex query for data. However, the server may\ + \ not respond with the search results immediately. \nIf a server needs more\ + \ time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}`\ \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." @@ -1618,10 +1820,10 @@ paths: content: application/json: schema: - $ref: "#/components/schemas/ObservationVariableSearchRequest" + $ref: "#/components/schemas/ObservationUnitSearchRequest" responses: "200": - $ref: "#/components/responses/ObservationVariableListResponse" + $ref: "#/components/responses/ObservationUnitListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" "400": @@ -1664,14 +1866,14 @@ paths: $ref: "#/components/responses/ImageListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/observations/{searchResultsDbId}: get: tags: @@ -1706,14 +1908,14 @@ paths: $ref: "#/components/responses/ObservationListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/observationunits/{searchResultsDbId}: get: tags: @@ -1749,57 +1951,14 @@ paths: $ref: "#/components/responses/ObservationUnitListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" - /search/variables/{searchResultsDbId}: - get: - tags: - - ObservationVariables - summary: "Submit a search request for `ObservationVariable`
\nSearch requests\ - \ allow a client to send a complex query for data. However, the server may\ - \ not respond with the search results immediately. \nIf a server needs more\ - \ time to process the request, it might respond with a `searchResultsDbId`.\ - \ \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}`\ - \ to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details." - description: "Get the results of a `ObservationVariable` search request
\n\ - Clients should submit a search request using the corresponding `POST /search/observationVariable`\ - \ endpoint.\nSearch requests allow a client to send a complex query for data.\ - \ However, the server may not respond with the search results immediately.\ - \ \nIf a server needs more time to process the request, it might respond with\ - \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ - \ search.
\nReview the Search Services documentation for additional implementation details." - parameters: - - name: searchResultsDbId - in: path - description: searchResultsDbId - required: true - schema: - type: string - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/ObservationVariableListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" "404": $ref: "#/components/responses/404NotFound" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" components: schemas: AdditionalInfo: @@ -1842,19 +2001,21 @@ components: items: type: string dataMatrixAbbreviations: - type: string - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." nullable: true - example: "GT,RD" + items: + type: string dataMatrixNames: - type: string - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." nullable: true - example: "Genotype,Read Depth" + items: + type: string dimensionCallSetPage: type: integer description: The requested page number for the CallSet dimension of the @@ -2058,9 +2219,9 @@ components: method: $ref: "#/components/schemas/Method" ontologyReference: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/OntologyReference" - - type: "null" scale: $ref: "#/components/schemas/Scale" scientist: @@ -2750,7 +2911,8 @@ components: nullable: true GeoJSONGeometry: type: object - nullable: true + discriminator: + propertyName: type oneOf: - required: - coordinates @@ -3304,6 +3466,28 @@ components: description: The human readable name of a trial to search for items: type: string + HeaderRow: + type: string + description: valid header fields + enum: + - observationTimeStamp + - observationUnitDbId + - observationUnitName + - studyDbId + - studyName + - germplasmDbId + - germplasmName + - positionCoordinateX + - positionCoordinateY + - year + - field + - plot + - sub-plot + - plant + - pot + - block + - entry + - rep Image: allOf: - $ref: "#/components/schemas/ImageNewRequest" @@ -3383,10 +3567,18 @@ components: format: int32 nullable: true mimeType: + pattern: image/.* type: string description: "The file type of the image. Examples 'image/jpeg', 'image/png',\ \ 'image/svg', etc" nullable: true + observationDbIds: + type: array + description: "A list of observation Ids this image is associated with, if\ + \ applicable." + nullable: true + items: + type: string observationUnitDbId: type: string nullable: true @@ -3719,7 +3911,9 @@ components: items: type: string listType: - $ref: "#/components/schemas/ListType" + nullable: true + allOf: + - $ref: "#/components/schemas/ListType" programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -4066,16 +4260,14 @@ components: observationUnitName: type: string nullable: true - observationVariableDbId: - type: string - nullable: true - observationVariableName: - type: string + observationVariable: nullable: true + allOf: + - $ref: "#/components/schemas/ObservationVariable" season: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/Season" - - type: "null" studyDbId: type: string nullable: true @@ -4460,6 +4652,77 @@ components: type: string description: A value assigned for a specific ObservationVariable when observing a specific ObservationUnit. + ObservationTable: + type: object + properties: + data: + type: array + description: "The 2D matrix of observation data. ObservationVariables and\ + \ other metadata are the columns, ObservationUnits are the rows." + items: + type: array + items: + type: string + headerRow: + type: array + description: "

The table is REQUIRED to have the following columns

\n\ +
    \n
  • observationUnitDbId - Each row is related to one Observation\ + \ Unit
    • \n
  • observationTimeStamp - Each row is has a time stamp\ + \ for when the observation was taken
    • \n
  • At least one column with\ + \ an observationVariableDbId
    • \n
\n

The table may have any or\ + \ all of the following OPTIONAL columns. Included columns are decided\ + \ by the server developer

\n
    \n
  • observationUnitName
    • \n\ + \
  • studyDbId
    • \n
  • studyName
    • \n
  • germplasmDbId
    • \n\ + \
  • germplasmName
    • \n
  • positionCoordinateX
    • \n
  • positionCoordinateY
    • \n\ + \
  • year
    • \n
\n

The table also may have any number of Observation\ + \ Unit Hierarchy Level columns. For example:

\n
    \n
  • field
    • \n\ + \
  • plot
    • \n
  • sub-plot
    • \n
  • plant
    • \n
  • pot
    • \n\ + \
  • block
    • \n
  • entry
    • \n
  • rep
    • \n
\n

The JSON\ + \ representation provides a pair of extra arrays for defining the headers\ + \ of the table. \nThe first array \"headerRow\" will always contain \"\ + observationUnitDbId\" and any or all of the OPTIONAL column header names.\ + \ \nThe second array \"observationVariables\" contains the names and DbIds\ + \ for the Observation Variables represented in the table. \nBy appending\ + \ the two arrays, you can construct the complete header row of the table.\ + \

" + items: + type: string + description: valid header fields + enum: + - observationTimeStamp + - observationUnitDbId + - observationUnitName + - studyDbId + - studyName + - germplasmDbId + - germplasmName + - positionCoordinateX + - positionCoordinateY + - year + - field + - plot + - sub-plot + - plant + - pot + - block + - entry + - rep + observationVariables: + type: array + description: The list of observation variables which have values recorded + for them in the data matrix. Append to the 'headerRow' for complete header + row of the table. + items: + type: object + properties: + observationVariableDbId: + type: string + description: Variable unique identifier + example: 367aa1a9 + observationVariableName: + type: string + description: Variable name (usually a short name) + example: Plant height ObservationTreatment: type: object properties: @@ -4532,6 +4795,47 @@ components: \ associated observed variable (see observed variables). \nAlternatively,\ \ it is possible to use samples for more detailed tracing of sub-plant units,\ \ attaching the observations to them instead.\" " + ObservationUnitHierarchyLevelRequest: + type: object + properties: + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string ObservationUnitLevel: type: object properties: @@ -4713,259 +5017,47 @@ components: - TEST - FILLER geoCoordinates: - type: array - description: |- - One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - - Copied from RFC 7946 Section 3.1.1 - - A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. - nullable: true - items: - $ref: "#/components/schemas/GeoJSON" + $ref: "#/components/schemas/GeoJSON" observationLevel: $ref: "#/components/schemas/ObservationUnitLevel" observationLevelRelationships: type: array - description: "Observation levels indicate the granularity level at which\ - \ the measurements are taken. `levelName` \ndefines the level, `levelOrder`\ - \ defines where that level exists in the hierarchy of levels. \n`levelOrder`s\ - \ lower numbers are at the top of the hierarchy (ie field > 0) and higher\ - \ numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode`\ - \ is an ID code for this level tag. Identify \nthis observation unit by\ - \ each level of the hierarchy where it exists. \n\nFor more information\ - \ on Observation Levels, please review the Observation Levels\ - \ documentation. \n\n**Standard Level Names: study, field, entry,\ - \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** " - nullable: true - items: - $ref: "#/components/schemas/ObservationUnitLevelRelationship" - positionCoordinateX: - type: string - description: The X position coordinate for an observation unit. Different - systems may use different coordinate systems. - nullable: true - positionCoordinateXType: - anyOf: - - $ref: "#/components/schemas/PositionCoordinateType" - - type: "null" - positionCoordinateY: - type: string - description: The Y position coordinate for an observation unit. Different - systems may use different coordinate systems. - nullable: true - positionCoordinateYType: - anyOf: - - $ref: "#/components/schemas/PositionCoordinateType" - - type: "null" - description: All positional and layout information related to this Observation - Unit - nullable: true - ObservationUnitRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - includeObservations: - type: boolean - description: "Use this parameter to include a list of observations embedded\ - \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ - \ your own risk. It may return large, unpaginated lists of observation\ - \ data. Only set this value to True if you are sure you need to." - nullable: true - example: false - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - observationLevelRelationships: - type: array - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships - nullable: true - items: - $ref: "#/components/schemas/ObservationUnitLevelRelationship" - observationLevels: - type: array - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel - nullable: true - items: - $ref: "#/components/schemas/ObservationUnitLevel" - observationUnitDbIds: - type: array - description: The unique id of an observation unit - nullable: true - items: - type: string - observationUnitLevelCodes: - type: array - description: "The Observation Unit Level Code. This parameter should be\ - \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ - \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelNames: - type: array - description: "The Observation Unit Level. Returns only the observation unit\ - \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ - \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ - \ plot, sub-plot, plant, pot, sample** \n
For more information on\ - \ Observation Levels, please review the Observation Levels documentation. " - items: - type: string - observationUnitLevelOrders: - type: array - description: "The Observation Unit Level Order Number. Returns only the\ - \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipCodes: - type: array - description: "The Observation Unit Level Code. \n
This parameter should\ - \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ - \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipDbIds: - type: array - description: "The observationUnitDbId associated with a particular level\ - \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ - \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipNames: - type: array - description: "The Observation Unit Level Relationship is a connection that\ - \ this observation unit has to another level of the hierarchy. \n
For\ - \ example, if you have several observation units at a 'plot' level, they\ - \ might all share a relationship to the same 'field' level. \n
Use\ - \ this parameter to identify groups of observation units that share a\ - \ relationship level. \n
**Standard Level Names: study, field, entry,\ - \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ - \ more information on Observation Levels, please review the Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipOrders: - type: array - description: "The Observation Unit Level Order Number. \n
Returns only\ - \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitNames: - type: array - description: The human readable identifier for an Observation Unit - nullable: true - items: - type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - seasonDbIds: - type: array - description: "The year or Phenotyping campaign of a multi-annual study (trees,\ - \ grape, ...)" - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for + description: "Observation levels indicate the granularity level at which\ + \ the measurements are taken. `levelName` \ndefines the level, `levelOrder`\ + \ defines where that level exists in the hierarchy of levels. \n`levelOrder`s\ + \ lower numbers are at the top of the hierarchy (ie field > 0) and higher\ + \ numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode`\ + \ is an ID code for this level tag. Identify \nthis observation unit by\ + \ each level of the hierarchy where it exists. \n\nFor more information\ + \ on Observation Levels, please review the Observation Levels\ + \ documentation. \n\n**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** " + nullable: true items: - type: string - ObservationUnitSearchRequest: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + positionCoordinateX: + type: string + description: The X position coordinate for an observation unit. Different + systems may use different coordinate systems. + nullable: true + positionCoordinateXType: + nullable: true + allOf: + - $ref: "#/components/schemas/PositionCoordinateType" + positionCoordinateY: + type: string + description: The Y position coordinate for an observation unit. Different + systems may use different coordinate systems. + nullable: true + positionCoordinateYType: + nullable: true + allOf: + - $ref: "#/components/schemas/PositionCoordinateType" + description: All positional and layout information related to this Observation + Unit + nullable: true + ObservationUnitRequest: type: object properties: commonCropNames: @@ -4979,27 +5071,6 @@ components: \ of available crops on a server." items: type: string - externalReferenceIDs: - type: array - description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ - \ Github issue number #460 \n
List of external reference IDs. Could\ - \ be a simple strings or a URIs. (use with `externalReferenceSources`\ - \ parameter)" - deprecated: true - items: - type: string - externalReferenceIds: - type: array - description: List of external reference IDs. Could be a simple strings or - a URIs. (use with `externalReferenceSources` parameter) - items: - type: string - externalReferenceSources: - type: array - description: List of identifiers for the source system or database of an - external reference (use with `externalReferenceIDs` parameter) - items: - type: string germplasmDbIds: type: array description: List of IDs which uniquely identify germplasm to search for @@ -5049,6 +5120,78 @@ components: nullable: true items: type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string observationUnitNames: type: array description: The human readable identifier for an Observation Unit @@ -5071,17 +5214,6 @@ components: \ usually in the form of a URI" items: type: string - page: - type: integer - description: Which result page is requested. The page indexing starts at - 0 (the first page is 'page'= 0). Default is `0`. - format: int32 - example: 0 - pageSize: - type: integer - description: The size of the pages to be returned. Default is `1000`. - format: int32 - example: 1000 programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -5107,155 +5239,27 @@ components: nullable: true items: type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - description: "A representation of the physical entity being observed during\ - \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ - \ but it could include things like Fields, Blocks, or Samples." - ObservationVariable: - allOf: - - $ref: "#/components/schemas/ObservationVariableNewRequest" - - required: - - observationVariableDbId - type: object - properties: - observationVariableDbId: - type: string - description: |- - Variable unique identifier - - MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. - ObservationVariableNewRequest: - required: - - method - - observationVariableName - - scale - - trait - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - description: "Crop name (examples: \"Maize\", \"Wheat\")" - nullable: true - contextOfUse: - type: array - description: "Indication of how trait is routinely used. (examples: [\"\ - Trial evaluation\", \"Nursery evaluation\"])" - nullable: true - items: - type: string - defaultValue: - type: string - description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" - nullable: true - documentationURL: - type: string - description: A URL to the human readable documentation of an object - format: uri - nullable: true - externalReferences: - type: array - description: An array of external reference ids. These are references to - this piece of data in an external system. Could be a simple string or - a URI. - nullable: true - items: - $ref: "#/components/schemas/ExternalReference" - growthStage: - type: string - description: "Growth stage at which measurement is made (examples: \"flowering\"\ - )" - nullable: true - institution: - type: string - description: Name of institution submitting the variable - nullable: true - language: - type: string - description: 2 letter ISO 639-1 code for the language of submission of the - variable. - nullable: true - method: - $ref: "#/components/schemas/Method" - observationVariableName: - type: string - description: |- - Variable name (usually a short name) - - MIAPPE V1.1 (DM-84) Variable name - Name of the variable. - observationVariablePUI: - type: string - description: "The Permanent Unique Identifier of a Observation Variable,\ - \ usually in the form of a URI" - nullable: true - ontologyReference: - anyOf: - - $ref: "#/components/schemas/OntologyReference" - - type: "null" - scale: - $ref: "#/components/schemas/Scale" - scientist: - type: string - description: Name of scientist submitting the variable. - nullable: true - status: - type: string - description: "Variable status. (examples: \"recommended\", \"obsolete\"\ - , \"legacy\", etc.)" - nullable: true - submissionTimestamp: - type: string - description: Timestamp when the Variable was added (ISO 8601) - format: date-time - nullable: true - synonyms: - type: array - description: Other variable names - nullable: true - items: - type: string - trait: - $ref: "#/components/schemas/Trait" - ObservationVariableParameters: - type: object - properties: - observationVariableDbIds: + studyDbIds: type: array - description: The DbIds of Variables to search for + description: List of study identifiers to search for items: type: string - observationVariableNames: + studyNames: type: array - description: The names of Variables to search for + description: List of study names to filter search results items: type: string - observationVariablePUIs: + trialDbIds: type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" + description: The ID which uniquely identifies a trial to search for items: type: string - ObservationVariableRequest: + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ObservationUnitSearchRequest: type: object properties: commonCropNames: @@ -5269,27 +5273,80 @@ components: \ of available crops on a server." items: type: string - dataTypes: + externalReferenceIDs: type: array - description: List of scale data types to filter search results + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true items: - $ref: "#/components/schemas/TraitDataType" - methodDbIds: + type: string + externalReferenceIds: type: array - description: List of methods to filter search results + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) items: type: string - methodNames: + externalReferenceSources: type: array - description: |- - Human readable name for the method -
MIAPPE V1.1 (DM-88) Method Name of the method of observation + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) items: type: string - methodPUIs: + germplasmDbIds: type: array - description: "The Permanent Unique Identifier of a Method, usually in the\ - \ form of a URI" + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + includeObservations: + type: boolean + description: "Use this parameter to include a list of observations embedded\ + \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ + \ your own risk. It may return large, unpaginated lists of observation\ + \ data. Only set this value to True if you are sure you need to." + nullable: true + example: false + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationUnitDbIds: + type: array + description: The unique id of an observation unit + nullable: true + items: + type: string + observationUnitNames: + type: array + description: The human readable identifier for an Observation Unit + nullable: true items: type: string observationVariableDbIds: @@ -5308,11 +5365,17 @@ components: \ usually in the form of a URI" items: type: string - ontologyDbIds: - type: array - description: List of ontology IDs to search for - items: - type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -5331,29 +5394,11 @@ components: Use `GET /programs` to find the list of available programs on a server. items: type: string - scaleDbIds: - type: array - description: The unique identifier for a Scale - items: - type: string - scaleNames: - type: array - description: |- - Name of the scale -
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable - items: - type: string - scalePUIs: - type: array - description: "The Permanent Unique Identifier of a Scale, usually in the\ - \ form of a URI" - items: - type: string - studyDbId: + seasonDbIds: type: array - description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ - \ number #483 \n
The unique ID of a studies to filter on" - deprecated: true + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + nullable: true items: type: string studyDbIds: @@ -5366,69 +5411,118 @@ components: description: List of study names to filter search results items: type: string - traitAttributePUIs: - type: array - description: |- - The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI -
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" - items: - type: string - traitAttributes: - type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the attribute is the observed feature (or characteristic) of the entity\ - \ e.g., for \"grain colour\", attribute = \"colour\"" - items: - type: string - traitClasses: - type: array - description: List of trait classes to filter search results - items: - type: string - traitDbIds: + trialDbIds: type: array - description: The unique identifier for a Trait + description: The ID which uniquely identifies a trial to search for items: type: string - traitEntities: + trialNames: type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the entity is the part of the plant that the trait refers to e.g., for\ - \ \"grain colour\", entity = \"grain\"" + description: The human readable name of a trial to search for items: type: string - traitEntityPUIs: + description: "A representation of the physical entity being observed during\ + \ a phenotype data collection process. Typically, this is a Plot or a Plant,\ + \ but it could include things like Fields, Blocks, or Samples." + ObservationUnitTable: + type: object + properties: + data: type: array - description: "The Permanent Unique Identifier of a Trait Entity, usually\ - \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ - \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ - \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + description: "The 2D matrix of observation data. ObservationVariables and\ + \ other metadata are the columns, ObservationUnits are the rows." items: - type: string - traitNames: - type: array - description: |- - The human readable name of a trait -
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + type: array + items: + type: string + headerRow: + type: array + description: "

The table is REQUIRED to have the following columns

\n\ +
    \n
  • observationUnitDbId - Each row is related to one Observation\ + \ Unit
    • \n
  • At least one column with an observationVariableDbId
    • \n\ +
\n

The table may have any or all of the following OPTIONAL columns.\ + \ Included columns are decided by the server developer

\n
    \n
  • observationUnitName
    • \n\ + \
  • studyDbId
    • \n
  • studyName
    • \n
  • germplasmDbId
    • \n\ + \
  • germplasmName
    • \n
  • positionCoordinateX
    • \n
  • positionCoordinateY
    • \n\ + \
  • year
    • \n
\n

The table also may have any number of Observation\ + \ Unit Hierarchy Level columns. For example:

\n
    \n
  • field
    • \n\ + \
  • plot
    • \n
  • sub-plot
    • \n
  • plant
    • \n
  • pot
    • \n\ + \
  • block
    • \n
  • entry
    • \n
  • rep
    • \n
\n

The JSON\ + \ representation provides a pair of extra arrays for defining the headers\ + \ of the table. \nThe first array \"headerRow\" will always contain \"\ + observationUnitDbId\" and any or all of the OPTIONAL column header names.\ + \ \nThe second array \"observationVariables\" contains the names and DbIds\ + \ for the Observation Variables represented in the table. \nBy appending\ + \ the two arrays, you can construct the complete header row of the table.\ + \

" + items: + type: string + description: valid header fields + enum: + - observationUnitDbId + - observationUnitName + - studyDbId + - studyName + - germplasmDbId + - germplasmName + - positionCoordinateX + - positionCoordinateY + - year + - field + - plot + - sub-plot + - plant + - pot + - block + - entry + - rep + observationVariables: + type: array + description: The list of observation variables which have values recorded + for them in the data matrix. Append to the 'headerRow' for complete header + row of the table. items: - type: string - traitPUIs: + type: object + properties: + observationVariableDbId: + type: string + description: Variable unique identifier + example: 367aa1a9 + observationVariableName: + type: string + description: Variable name (usually a short name) + example: Plant height + ObservationVariable: + type: object + properties: + observationVariableDbId: + type: string + description: Variable unique identifier + example: 367aa1a9 + observationVariableName: + type: string + description: Variable name (usually a short name) + example: Plant height + ObservationVariableParameters: + type: object + properties: + observationVariableDbIds: type: array - description: "The Permanent Unique Identifier of a Trait, usually in the\ - \ form of a URI" + description: The DbIds of Variables to search for items: type: string - trialDbIds: + observationVariableNames: type: array - description: The ID which uniquely identifies a trial to search for + description: The names of Variables to search for items: type: string - trialNames: + observationVariablePUIs: type: array - description: The human readable name of a trial to search for + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" items: type: string - ObservationVariableSearchRequest: + ObservationVariableRequest: type: object properties: commonCropNames: @@ -5447,27 +5541,6 @@ components: description: List of scale data types to filter search results items: $ref: "#/components/schemas/TraitDataType" - externalReferenceIDs: - type: array - description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ - \ Github issue number #460 \n
List of external reference IDs. Could\ - \ be a simple strings or a URIs. (use with `externalReferenceSources`\ - \ parameter)" - deprecated: true - items: - type: string - externalReferenceIds: - type: array - description: List of external reference IDs. Could be a simple strings or - a URIs. (use with `externalReferenceSources` parameter) - items: - type: string - externalReferenceSources: - type: array - description: List of identifiers for the source system or database of an - external reference (use with `externalReferenceIDs` parameter) - items: - type: string methodDbIds: type: array description: List of methods to filter search results @@ -5507,17 +5580,6 @@ components: description: List of ontology IDs to search for items: type: string - page: - type: integer - description: Which result page is requested. The page indexing starts at - 0 (the first page is 'page'= 0). Default is `0`. - format: int32 - example: 0 - pageSize: - type: integer - description: The size of the pages to be returned. Default is `1000`. - format: int32 - example: 1000 programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -6707,9 +6769,9 @@ components: \ other dataTypes when applicable." nullable: true validValues: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/ValidValues" - - type: "null" description: "A Scale describes the units and acceptable values for an ObservationVariable.\ \ \n
For example, an ObservationVariable might be defined with a Trait\ \ of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\"\ @@ -6854,7 +6916,64 @@ components: SeedLotTransactionRequest: type: object properties: - transactionDbIs: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seedLotDbIds: + type: array + description: Unique id for a seed lot on this server + items: + type: string + transactionDbIds: type: array description: Unique id for a Transaction that has occurred items: @@ -7478,9 +7597,9 @@ components: method: $ref: "#/components/schemas/Method" ontologyReference: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/OntologyReference" - - type: "null" scale: $ref: "#/components/schemas/Scale" scientist: @@ -7857,6 +7976,52 @@ components: description: The unique identifier representing a VariantSet items: type: string + VariantSetsExtractRequest: + type: object + properties: + callSetDbIds: + type: array + description: The CallSet to search. + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + example: "~" + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + example: '|' + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + unknownString: + type: string + description: The string used as a representation for missing data. + example: "-" + variantDbIds: + type: array + description: The Variant to search. + items: + type: string + variantSetDbIds: + type: array + description: The VariantSet to search. + items: + type: string + description: Request object for extracting data subsets as new Variant Sets basePagination: required: - currentPage @@ -8022,23 +8187,6 @@ components: totalCount: 10 totalPages: 1 responses: - ObservationVariableSingleResponse: - description: OK - content: - application/json: - schema: - title: ObservationVariableSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/ObservationVariable" VariantSingleResponse: description: OK content: @@ -8132,6 +8280,32 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/Study" + ObservationDeleteResponse: + description: OK + content: + application/json: + schema: + title: ObservationDeleteResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - observationDbIds + type: object + properties: + observationDbIds: + type: array + description: The unique ids of the Observation records which have + been successfully deleted + items: + type: string MarkerPositionListResponse: description: OK content: @@ -8361,30 +8535,6 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/ReferenceSet" - ObservationVariableListResponse: - description: OK - content: - application/json: - schema: - title: ObservationVariableListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/ObservationVariable" CrossListResponse: description: OK content: @@ -9063,6 +9213,32 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/GermplasmMCPD" + StudyObservationLevelsListResponse: + description: OK + content: + application/json: + schema: + title: StudyObservationLevelsListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: array + items: + $ref: "#/components/schemas/ObservationUnitHierarchyLevel" ReferenceSetListResponse: description: OK content: @@ -9179,6 +9355,32 @@ components: type: array items: $ref: "#/components/schemas/Ontology" + ImageDeleteResponse: + description: OK + content: + application/json: + schema: + title: ImageDeleteResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - imageDbIds + type: object + properties: + imageDbIds: + type: array + description: The unique ids of the Image records which have been + successfully deleted + items: + type: string "404NotFound": description: Not Found content: @@ -9356,6 +9558,30 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/Person" + ProgramCommonCropNameListResponse: + description: OK + content: + application/json: + schema: + title: ProgramCommonCropNameListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: string ImageListResponse: description: OK content: @@ -9445,6 +9671,29 @@ components: type: array items: $ref: "#/components/schemas/GermplasmAttributeValue" + ObservationTableResponse: + description: OK + content: + application/json: + schema: + title: ObservationTableResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Observation" + text/csv: + schema: + type: string + text/tsv: + schema: + type: string BreedingMethodListResponse: description: OK content: @@ -9510,6 +9759,29 @@ components: $ref: "#/components/schemas/metadata" result: $ref: "#/components/schemas/GermplasmAttributeValue" + ObservationUnitTableResponse: + description: OK + content: + application/json: + schema: + title: ObservationUnitTableResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ObservationUnit" + text/csv: + schema: + type: string + text/tsv: + schema: + type: string GenomeMapListResponse: description: OK content: diff --git a/Specification/Generated/BrAPI.yaml b/Specification/Generated/BrAPI.yaml new file mode 100644 index 00000000..34e38c81 --- /dev/null +++ b/Specification/Generated/BrAPI.yaml @@ -0,0 +1,8708 @@ +openapi: 3.0.0 +info: + title: BrAPI + version: "" +paths: + /lists: + get: + tags: + - Lists + summary: Get a filtered list of List + description: Get a list of List + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: listDbId + in: query + description: An array of primary database identifiers to identify a set of + Lists + required: false + schema: + type: string + - name: listName + in: query + description: An array of human readable names to identify a set of Lists + required: false + schema: + type: string + - name: listSource + in: query + description: "An array of terms identifying lists from different sources (ie\ + \ 'USER', 'SYSTEM', etc)" + required: false + schema: + type: string + - name: listType + in: query + required: false + schema: + $ref: "#/components/schemas/ListType" + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ListListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Lists + summary: Create new List + description: Add new List to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/ListNewRequest" + responses: + "200": + $ref: "#/components/responses/ListListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /locations: + get: + tags: + - Locations + summary: Get a filtered list of Location + description: Get a list of Location + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: locationDbId + in: query + description: The location ids to search for + required: false + schema: + type: string + - name: locationName + in: query + description: A human readable names to search for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: locationType + in: query + description: "The type of location this represents (ex. Breeding Location,\ + \ Storage Location, etc)" + required: false + schema: + type: string + - name: parentLocationDbId + in: query + description: "The unique identifier for a Location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \nFor\ + \ example, an Institution might have multiple Field Stations inside it and\ + \ each Field Station might have multiple Fields." + required: false + schema: + type: string + - name: parentLocationName + in: query + description: "A human readable name for a location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \nFor\ + \ example, an Institution might have multiple Field Stations inside it and\ + \ each Field Station might have multiple Fields." + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/LocationListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Locations + summary: Create new Location + description: Add new Location to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/LocationNewRequest" + responses: + "200": + $ref: "#/components/responses/LocationListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /people: + get: + tags: + - People + summary: Get a filtered list of Person + description: Get a list of Person + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: firstName + in: query + description: Persons first name + required: false + schema: + type: string + - name: lastName + in: query + description: Persons last name + required: false + schema: + type: string + - name: personDbId + in: query + description: Unique ID for this person + required: false + schema: + type: string + - name: userID + in: query + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + required: false + schema: + type: string + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/PersonListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - People + summary: Create new Person + description: Add new Person to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/PersonNewRequest" + responses: + "200": + $ref: "#/components/responses/PersonListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /programs: + get: + tags: + - Programs + summary: Get a filtered list of Program + description: Get a list of Program + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: programName + in: query + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + required: false + schema: + type: string + - name: abbreviation + in: query + description: A list of shortened human readable names for a set of Programs + required: false + schema: + type: string + - name: programType + in: query + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding " + required: false + schema: + type: string + description: |- + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding. + enum: + - STANDARD + - PROJECT + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ProgramListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Programs + summary: Create new Program + description: Add new Program to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/ProgramNewRequest" + responses: + "200": + $ref: "#/components/responses/ProgramListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /seasons: + get: + tags: + - Seasons + summary: Get a filtered list of Season + description: Get a list of Season + parameters: + - name: seasonDbId + in: query + description: "The unique identifier for a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'." + required: false + schema: + type: string + - name: season + in: query + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + required: false + schema: + type: string + - name: seasonName + in: query + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + required: false + schema: + type: string + - name: year + in: query + description: The 4 digit year of a season. Example 2017 + required: false + schema: + type: integer + format: int32 + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/SeasonListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Seasons + summary: Create new Season + description: Add new Season to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/Season" + responses: + "200": + $ref: "#/components/responses/SeasonListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /studies: + get: + tags: + - Studies + summary: Get a filtered list of Study + description: Get a list of Study + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: germplasmDbId + in: query + description: List of IDs which uniquely identify germplasm to search for + required: false + schema: + type: string + - name: locationDbId + in: query + description: The location ids to search for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: studyName + in: query + description: List of study names to filter search results + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: observationVariableDbId + in: query + description: The DbIds of Variables to search for + required: false + schema: + type: string + - name: active + in: query + description: A flag to indicate if a Study is currently active and ongoing + required: false + schema: + type: boolean + - name: seasonDbId + in: query + description: The ID which uniquely identifies a season + required: false + schema: + type: string + - name: studyType + in: query + description: "The type of study being performed. ex. \"Yield Trial\", etc" + required: false + schema: + type: string + - name: studyCode + in: query + description: A short human readable code for a study + required: false + schema: + type: string + - name: studyPUI + in: query + description: "Permanent unique identifier associated with study data. For\ + \ example, a URI or DOI" + required: false + schema: + type: string + - name: sortBy + in: query + description: Name of the field to sort by. + required: false + schema: + type: string + description: Name of the field to sort by. + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + - germplasmDbId + - observationVariableDbId + - name: sortOrder + in: query + description: Sort order direction. Ascending/Descending. + required: false + schema: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - ASC + - DESC + - asc + - desc + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/StudyListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Studies + summary: Create new Study + description: Add new Study to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/StudyNewRequest" + responses: + "200": + $ref: "#/components/responses/StudyListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /trials: + get: + tags: + - Trials + summary: Get a filtered list of Trial + description: Get a list of Trial + parameters: + - name: commonCropName + in: query + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at a\ + \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ + \ crop names.\n\nUse this parameter to only return results associated with\ + \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ + \ crops on a server." + required: false + schema: + type: string + - name: locationDbId + in: query + description: The location ids to search for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - name: trialName + in: query + description: The human readable name of a trial to search for + required: false + schema: + type: string + - name: active + in: query + description: A flag to indicate if a Trial is currently active and ongoing + required: false + schema: + type: boolean + - name: contactDbId + in: query + description: List of contact entities associated with this trial + required: false + schema: + type: string + - name: searchDateRangeStart + in: query + description: "The start of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of\ + \ the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate`\ + \ AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n\ + - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + required: false + schema: + type: string + format: date + - name: searchDateRangeEnd + in: query + description: "The end of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of\ + \ the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate`\ + \ AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n\ + - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + required: false + schema: + type: string + format: date + - name: trialPUI + in: query + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + required: false + schema: + type: string + - name: sortBy + in: query + description: Name of the field to sort by. + required: false + schema: + type: string + description: Name of the field to sort by. + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + - name: sortOrder + in: query + description: Sort order direction. Ascending/Descending. + required: false + schema: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - ASC + - DESC + - asc + - desc + - $ref: "#/components/parameters/externalReferenceId" + - $ref: "#/components/parameters/externalReferenceID" + - $ref: "#/components/parameters/externalReferenceSource" + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/TrialListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + post: + tags: + - Trials + summary: Create new Trial + description: Add new Trial to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/TrialNewRequest" + responses: + "200": + $ref: "#/components/responses/TrialListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /commoncropnames: + get: + tags: + - Programs + summary: Get the commonCropNames of Program + description: List all available Program commonCropNames + parameters: + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ProgramCommonCropNameListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /observationlevels: + get: + tags: + - Studies + summary: Get the observationLevelses of Study + description: List all available Study observationLevelses + parameters: + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/StudyObservationLevelsListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /studytypes: + get: + tags: + - Studies + summary: Get the studyTypes of Study + description: List all available Study studyTypes + parameters: + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/StudyStudyTypeListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /lists/{listDbId}: + get: + tags: + - Lists + summary: Get the details of a specific List + description: Get details for a List + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: listDbId + in: path + description: The unique identifier for a List + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/ListSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + put: + tags: + - Lists + summary: Update the details for an existing List + description: Update the details for an existing List + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: listDbId + in: path + description: The unique identifier for a List + required: true + schema: + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ListNewRequest" + responses: + "200": + $ref: "#/components/responses/ListSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /lists/{listDbId}/data: + post: + tags: + - Lists + summary: Create new string + description: Add new string to database + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: listDbId + in: path + description: The unique identifier for a List + required: true + schema: + type: string + requestBody: + content: + application/json: + schema: + type: string + responses: + "200": + $ref: "#/components/responses/ListSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /locations/{locationDbId}: + get: + tags: + - Locations + summary: Get the details of a specific Location + description: Get details for a Location + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: locationDbId + in: path + description: The unique identifier for a Location + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/LocationSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + put: + tags: + - Locations + summary: Update the details for an existing Location + description: Update the details for an existing Location + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: locationDbId + in: path + description: The unique identifier for a Location + required: true + schema: + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/LocationNewRequest" + responses: + "200": + $ref: "#/components/responses/LocationSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /people/{personDbId}: + get: + tags: + - People + summary: Get the details of a specific Person + description: Get details for a Person + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: personDbId + in: path + description: Unique ID for a person + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/PersonSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + put: + tags: + - People + summary: Update the details for an existing Person + description: Update the details for an existing Person + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: personDbId + in: path + description: Unique ID for a person + required: true + schema: + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PersonNewRequest" + responses: + "200": + $ref: "#/components/responses/PersonSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /programs/{programDbId}: + get: + tags: + - Programs + summary: Get the details of a specific Program + description: Get details for a Program + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: programDbId + in: path + description: The ID which uniquely identifies the program + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/ProgramSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + put: + tags: + - Programs + summary: Update the details for an existing Program + description: Update the details for an existing Program + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: programDbId + in: path + description: The ID which uniquely identifies the program + required: true + schema: + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ProgramNewRequest" + responses: + "200": + $ref: "#/components/responses/ProgramSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /seasons/{seasonDbId}: + get: + tags: + - Seasons + summary: Get the details of a specific Season + description: Get details for a Season + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: seasonDbId + in: path + description: "The ID which uniquely identifies a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'" + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/SeasonSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + put: + tags: + - Seasons + summary: Update the details for an existing Season + description: Update the details for an existing Season + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: seasonDbId + in: path + description: "The ID which uniquely identifies a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'" + required: true + schema: + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/Season" + responses: + "200": + $ref: "#/components/responses/SeasonSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /studies/{studyDbId}: + get: + tags: + - Studies + summary: Get the details of a specific Study + description: Get details for a Study + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: studyDbId + in: path + description: |- + The ID which uniquely identifies a study within the given database server + + MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/StudySingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + put: + tags: + - Studies + summary: Update the details for an existing Study + description: Update the details for an existing Study + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: studyDbId + in: path + description: |- + The ID which uniquely identifies a study within the given database server + + MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + required: true + schema: + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/StudyNewRequest" + responses: + "200": + $ref: "#/components/responses/StudySingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /trials/{trialDbId}: + get: + tags: + - Trials + summary: Get the details of a specific Trial + description: Get details for a Trial + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: trialDbId + in: path + description: |- + The ID which uniquely identifies a trial + + MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + required: true + schema: + type: string + responses: + "200": + $ref: "#/components/responses/TrialSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + put: + tags: + - Trials + summary: Update the details for an existing Trial + description: Update the details for an existing Trial + parameters: + - $ref: "#/components/parameters/authorizationHeader" + - name: trialDbId + in: path + description: |- + The ID which uniquely identifies a trial + + MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + required: true + schema: + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/TrialNewRequest" + responses: + "200": + $ref: "#/components/responses/TrialSingleResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /search/lists: + post: + tags: + - Lists + summary: Submit a search request for `List` + description: "Submit a search request for `List`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ListSearchRequest" + responses: + "200": + $ref: "#/components/responses/ListListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/locations: + post: + tags: + - Locations + summary: Submit a search request for `Location` + description: "Submit a search request for `Location`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/location/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/LocationSearchRequest" + responses: + "200": + $ref: "#/components/responses/LocationListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/people: + post: + tags: + - People + summary: Submit a search request for `Person` + description: "Submit a search request for `Person`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/person/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/PersonSearchRequest" + responses: + "200": + $ref: "#/components/responses/PersonListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/programs: + post: + tags: + - Programs + summary: Submit a search request for `Program` + description: "Submit a search request for `Program`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/program/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ProgramSearchRequest" + responses: + "200": + $ref: "#/components/responses/ProgramListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/studies: + post: + tags: + - Studies + summary: Submit a search request for `Study` + description: "Submit a search request for `Study`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/StudySearchRequest" + responses: + "200": + $ref: "#/components/responses/StudyListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/trials: + post: + tags: + - Trials + summary: Submit a search request for `Trial` + description: "Submit a search request for `Trial`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + parameters: + - $ref: "#/components/parameters/authorizationHeader" + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/TrialSearchRequest" + responses: + "200": + $ref: "#/components/responses/TrialListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /search/lists/{searchResultsDbId}: + get: + tags: + - Lists + summary: "Submit a search request for `List`
\nSearch requests allow a client\ + \ to send a complex query for data. However, the server may not respond with\ + \ the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `List` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/list` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ListListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /search/locations/{searchResultsDbId}: + get: + tags: + - Locations + summary: "Submit a search request for `Location`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/location/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Location` search request
\nClients\ + \ should submit a search request using the corresponding `POST /search/location`\ + \ endpoint.\nSearch requests allow a client to send a complex query for data.\ + \ However, the server may not respond with the search results immediately.\ + \ \nIf a server needs more time to process the request, it might respond with\ + \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/LocationListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /search/people/{searchResultsDbId}: + get: + tags: + - People + summary: "Submit a search request for `Person`
\nSearch requests allow a\ + \ client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/person/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Person` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/person` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/PersonListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /search/programs/{searchResultsDbId}: + get: + tags: + - Programs + summary: "Submit a search request for `Program`
\nSearch requests allow\ + \ a client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/program/{searchResultsDbId}` to retrieve the results of the\ + \ search.
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Program` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/program` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ProgramListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /search/studies/{searchResultsDbId}: + get: + tags: + - Studies + summary: "Submit a search request for `Study`
\nSearch requests allow a\ + \ client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Study` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/study` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/StudyListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /search/trials/{searchResultsDbId}: + get: + tags: + - Trials + summary: "Submit a search request for `Trial`
\nSearch requests allow a\ + \ client to send a complex query for data. However, the server may not respond\ + \ with the search results immediately. \nIf a server needs more time to process\ + \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ + \ `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.\ + \
\nReview the Search Services documentation for additional implementation details." + description: "Get the results of a `Trial` search request
\nClients should\ + \ submit a search request using the corresponding `POST /search/trial` endpoint.\n\ + Search requests allow a client to send a complex query for data. However,\ + \ the server may not respond with the search results immediately. \nIf a server\ + \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ + \ \nUse this endpoint to retrieve the results of the search.
\nReview\ + \ the Search Services documentation for additional implementation details." + parameters: + - name: searchResultsDbId + in: path + description: searchResultsDbId + required: true + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/TrialListResponse" + "202": + $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" + /serverinfo: + get: + tags: + - Server Info + summary: Get the list of implemented Calls + description: "Implementation Notes\n\nHaving a consistent structure for the\ + \ path string of each call is very \nimportant for teams to be able to connect\ + \ and find errors. Read more on Github.\n\nHere are the rules for the path\ + \ of each call that should be returned\n\nEvery word in the call path should\ + \ match the documentation exactly, both in \nspelling and capitalization.\ + \ Note that path strings are all lower case, but \npath parameters are camel\ + \ case.\n\nEach path should start relative to \\\"/\\\" and therefore should\ + \ not include \\\"/\\\"\n\nNo leading or trailing slashes (\\\"/\\\") \n\n\ + Path parameters are wrapped in curly braces (\\\"{}\\\"). The name of the\ + \ path parameter \nshould be spelled exactly as it is specified in the documentation.\n\ + \nExamples \n\nGOOD \"call\": \"germplasm/{germplasmDbId}/pedigree\" \n\n\ + BAD \"call\": \"germplasm/{id}/pedigree\"\n\nBAD \"call\": \"germplasm/{germplasmDBid}/pedigree\"\ + \ \n\nBAD \"call\": \"brapi/v2/germplasm/{germplasmDbId}/pedigree\" \n\n\ + BAD \"call\": \"/germplasm/{germplasmDbId}/pedigree/\" \n\nBAD \"call\"\ + : \"germplasm//pedigree\"" + parameters: + - name: contentType + in: query + description: Filter the list of endpoints based on the response content type. + required: false + style: form + explode: true + schema: + $ref: "#/components/schemas/ContentTypes" + - name: dataType + in: query + description: |- + **Deprecated in v2.1** Please use `contentType`. Github issue number #443 +
The data format supported by the call. + required: false + deprecated: true + style: form + explode: true + schema: + $ref: "#/components/schemas/ContentTypes" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + description: OK + content: + application/json: + schema: + title: ServerInfoResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ServerInfo" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" +components: + schemas: + AdditionalInfo: + type: string + additionalProperties: + description: A free space containing any additional information related to + a particular object. + description: "A free space containing any additional information related to\ + \ a particular object. A data source may provide any JSON object, unrestricted\ + \ by the BrAPI specification." + nullable: true + AlleleMatrixPagination: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension of + the matrix + format: int32 + example: 500 + AlleleMatrixRequest: + type: object + properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + items: + type: string + dataMatrixAbbreviations: + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." + nullable: true + items: + type: string + dataMatrixNames: + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." + nullable: true + items: + type: string + dimensionCallSetPage: + type: integer + description: The requested page number for the CallSet dimension of the + matrix + format: int32 + nullable: true + dimensionCallSetPageSize: + type: integer + description: The requested page size for the CallSet dimension of the matrix + format: int32 + nullable: true + dimensionVariantPage: + type: integer + description: The requested page number for the Variant dimension of the + matrix + format: int32 + nullable: true + dimensionVariantPageSize: + type: integer + description: The requested page size for the Variant dimension of the matrix + format: int32 + nullable: true + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + nullable: true + example: true + germplasmDbIds: + type: array + description: A list of IDs which uniquely identify `Germplasm` within the + given database server + nullable: true + items: + type: string + germplasmNames: + type: array + description: A list of human readable `Germplasm` names + nullable: true + items: + type: string + germplasmPUIs: + type: array + description: A list of permanent unique identifiers associated with `Germplasm` + nullable: true + items: + type: string + pagination: + type: array + description: Pagination for the matrix + nullable: true + items: + type: object + properties: + dimension: + type: string + description: the dimension of the matrix being paginated + example: VARIANTS + enum: + - CALLSETS + - VARIANTS + page: + type: integer + description: the requested page number (zero indexed) + format: int32 + example: 0 + pageSize: + type: integer + description: the maximum number of elements per page in this dimension + of the matrix + format: int32 + example: 500 + positionRanges: + type: array + description: "The postion range to search\n
\nUses the format \":-\"\ + \ where is the chromosome name, is \nthe starting position\ + \ of the range, and is the ending position of the range" + nullable: true + items: + type: string + preview: + type: boolean + description: "Default Value = false\n
\nIf 'preview' is set to true,\ + \ then the server should only return the lists of 'callSetDbIds', \n'variantDbIds',\ + \ and 'variantSetDbIds'. The server should not return any matrix data.\ + \ This\nis intended to be a preview and give the client a sense of how\ + \ large the matrix returned will be\n
\nIf 'preview' is set to false\ + \ or not set (default), then the server should return all the matrix\n\ + data as requested." + example: true + default: false + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + nullable: true + items: + type: string + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + nullable: true + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + nullable: true + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + nullable: true + example: "." + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server + nullable: true + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + nullable: true + items: + type: string + Attribute: + required: + - attributeName + - method + - scale + - trait + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + attributeCategory: + type: string + description: General category for the attribute. very similar to Trait class. + example: Morphological + attributeDbId: + type: string + description: The ID which uniquely identifies this attribute within the + given database server + attributeDescription: + type: string + description: A human readable description of this attribute + example: Height of the plant measured in meters by a tape + attributeName: + type: string + description: A human readable name for this attribute + example: Plant Height 1 + attributePUI: + type: string + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + example: http://my-traits.com/trait/CO_123:0008012 + commonCropName: + type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true + contextOfUse: + type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true + items: + type: string + defaultValue: + type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true + documentationURL: + type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + growthStage: + type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true + institution: + type: string + description: Name of institution submitting the variable + nullable: true + language: + type: string + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true + method: + $ref: "#/components/schemas/Method" + ontologyReference: + nullable: true + allOf: + - $ref: "#/components/schemas/OntologyReference" + scale: + $ref: "#/components/schemas/Scale" + scientist: + type: string + description: Name of scientist submitting the variable. + nullable: true + status: + type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true + submissionTimestamp: + type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true + synonyms: + type: array + description: Other variable names + nullable: true + items: + type: string + trait: + $ref: "#/components/schemas/Trait" + CallRequest: + type: object + properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + nullable: true + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + nullable: true + example: true + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + deprecated: true + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + nullable: true + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + nullable: true + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + nullable: true + example: "." + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variant` within the + given database server + nullable: true + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + nullable: true + items: + type: string + CallSetRequest: + type: object + properties: + callSetDbIds: + type: array + description: A list of IDs which uniquely identify `CallSets` within the + given database server + nullable: true + items: + type: string + callSetNames: + type: array + description: A list of human readable names associated with `CallSets` + nullable: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: A list of IDs which uniquely identify `Samples` within the + given database server + nullable: true + items: + type: string + sampleNames: + type: array + description: A list of human readable names associated with `Samples` + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` within + the given database server + nullable: true + items: + type: string + CommonCropNamesParameters: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + Contact: + required: + - contactDbId + type: object + properties: + contactDbId: + type: string + description: |- + The ID which uniquely identifies this contact + + MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. + email: + type: string + description: |- + The contacts email address + + MIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person. + nullable: true + instituteName: + type: string + description: |- + The name of the institution which this contact is part of + + MIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to + nullable: true + name: + type: string + description: |- + The full name of this contact person + + MIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications) + nullable: true + orcid: + type: string + description: |- + The Open Researcher and Contributor ID for this contact person (orcid.org) + + MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. + nullable: true + type: + type: string + description: |- + The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.) + + MIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation + nullable: true + description: A persons contact information + ContentTypes: + type: string + enum: + - application/json + - text/csv + - text/tsv + - application/flapjack + Context: + title: context + type: array + description: "The JSON-LD Context is used to provide JSON-LD definitions to\ + \ each field in a JSON object. By providing an array of context file urls,\ + \ a BrAPI response object becomes JSON-LD compatible. \n\nFor more information,\ + \ see https://w3c.github.io/json-ld-syntax/#the-context" + example: + - https://brapi.org/jsonld/context/metadata.jsonld + items: + type: string + format: uri + CrossRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + CrossStatus: + type: string + enum: + - TODO + - DONE + - SKIPPED + CrossingProjectRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + includePotentialParents: + type: boolean + description: "If the parameter 'includePotentialParents' is false, the array\ + \ 'potentialParents' should be empty, null, or excluded from the response\ + \ object." + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + DataLink: + type: object + properties: + dataFormat: + type: string + description: |- + The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy) + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + nullable: true + description: + type: string + description: |- + The general description of this data link + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + nullable: true + fileFormat: + type: string + description: |- + The MIME type of the file (ie text/csv, application/excel, application/zip). + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + nullable: true + name: + type: string + description: |- + The name of the external data link + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + nullable: true + provenance: + type: string + description: "The description of the origin or ownership of this linked\ + \ data. Could be a formal reference to software, method, or workflow." + nullable: true + scientificType: + type: string + description: "The general type of data. For example- Genotyping, Phenotyping\ + \ raw data, Phenotyping reduced data, Environmental, etc" + nullable: true + url: + type: string + description: |- + URL describing the location of this data file to view or download + + MIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission. + format: uri + nullable: true + version: + type: string + description: "The version number for this data \n\nMIAPPE V1.1 (DM-39) Data\ + \ file version - The version of the dataset (the actual data)." + nullable: true + description: "A link to extra data files associated with this study. Extra data\ + \ could include notes, images, and reference data." + DatasetAuthorships: + type: object + properties: + datasetPUI: + type: string + description: The DOI or other permanent unique identifier for this published + dataset + nullable: true + license: + type: string + description: MIAPPE V1.1 (DM-7) License - License for the reuse of the data + associated with this investigation. The Creative Commons licenses cover + most use cases and are recommended. + nullable: true + publicReleaseDate: + type: string + description: MIAPPE V1.1 (DM-6) Public release date - Date of first public + release of the dataset presently being described. + nullable: true + submissionDate: + type: string + description: MIAPPE V1.1 (DM-5) Submission date - Date of submission of + the dataset presently being described to a host repository. + nullable: true + description: License and citation information for the data in this trial + Dimension: + type: string + description: the dimension of the matrix being paginated + enum: + - CALLSETS + - VARIANTS + EnvironmentParameter: + required: + - description + - parameterName + type: object + properties: + description: + type: string + description: Human-readable value of the environment parameter (defined + above) constant within the experiment + parameterName: + type: string + description: "Name of the environment parameter constant within the experiment\n\ + \nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment\ + \ parameter constant within the experiment. " + parameterPUI: + type: string + description: URI pointing to an ontology class for the parameter + nullable: true + unit: + type: string + description: Unit of the value for this parameter + nullable: true + unitPUI: + type: string + description: URI pointing to an ontology class for the unit + nullable: true + value: + type: string + description: |- + Numerical or categorical value + + MIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment. + nullable: true + valuePUI: + type: string + description: URI pointing to an ontology class for the parameter value + nullable: true + description: "Environmental parameters that were kept constant throughout the\ + \ study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57)\ + \ Environment - Environmental parameters that were kept constant throughout\ + \ the study and did not change between observation units or assays. Environment\ + \ characteristics that vary over time, i.e. environmental variables, should\ + \ be recorded as Observed Variables (see below)." + EventRequest: + type: object + properties: + dateRangeEnd: + type: string + description: Filter based on an Event start date. + format: date-time + dateRangeStart: + type: string + description: Filter based on an Event start date. + format: date-time + eventDbIds: + type: array + description: Filter based on an Event DbId. + items: + type: string + eventTypes: + type: array + description: Filter based on an Event Type + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + ExperimentalDesign: + type: object + properties: + PUI: + type: string + description: "MIAPPE V1.1 (DM-23) Type of experimental design - Type of\ + \ experimental design of the study, in the form of an accession number\ + \ from the Crop Ontology." + nullable: true + description: + type: string + description: "MIAPPE V1.1 (DM-22) Description of the experimental design\ + \ - Short description of the experimental design, possibly including statistical\ + \ design. In specific cases, e.g. legacy datasets or data computed from\ + \ several studies, the experimental design can be \"unknown\"/\"NA\",\ + \ \"aggregated/reduced data\", or simply 'none'." + nullable: true + description: The experimental and statistical design full description plus a + category PUI taken from crop research ontology or agronomy ontology + nullable: true + ExternalReference: + type: object + properties: + referenceID: + type: string + description: "**Deprecated in v2.1** Please use `referenceId`. Github issue\ + \ number #460
The external reference ID. Could be a simple string\ + \ or a URI." + nullable: true + deprecated: true + referenceId: + type: string + description: The external reference ID. Could be a simple string or a URI. + referenceSource: + type: string + description: An identifier for the source system or database of this reference + ExternalReferencesParameters: + type: object + properties: + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + GenomeMapRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + mapDbIds: + type: array + description: The ID which uniquely identifies a `GenomeMap` + items: + type: string + mapPUIs: + type: array + description: The DOI or other permanent identifier for a `GenomeMap` + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scientificName: + type: array + description: "Full scientific binomial format name. This includes Genus,\ + \ Species, and Sub-species" + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + types: + type: array + description: "The type of map, usually \"Genetic\" or \"Physical\"" + items: + type: string + GeoJSON: + type: object + properties: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + type: + type: string + description: The literal string "Feature" + example: Feature + default: Feature + description: |- + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + nullable: true + GeoJSONGeometry: + type: object + discriminator: + propertyName: type + oneOf: + - required: + - coordinates + - type + type: object + properties: + coordinates: + type: array + description: A single position + items: + type: number + type: + type: string + description: The literal string "Point" + default: Point + description: |- + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + - required: + - coordinates + - type + type: object + properties: + coordinates: + type: array + description: An array of linear rings + items: + type: array + items: + type: array + items: + type: number + type: + type: string + description: The literal string "Polygon" + default: Polygon + description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ + \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ + \ The first two elements are longitude and latitude, or\neasting and northing,\ + \ precisely in that order and using decimal numbers. Altitude or elevation\ + \ MAY be included as an optional third element." + GeoJSONPoint: + required: + - coordinates + - type + type: object + properties: + coordinates: + type: array + description: A single position + items: + type: number + type: + type: string + description: The literal string "Point" + default: Point + description: |- + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + GeoJSONPolygon: + required: + - coordinates + - type + type: object + properties: + coordinates: + type: array + description: An array of linear rings + items: + type: array + items: + type: array + items: + type: number + type: + type: string + description: The literal string "Polygon" + default: Polygon + description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ + \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ + \ The first two elements are longitude and latitude, or\neasting and northing,\ + \ precisely in that order and using decimal numbers. Altitude or elevation\ + \ MAY be included as an optional third element." + GeoJSONSearchArea: + type: object + properties: + geometry: + $ref: "#/components/schemas/GeoJSONGeometry" + type: + type: string + description: The literal string "Feature" + example: Feature + default: Feature + GermplasmAttributeRequest: + type: object + properties: + attributeCategories: + type: array + description: General category for the attribute. very similar to Trait class. + nullable: true + items: + type: string + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + nullable: true + items: + type: string + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + nullable: true + items: + type: string + attributePUIs: + type: array + description: "The Permanent Unique Identifier of an Attribute, usually in\ + \ the form of a URI" + nullable: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + GermplasmAttributeValueRequest: + type: object + properties: + attributeDbIds: + type: array + description: List of Germplasm Attribute IDs to search for + nullable: true + items: + type: string + attributeNames: + type: array + description: List of human readable Germplasm Attribute names to search + for + nullable: true + items: + type: string + attributeValueDbIds: + type: array + description: List of Germplasm Attribute Value IDs to search for + nullable: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + nullable: true + items: + $ref: "#/components/schemas/TraitDataType" + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + methodDbIds: + type: array + description: List of methods to filter search results + nullable: true + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: List of scales to filter search results + nullable: true + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + nullable: true + items: + type: string + traitDbIds: + type: array + description: List of trait unique ID to filter search results + nullable: true + items: + type: string + GermplasmParameters: + type: object + properties: + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + GermplasmRequest: + type: object + properties: + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + nullable: true + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + nullable: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + nullable: true + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + nullable: true + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + nullable: true + items: + type: string + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + nullable: true + items: + type: string + parentDbIds: + type: array + description: Search for Germplasm with these parents + nullable: true + items: + type: string + progenyDbIds: + type: array + description: Search for Germplasm with these children + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + nullable: true + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + GrowthFacility: + type: object + properties: + PUI: + type: string + description: "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth\ + \ facility in which the study was carried out, in the form of an accession\ + \ number from the Crop Ontology." + description: + type: string + description: MIAPPE V1.1 (DM-26) Description of growth facility - Short + description of the facility in which the study was carried out. + nullable: true + description: Short description of the facility in which the study was carried + out. + nullable: true + ImageRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + descriptiveOntologyTerms: + type: array + description: "A list of terms to formally describe the image to search for.\ + \ Each item could be a simple Tag, an Ontology reference Id, or a full\ + \ ontology URL." + items: + type: string + imageDbIds: + type: array + description: A list of image Ids to search for + items: + type: string + imageFileNames: + type: array + description: Image file names to search for. + items: + type: string + imageFileSizeMax: + type: integer + description: A maximum image file size to search for. + format: int32 + example: 20000000 + imageFileSizeMin: + type: integer + description: A minimum image file size to search for. + format: int32 + example: 1000 + imageHeightMax: + type: integer + description: A maximum image height to search for. + format: int32 + example: 1080 + imageHeightMin: + type: integer + description: A minimum image height to search for. + format: int32 + example: 720 + imageLocation: + $ref: "#/components/schemas/GeoJSONSearchArea" + imageNames: + type: array + description: Human readable names to search for. + items: + type: string + imageTimeStampRangeEnd: + type: string + description: The latest timestamp to search for. + format: date-time + imageTimeStampRangeStart: + type: string + description: The earliest timestamp to search for. + format: date-time + imageWidthMax: + type: integer + description: A maximum image width to search for. + format: int32 + example: 1920 + imageWidthMin: + type: integer + description: A minimum image width to search for. + format: int32 + example: 1280 + mimeTypes: + type: array + description: A set of image file types to search for. + items: + type: string + observationDbIds: + type: array + description: A list of observation Ids this image is associated with to + search for + items: + type: string + observationUnitDbIds: + type: array + description: A set of observation unit identifiers to search for. + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + LastUpdate: + type: object + properties: + timestamp: + type: string + description: The timestamp of the update. + format: date-time + nullable: true + version: + type: string + description: The version of the update. + nullable: true + description: The date and time when this study was last modified + nullable: true + List: + allOf: + - $ref: "#/components/schemas/ListNewRequest" + - required: + - listDbId + type: object + properties: + listDbId: + type: string + description: The unique identifier for a List + description: "A List represents a collection of other BrAPI data objects.\ + \ Typically these are custom lists generated by a user to keep track of\ + \ interesting data. For example, a user might build a List of Germplasm\ + \ that they have manually marked for further study." + ListNewRequest: + required: + - listName + - listType + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + data: + type: array + description: The array of DbIds of the BrAPI objects contained in a List + nullable: true + items: + type: string + dateCreated: + type: string + description: Timestamp when the entity was first created + format: date-time + nullable: true + dateModified: + type: string + description: Timestamp when the entity was last updated + format: date-time + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + listDescription: + type: string + description: Description of a List + nullable: true + listName: + type: string + description: Human readable name of a List + listOwnerName: + type: string + description: Human readable name of a List Owner. (usually a user or person) + nullable: true + listOwnerPersonDbId: + type: string + listSize: + type: integer + description: The number of elements in a List + format: int32 + nullable: true + listSource: + type: string + description: The description of where a List originated from + nullable: true + listType: + $ref: "#/components/schemas/ListType" + description: "A List represents a collection of other BrAPI data objects. Typically\ + \ these are custom lists generated by a user to keep track of interesting\ + \ data. For example, a user might build a List of Germplasm that they have\ + \ manually marked for further study." + ListRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dateCreatedRangeEnd: + type: string + description: Define the end for an interval of time and only include Lists + that are created within this interval. + format: date-time + nullable: true + dateCreatedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are created within this interval. + format: date-time + nullable: true + dateModifiedRangeEnd: + type: string + description: Define the end for an interval of time and only include Lists + that are modified within this interval. + format: date-time + nullable: true + dateModifiedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are modified within this interval. + format: date-time + nullable: true + listDbIds: + type: array + description: An array of primary database identifiers to identify a set + of Lists + nullable: true + items: + type: string + listNames: + type: array + description: An array of human readable names to identify a set of Lists + nullable: true + items: + type: string + listOwnerNames: + type: array + description: An array of names for the people or entities who are responsible + for a set of Lists + nullable: true + items: + type: string + listOwnerPersonDbIds: + type: array + description: An array of primary database identifiers to identify people + or entities who are responsible for a set of Lists + nullable: true + items: + type: string + listSources: + type: array + description: "An array of terms identifying lists from different sources\ + \ (ie 'USER', 'SYSTEM', etc)" + nullable: true + items: + type: string + listType: + nullable: true + allOf: + - $ref: "#/components/schemas/ListType" + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + ListSearchRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dateCreatedRangeEnd: + type: string + description: Define the end for an interval of time and only include Lists + that are created within this interval. + format: date-time + nullable: true + dateCreatedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are created within this interval. + format: date-time + nullable: true + dateModifiedRangeEnd: + type: string + description: Define the end for an interval of time and only include Lists + that are modified within this interval. + format: date-time + nullable: true + dateModifiedRangeStart: + type: string + description: Define the beginning for an interval of time and only include + Lists that are modified within this interval. + format: date-time + nullable: true + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + listDbIds: + type: array + description: An array of primary database identifiers to identify a set + of Lists + nullable: true + items: + type: string + listNames: + type: array + description: An array of human readable names to identify a set of Lists + nullable: true + items: + type: string + listOwnerNames: + type: array + description: An array of names for the people or entities who are responsible + for a set of Lists + nullable: true + items: + type: string + listOwnerPersonDbIds: + type: array + description: An array of primary database identifiers to identify people + or entities who are responsible for a set of Lists + nullable: true + items: + type: string + listSources: + type: array + description: "An array of terms identifying lists from different sources\ + \ (ie 'USER', 'SYSTEM', etc)" + nullable: true + items: + type: string + listType: + nullable: true + allOf: + - $ref: "#/components/schemas/ListType" + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + description: "A List represents a collection of other BrAPI data objects. Typically\ + \ these are custom lists generated by a user to keep track of interesting\ + \ data. For example, a user might build a List of Germplasm that they have\ + \ manually marked for further study." + ListType: + type: string + description: The type of objects that are referenced in a List + enum: + - germplasm + - markers + - variants + - programs + - trials + - studies + - observationUnits + - observations + - observationVariables + - samples + Location: + allOf: + - $ref: "#/components/schemas/LocationNewRequest" + - required: + - locationDbId + type: object + properties: + locationDbId: + type: string + description: The unique identifier for a Location + description: "A geographic Location on earth. This is usually used to describe\ + \ the general area where an experiment took place. For example, a natural\ + \ site, an experimental field, a greenhouse, a phenotyping facility, etc." + LocationNewRequest: + required: + - locationName + type: object + properties: + abbreviation: + type: string + description: A shortened version of the human readable name for a Location + nullable: true + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + coordinateDescription: + type: string + description: "Describes the precision and landmarks of the coordinate values\ + \ used for a Location. (ex. the site, the nearest town, a 10 kilometers\ + \ radius circle, +/- 20 meters, etc)" + nullable: true + coordinateUncertainty: + type: string + description: Uncertainty associated with the coordinates in meters. Leave + the value empty if the uncertainty is unknown. + nullable: true + coordinates: + $ref: "#/components/schemas/GeoJSON" + countryCode: + type: string + description: |- + [ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec +
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.' + nullable: true + countryName: + type: string + description: |- + The full name of the country where a Location is located +
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code. + nullable: true + documentationURL: + type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + environmentType: + type: string + description: "Describes the general type of environment of a Location. (ex.\ + \ forest, field, nursery, etc)" + nullable: true + exposure: + type: string + description: Describes the level of protection/exposure for things like + sun light and wind at a particular Location + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + instituteAddress: + type: string + description: |- + The street address of the institute at a particular Location +
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. + nullable: true + instituteName: + type: string + description: |- + The full name of the institute at a particular Location +
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. + nullable: true + locationName: + type: string + description: |- + A human readable name for a Location +
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place. + locationType: + type: string + description: "A short description of a type of Location (ex. Field Station,\ + \ Breeding Location, Storage Location, etc)" + nullable: true + parentLocationDbId: + type: string + nullable: true + parentLocationName: + type: string + nullable: true + siteStatus: + type: string + description: "Description of the accessibility of the location (ex. Public,\ + \ Private)" + nullable: true + slope: + type: string + description: Describes the approximate slope (height/distance) of a Location. + nullable: true + topography: + type: string + description: "Describes the topography of the land at a Location. (ex. Plateau,\ + \ Cirque, Hill, Valley, etc)" + nullable: true + description: "A geographic Location on earth. This is usually used to describe\ + \ the general area where an experiment took place. For example, a natural\ + \ site, an experimental field, a greenhouse, a phenotyping facility, etc." + LocationParameters: + type: object + properties: + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + LocationRequest: + type: object + properties: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Locations + nullable: true + items: + type: string + altitudeMax: + type: number + description: The maximum altitude to search for + nullable: true + example: 200 + altitudeMin: + type: number + description: The minimum altitude to search for + nullable: true + example: 20 + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + coordinates: + anyOf: + - $ref: "#/components/schemas/GeoJSONSearchArea" + - type: "null" + countryCodes: + type: array + description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ + \ spec" + nullable: true + items: + type: string + countryNames: + type: array + description: The full name of the country to search for + nullable: true + items: + type: string + instituteAddresses: + type: array + description: The street address of the institute to search for + nullable: true + items: + type: string + instituteNames: + type: array + description: The name of the institute to search for + nullable: true + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + locationTypes: + type: array + description: "The type of location this represents (ex. Breeding Location,\ + \ Storage Location, etc)" + nullable: true + items: + type: string + parentLocationDbIds: + type: array + description: "The unique identifier for a Location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + nullable: true + items: + type: string + parentLocationNames: + type: array + description: "A human readable name for a location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + LocationSearchRequest: + type: object + properties: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Locations + nullable: true + items: + type: string + altitudeMax: + type: number + description: The maximum altitude to search for + nullable: true + example: 200 + altitudeMin: + type: number + description: The minimum altitude to search for + nullable: true + example: 20 + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + coordinates: + anyOf: + - $ref: "#/components/schemas/GeoJSONSearchArea" + - type: "null" + countryCodes: + type: array + description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ + \ spec" + nullable: true + items: + type: string + countryNames: + type: array + description: The full name of the country to search for + nullable: true + items: + type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + instituteAddresses: + type: array + description: The street address of the institute to search for + nullable: true + items: + type: string + instituteNames: + type: array + description: The name of the institute to search for + nullable: true + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + locationTypes: + type: array + description: "The type of location this represents (ex. Breeding Location,\ + \ Storage Location, etc)" + nullable: true + items: + type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + parentLocationDbIds: + type: array + description: "The unique identifier for a Location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + nullable: true + items: + type: string + parentLocationNames: + type: array + description: "A human readable name for a location\n
The Parent Location\ + \ defines the encompassing location that this location belongs to. \n\ + For example, an Institution might have multiple Field Stations inside\ + \ it and each Field Station might have multiple Fields." + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + description: "A geographic Location on earth. This is usually used to describe\ + \ the general area where an experiment took place. For example, a natural\ + \ site, an experimental field, a greenhouse, a phenotyping facility, etc." + MarkerPositionRequest: + type: object + properties: + linkageGroupNames: + type: array + description: A list of Uniquely Identifiable linkage group names + nullable: true + items: + type: string + mapDbIds: + type: array + description: A list of IDs which uniquely identify `GenomeMaps` within the + given database server + nullable: true + items: + type: string + maxPosition: + type: integer + description: The maximum position of markers in a given map + format: int32 + nullable: true + example: 4000 + minPosition: + type: integer + description: The minimum position of markers in a given map + format: int32 + nullable: true + example: 250 + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` within the + given database server + nullable: true + items: + type: string + MethodRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + methodDbIds: + type: array + description: The unique identifier for a method. + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + ObservationRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationDbIds: + type: array + description: The unique id of an Observation + nullable: true + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationTimeStampRangeEnd: + type: string + description: Timestamp range end + format: date-time + nullable: true + observationTimeStampRangeStart: + type: string + description: Timestamp range start + format: date-time + nullable: true + observationUnitDbIds: + type: array + description: The unique id of an Observation Unit + nullable: true + items: + type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ObservationUnitHierarchyLevel: + type: object + properties: + levelName: + type: string + description: "A name for this level \n\n**Standard Level Names: study, field,\ + \ entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\ + \nFor more information on Observation Levels, please review the Observation Levels documentation. " + nullable: true + levelOrder: + type: integer + description: "`levelOrder` defines where that level exists in the hierarchy\ + \ of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy\ + \ (ie field -> 1) and higher numbers are at the bottom of the hierarchy\ + \ (ie plant -> 9). \n\nFor more information on Observation Levels, please\ + \ review the Observation Levels documentation. " + format: int32 + nullable: true + description: "The exact level and level code of an observation unit. \n\nFor\ + \ more information on Observation Levels, please review the Observation\ + \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ + Type of observation unit in textual form, usually one of the following: study,\ + \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ + \ types is possible but not recommended. \nThe observation unit type can not\ + \ be used to indicate sub-plant levels. However, observations can still be\ + \ made on the sub-plant level, as long as the details are indicated in the\ + \ associated observed variable (see observed variables). \nAlternatively,\ + \ it is possible to use samples for more detailed tracing of sub-plant units,\ + \ attaching the observations to them instead.\" " + ObservationUnitHierarchyLevelRequest: + type: object + properties: + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ObservationUnitRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + includeObservations: + type: boolean + description: "Use this parameter to include a list of observations embedded\ + \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ + \ your own risk. It may return large, unpaginated lists of observation\ + \ data. Only set this value to True if you are sure you need to." + nullable: true + example: false + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationLevelRelationships: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships + nullable: true + items: + $ref: "#/components/schemas/ObservationUnitLevelRelationship" + observationLevels: + type: array + description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel + nullable: true + items: + $ref: "#/components/schemas/ObservationUnitLevel" + observationUnitDbIds: + type: array + description: The unique id of an observation unit + nullable: true + items: + type: string + observationUnitLevelCodes: + type: array + description: "The Observation Unit Level Code. This parameter should be\ + \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelNames: + type: array + description: "The Observation Unit Level. Returns only the observation unit\ + \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ + \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ + \ plot, sub-plot, plant, pot, sample** \n
For more information on\ + \ Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelOrders: + type: array + description: "The Observation Unit Level Order Number. Returns only the\ + \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipCodes: + type: array + description: "The Observation Unit Level Code. \n
This parameter should\ + \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ + \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipDbIds: + type: array + description: "The observationUnitDbId associated with a particular level\ + \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ + \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipNames: + type: array + description: "The Observation Unit Level Relationship is a connection that\ + \ this observation unit has to another level of the hierarchy. \n
For\ + \ example, if you have several observation units at a 'plot' level, they\ + \ might all share a relationship to the same 'field' level. \n
Use\ + \ this parameter to identify groups of observation units that share a\ + \ relationship level. \n
**Standard Level Names: study, field, entry,\ + \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ + \ more information on Observation Levels, please review the Observation Levels documentation. " + items: + type: string + observationUnitLevelRelationshipOrders: + type: array + description: "The Observation Unit Level Order Number. \n
Returns only\ + \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ + \ \n
For more information on Observation Levels, please review the\ + \ Observation Levels documentation. " + items: + type: string + observationUnitNames: + type: array + description: The human readable identifier for an Observation Unit + nullable: true + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: "The year or Phenotyping campaign of a multi-annual study (trees,\ + \ grape, ...)" + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ObservationVariableParameters: + type: object + properties: + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + ObservationVariableRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + OntologyParameters: + type: object + properties: + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + OntologyRequest: + type: object + properties: + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + ontologyNames: + type: array + description: The human readable identifier for an ontology definition. + items: + type: string + OntologyTerm: + type: object + properties: + term: + type: string + description: Ontology term - the label of the ontology term the termId is + pointing to. + nullable: true + termURI: + type: string + description: Ontology term identifier - the CURIE for an ontology term. + It differs from the standard GA4GH schema's :ref:`id ` in that it is a + CURIE pointing to an information resource outside of the scope of the + schema or its resource implementation. + nullable: true + description: A pointer to an ontology used by a genomic reference + PagingParameters: + type: object + properties: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + PedigreeNodeRequest: + type: object + properties: + accessionNumbers: + type: array + description: |- + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + nullable: true + items: + type: string + binomialNames: + type: array + description: List of the full binomial name (scientific name) to identify + a germplasm + nullable: true + items: + type: string + collections: + type: array + description: A specific panel/collection/population name this germplasm + belongs to. + nullable: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + familyCodes: + type: array + description: A familyCode representing the family this germplasm belongs + to. + nullable: true + items: + type: string + genus: + type: array + description: List of Genus names to identify germplasm + nullable: true + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + germplasmPUIs: + type: array + description: List of Permanent Unique Identifiers to identify germplasm + nullable: true + items: + type: string + includeFullTree: + type: boolean + description: "If this parameter is true, recursively include ALL of the\ + \ nodes available in this pedigree tree" + nullable: true + example: true + includeParents: + type: boolean + description: "If this parameter is true, include the array of parents in\ + \ the response" + nullable: true + example: true + includeProgeny: + type: boolean + description: "If this parameter is true, include the array of progeny in\ + \ the response" + nullable: true + example: true + includeSiblings: + type: boolean + description: "If this parameter is true, include the array of siblings in\ + \ the response" + nullable: true + example: true + instituteCodes: + type: array + description: "The code for the institute that maintains the material. \n\ +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ + \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ + \ country code of the country where the institute is located plus a number\ + \ (e.g. PER001). The current set of institute codes is available from\ + \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ + \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ + \ rules (v)\"." + nullable: true + items: + type: string + pedigreeDepth: + type: integer + description: "Recursively include this number of levels up the tree in the\ + \ response (parents, grand-parents, great-grand-parents, etc)" + format: int32 + example: 3 + progenyDepth: + type: integer + description: "Recursively include this number of levels down the tree in\ + \ the response (children, grand-children, great-grand-children, etc)" + format: int32 + example: 3 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + species: + type: array + description: List of Species names to identify germplasm + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + synonyms: + type: array + description: List of alternative names or IDs used to reference this germplasm + nullable: true + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + Person: + allOf: + - $ref: "#/components/schemas/PersonNewRequest" + - required: + - personDbId + type: object + properties: + personDbId: + type: string + description: Unique ID for a person + description: "A generic object used to maintain the metadata needed to describe\ + \ a human. The Person might be a software user, a field technician, or a\ + \ primary contact for a Program." + PersonNewRequest: + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + description: + type: string + description: description of this person + nullable: true + emailAddress: + type: string + description: email address for this person + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + firstName: + type: string + description: Persons first name + nullable: true + lastName: + type: string + description: Persons last name + nullable: true + mailingAddress: + type: string + description: physical address of this person + nullable: true + middleName: + type: string + description: Persons middle name + nullable: true + phoneNumber: + type: string + description: phone number of this person + nullable: true + userID: + type: string + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + nullable: true + description: "A generic object used to maintain the metadata needed to describe\ + \ a human. The Person might be a software user, a field technician, or a primary\ + \ contact for a Program." + PersonRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + emailAddresses: + type: array + description: email address for this person + nullable: true + items: + type: string + firstNames: + type: array + description: Persons first name + nullable: true + items: + type: string + lastNames: + type: array + description: Persons last name + nullable: true + items: + type: string + mailingAddresses: + type: array + description: physical address of this person + nullable: true + items: + type: string + middleNames: + type: array + description: Persons middle name + nullable: true + items: + type: string + personDbIds: + type: array + description: Unique ID for this person + nullable: true + items: + type: string + phoneNumbers: + type: array + description: phone number of this person + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + userIDs: + type: array + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + nullable: true + items: + type: string + PersonSearchRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + emailAddresses: + type: array + description: email address for this person + nullable: true + items: + type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + firstNames: + type: array + description: Persons first name + nullable: true + items: + type: string + lastNames: + type: array + description: Persons last name + nullable: true + items: + type: string + mailingAddresses: + type: array + description: physical address of this person + nullable: true + items: + type: string + middleNames: + type: array + description: Persons middle name + nullable: true + items: + type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + personDbIds: + type: array + description: Unique ID for this person + nullable: true + items: + type: string + phoneNumbers: + type: array + description: phone number of this person + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + userIDs: + type: array + description: A systems user ID associated with this person. Different from + personDbId because you could have a person who is not a user of the system. + nullable: true + items: + type: string + description: "A generic object used to maintain the metadata needed to describe\ + \ a human. The Person might be a software user, a field technician, or a primary\ + \ contact for a Program." + PlannedCrossRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossingProjectDbIds: + type: array + description: Search for Crossing Projects with this unique id + items: + type: string + crossingProjectNames: + type: array + description: The human readable name for a crossing project + items: + type: string + plannedCrossDbIds: + type: array + description: Search for Planned Cross with this unique id + items: + type: string + plannedCrossNames: + type: array + description: Search for Planned Cross with this human readable name + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + statuses: + type: array + description: "The status of this planned cross. Is it waiting to be performed\ + \ ('TODO'), has it been completed successfully ('DONE'), or has it not\ + \ been done on purpose ('SKIPPED')." + items: + type: string + enum: + - TODO + - DONE + - SKIPPED + PlateRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an observation unit + nullable: true + items: + type: string + plateBarcodes: + type: array + description: A unique identifier physically attached to the plate + nullable: true + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a plate of samples + nullable: true + items: + type: string + plateNames: + type: array + description: The human readable name of a plate of samples + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a sample + nullable: true + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related Samples + nullable: true + items: + type: string + sampleNames: + type: array + description: The human readable name of the sample + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + Program: + allOf: + - $ref: "#/components/schemas/ProgramNewRequest" + - required: + - programDbId + type: object + properties: + programDbId: + type: string + description: The ID which uniquely identifies the program + description: A BrAPI Program represents the high level organization or group + who is responsible for conducting trials and studies. Things like Breeding + Programs and Funded Projects are considered BrAPI Programs. A Program can + contain multiple Trials. A Trial can contain multiple Studies. + ProgramNewRequest: + required: + - programName + type: object + properties: + abbreviation: + type: string + description: A shortened version of the human readable name for a Program + nullable: true + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + description: Common name for the crop which this program is for + nullable: true + documentationURL: + type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + fundingInformation: + type: string + description: Information describing the grant or funding source for this + program + nullable: true + leadPersonDbId: + type: string + nullable: true + leadPersonName: + type: string + nullable: true + objective: + type: string + description: The primary objective of the program + nullable: true + programName: + type: string + description: Human readable name of the program + programType: + type: string + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding\ + \ " + enum: + - STANDARD + - PROJECT + description: A BrAPI Program represents the high level organization or group + who is responsible for conducting trials and studies. Things like Breeding + Programs and Funded Projects are considered BrAPI Programs. A Program can + contain multiple Trials. A Trial can contain multiple Studies. + ProgramParameters: + type: object + properties: + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + ProgramRequest: + type: object + properties: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Programs + nullable: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + leadPersonDbIds: + type: array + description: The person DbIds of the program leader to search for + nullable: true + items: + type: string + leadPersonNames: + type: array + description: The names of the program leader to search for + nullable: true + items: + type: string + objectives: + type: array + description: A program objective to search for + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + programTypes: + type: array + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding " + nullable: true + items: + type: string + description: |- + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding. + enum: + - STANDARD + - PROJECT + ProgramSearchRequest: + type: object + properties: + abbreviations: + type: array + description: A list of shortened human readable names for a set of Programs + nullable: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + leadPersonDbIds: + type: array + description: The person DbIds of the program leader to search for + nullable: true + items: + type: string + leadPersonNames: + type: array + description: The names of the program leader to search for + nullable: true + items: + type: string + objectives: + type: array + description: A program objective to search for + nullable: true + items: + type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + programTypes: + type: array + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding " + nullable: true + items: + type: string + description: |- + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding. + enum: + - STANDARD + - PROJECT + description: A BrAPI Program represents the high level organization or group + who is responsible for conducting trials and studies. Things like Breeding + Programs and Funded Projects are considered BrAPI Programs. A Program can + contain multiple Trials. A Trial can contain multiple Studies. + ProgramType: + type: string + description: "The type of program entity this object represents\n
'STANDARD'\ + \ represents a standard, permanent breeding program\n
'PROJECT' represents\ + \ a short term project, usually with a set time limit based on funding " + enum: + - STANDARD + - PROJECT + Publication: + type: object + properties: + publicationPUI: + type: string + description: The permanent unique identifier of the publication. + nullable: true + publicationReference: + type: string + description: The publication reference. + nullable: true + description: MIAPPE V1.1 (DM-9) Associated publication - An identifier for a + literature publication where the investigation is described. Use of DOIs is + recommended. + ReferenceBasesRequest: + type: object + properties: + end: + type: integer + description: "The end position (0-based, exclusive) of this query. Defaults\ + \ to the length of this `Reference`." + format: int32 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + start: + type: integer + description: |- + The start position (0-based) of this query. Defaults to 0. + Genomic positions are non-negative integers less than reference length. + Requests spanning the join of circular genomes are represented as + two requests one on each side of the join (position 0). + format: int32 + ReferenceRequest: + type: object + properties: + accessions: + type: array + description: "If specified, return the references for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + nullable: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + isDerived: + type: boolean + description: "A sequence X is said to be derived from source sequence Y,\ + \ if X and Y are of the same length and the per-base sequence divergence\ + \ at A/C/G/T bases is sufficiently small. Two sequences derived from the\ + \ same official sequence share the same coordinates and annotations, and\ + \ can be replaced with the official sequence for certain use cases." + format: boolean + nullable: true + maxLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 90000 + md5checksums: + type: array + description: "If specified, return the references for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + nullable: true + items: + type: string + minLength: + type: integer + description: The minimum length of this `References` sequence. + format: int32 + example: 4000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: A list of IDs which uniquely identify `References` within the + given database server + nullable: true + items: + type: string + referenceSetDbIds: + type: array + description: A list of IDs which uniquely identify `ReferenceSets` within + the given database server + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ReferenceSetRequest: + type: object + properties: + accessions: + type: array + description: "If set, return the reference sets for which the `accession`\ + \ matches this string (case-sensitive, exact match)." + nullable: true + items: + type: string + assemblyPUIs: + type: array + description: "If set, return the reference sets for which the `assemblyId`\ + \ matches this string (case-sensitive, exact match)." + nullable: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + md5checksums: + type: array + description: "If set, return the reference sets for which the `md5checksum`\ + \ matches this string (case-sensitive, exact match)." + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceSetDbIds: + type: array + description: The `ReferenceSets` to search. + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + SampleRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + observationUnitDbIds: + type: array + description: The ID which uniquely identifies an `ObservationUnit` + nullable: true + items: + type: string + plateDbIds: + type: array + description: The ID which uniquely identifies a `Plate` of `Samples` + nullable: true + items: + type: string + plateNames: + type: array + description: The human readable name of a `Plate` of `Samples` + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + sampleDbIds: + type: array + description: The ID which uniquely identifies a `Sample` + nullable: true + items: + type: string + sampleGroupDbIds: + type: array + description: The unique identifier for a group of related `Samples` + nullable: true + items: + type: string + sampleNames: + type: array + description: The human readable name of the `Sample` + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + ScaleRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a scale. + items: + type: string + Season: + required: + - seasonDbId + type: object + properties: + seasonDbId: + type: string + description: "The ID which uniquely identifies a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'" + seasonName: + type: string + description: "Name of the season. ex. 'Spring', 'Q2', 'Season A', etc." + nullable: true + year: + type: integer + description: The 4 digit year of the season. + format: int32 + nullable: true + description: "A Season defines a period in time. A Season is made of two parts;\ + \ (1) the primary year and (2) a term which defines a segment of the year.\ + \ This term could be a traditional season, like \"Spring\" or \"Summer\",\ + \ or this term could be a month, like \"May\" or \"June\", or this could be\ + \ an arbitrary season name which is meaningful to the breeding Program like\ + \ \"PlantingTime_3\" or \"Season E\"." + SeasonRequest: + type: object + properties: + seasonDbIds: + type: array + description: "The unique identifier for a season. For backward compatibility\ + \ it can be a string like '2012', '1957-2004'." + items: + type: string + seasonNames: + type: array + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + items: + type: string + seasons: + type: array + description: The term to describe a given season. Example "Spring" OR "May" + OR "Planting_Time_7". + items: + type: string + years: + type: array + description: The 4 digit year of a season. Example 2017 + items: + type: integer + format: int32 + SeedLotRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seedLotDbIds: + type: array + description: Unique id for a seed lot on this server + items: + type: string + SeedLotTransactionRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seedLotDbIds: + type: array + description: Unique id for a seed lot on this server + items: + type: string + transactionDbIds: + type: array + description: Unique id for a Transaction that has occurred + items: + type: string + transactionDirection: + type: string + description: "Filter results to only include transactions directed to the\ + \ specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both\ + \ (BOTH). The default value for this parameter is BOTH" + nullable: true + enum: + - TO + - FROM + - BOTH + SortBy: + type: string + description: Name of the field to sort by. + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + SortOrder: + type: string + description: Sort order direction. Ascending/Descending. + enum: + - ASC + - DESC + - asc + - desc + Study: + allOf: + - $ref: "#/components/schemas/StudyNewRequest" + - required: + - studyDbId + type: object + properties: + studyDbId: + type: string + description: |- + The ID which uniquely identifies a study within the given database server + + MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + description: A Study represents an experiment that has taken place at a single + location. The Study contains metadata about the parameters and design of + the experiment. It can also be used to group results and data sets generated + from the experiment. A Trial can represent a collection of one or more Studies. + StudyNewRequest: + required: + - studyName + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Study is currently active and ongoing + nullable: true + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + description: Common name for the crop associated with this study + nullable: true + contacts: + type: array + description: List of contact entities associated with this study + nullable: true + items: + $ref: "#/components/schemas/Contact" + culturalPractices: + type: string + description: MIAPPE V1.1 (DM-28) Cultural practices - General description + of the cultural practices of the study. + nullable: true + dataLinks: + type: array + description: "List of links to extra data files associated with this study.\ + \ Extra data could include notes, images, and reference data." + nullable: true + items: + $ref: "#/components/schemas/DataLink" + documentationURL: + type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + endDate: + type: string + description: |- + The date the study ends + + MIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended + format: date-time + nullable: true + environmentParameters: + type: array + description: |- + Environmental parameters that were kept constant throughout the study and did not change between observation units. + + MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). + nullable: true + items: + $ref: "#/components/schemas/EnvironmentParameter" + experimentalDesign: + $ref: "#/components/schemas/ExperimentalDesign" + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + growthFacility: + $ref: "#/components/schemas/GrowthFacility" + lastUpdate: + $ref: "#/components/schemas/LastUpdate" + license: + type: string + description: The usage license associated with the study data + nullable: true + locationDbId: + type: string + nullable: true + locationName: + type: string + nullable: true + observationLevels: + type: array + description: "Observation levels indicate the granularity level at which\ + \ the measurements are taken. `levelName` \ndefines the level, `levelOrder`\ + \ defines where that level exists in the hierarchy of levels. \n`levelOrder`s\ + \ lower numbers are at the top of the hierarchy (ie field > 0) and higher\ + \ numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard\ + \ Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot,\ + \ plant, pot, sample** \n\nFor more information on Observation Levels,\ + \ please review the Observation Levels documentation. " + nullable: true + items: + $ref: "#/components/schemas/ObservationUnitHierarchyLevel" + observationUnitsDescription: + type: string + description: MIAPPE V1.1 (DM-25) Observation unit description - General + description of the observation units in the study. + nullable: true + observationVariableDbIds: + type: array + description: "The list of Observation Variables being used in this study.\ + \ \n\nThis list is intended to be the wishlist of variables to collect\ + \ in this study. It may or may not match the set of variables used in\ + \ the collected observation records. " + items: + type: string + seasons: + type: array + description: List of seasons over which this study was performed. + nullable: true + items: + type: string + startDate: + type: string + description: |- + The date this study started + + MIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started + format: date-time + nullable: true + studyCode: + type: string + description: A short human readable code for a study + nullable: true + studyDescription: + type: string + description: |- + The description of this study + + MIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study + studyName: + type: string + description: |- + The human readable name for a study + + MIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study + nullable: true + studyPUI: + type: string + description: "A permanent unique identifier associated with this study data.\ + \ For example, a URI or DOI" + nullable: true + studyType: + type: string + description: "The type of study being performed. ex. \"Yield Trial\", etc" + nullable: true + trialDbId: + type: string + trialName: + type: string + description: A Study represents an experiment that has taken place at a single + location. The Study contains metadata about the parameters and design of the + experiment. It can also be used to group results and data sets generated from + the experiment. A Trial can represent a collection of one or more Studies. + StudyParameters: + type: object + properties: + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + StudyRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Study is currently active and ongoing + nullable: true + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: The ID which uniquely identifies a season + nullable: true + items: + type: string + sortBy: + type: string + description: Name of the field to sort by. + nullable: true + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + - germplasmDbId + - observationVariableDbId + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + nullable: true + enum: + - ASC + - DESC + - asc + - desc + studyCodes: + type: array + description: A short human readable code for a study + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + studyPUIs: + type: array + description: "Permanent unique identifier associated with study data. For\ + \ example, a URI or DOI" + nullable: true + items: + type: string + studyTypes: + type: array + description: "The type of study being performed. ex. \"Yield Trial\", etc" + nullable: true + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + StudySearchRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Study is currently active and ongoing + nullable: true + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + observationVariableDbIds: + type: array + description: The DbIds of Variables to search for + items: + type: string + observationVariableNames: + type: array + description: The names of Variables to search for + items: + type: string + observationVariablePUIs: + type: array + description: "The Permanent Unique Identifier of an Observation Variable,\ + \ usually in the form of a URI" + items: + type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seasonDbIds: + type: array + description: The ID which uniquely identifies a season + nullable: true + items: + type: string + sortBy: + type: string + description: Name of the field to sort by. + nullable: true + enum: + - studyDbId + - trialDbId + - programDbId + - locationDbId + - seasonDbId + - studyType + - studyName + - studyLocation + - programName + - germplasmDbId + - observationVariableDbId + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + nullable: true + enum: + - ASC + - DESC + - asc + - desc + studyCodes: + type: array + description: A short human readable code for a study + nullable: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + studyPUIs: + type: array + description: "Permanent unique identifier associated with study data. For\ + \ example, a URI or DOI" + nullable: true + items: + type: string + studyTypes: + type: array + description: "The type of study being performed. ex. \"Yield Trial\", etc" + nullable: true + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + description: A Study represents an experiment that has taken place at a single + location. The Study contains metadata about the parameters and design of the + experiment. It can also be used to group results and data sets generated from + the experiment. A Trial can represent a collection of one or more Studies. + TokenPagingParameters: + type: object + properties: + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + pageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
Used to request a specific page of data to be returned.\n\ +
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken from\ + \ a prior response to construct a query and move to the next or previous\ + \ page respectively. " + example: 33c27874 + deprecated: true + TraitDataType: + type: string + description: |- +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ enum: + - Code + - Date + - Duration + - Nominal + - Numerical + - Ordinal + - Text + TraitRequest: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + observationVariableDbIds: + type: array + description: The unique identifier for an observation variable. + items: + type: string + ontologyDbIds: + type: array + description: "The unique identifier for an ontology definition. Use this\ + \ parameter to filter results based on a specific ontology \n\n Use `GET\ + \ /ontologies` to find the list of available ontologies on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a trait. + items: + type: string + TransactionDirection: + type: string + description: "Filter results to only include transactions directed to the specific\ + \ Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The\ + \ default value for this parameter is BOTH" + enum: + - TO + - FROM + - BOTH + Trial: + allOf: + - $ref: "#/components/schemas/TrialNewRequest" + - required: + - trialDbId + type: object + properties: + trialDbId: + type: string + description: |- + The ID which uniquely identifies a trial + + MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + description: "A Trial represents a collection of Study objects, and the metadata\ + \ associated with that collection. A Trial could represent a multi-location\ + \ experiment, and could contain information related to publications and\ + \ data licensing." + TrialNewRequest: + required: + - trialName + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Trial is currently active and ongoing + nullable: true + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + description: Common name for the crop associated with this trial + nullable: true + contacts: + type: array + description: List of contact entities associated with this trial + nullable: true + items: + $ref: "#/components/schemas/Contact" + datasetAuthorships: + type: array + description: License and citation information for the data in this trial + nullable: true + items: + $ref: "#/components/schemas/DatasetAuthorships" + documentationURL: + type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + endDate: + type: string + description: The date this trial ends + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + programDbId: + type: string + nullable: true + programName: + type: string + nullable: true + publications: + type: array + description: MIAPPE V1.1 (DM-9) Associated publication - An identifier for + a literature publication where the investigation is described. Use of + DOIs is recommended. + nullable: true + items: + $ref: "#/components/schemas/Publication" + startDate: + type: string + description: The date this trial started + nullable: true + trialDescription: + type: string + description: |- + The human readable description of a trial + + MIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail. + nullable: true + trialName: + type: string + description: |- + The human readable name of a trial + + MIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation. + trialPUI: + type: string + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + nullable: true + description: "A Trial represents a collection of Study objects, and the metadata\ + \ associated with that collection. A Trial could represent a multi-location\ + \ experiment, and could contain information related to publications and data\ + \ licensing." + TrialParameters: + type: object + properties: + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + TrialRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Trial is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + contactDbIds: + type: array + description: List of contact entities associated with this trial + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + searchDateRangeEnd: + type: string + description: "The end of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + searchDateRangeStart: + type: string + description: "The start of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + sortBy: + type: string + description: Name of the field to sort by. + nullable: true + enum: + - trialDbId + - trialName + - programDbId + - programName + - locationDbId + - startDate + - endDate + sortOrder: + type: string + description: Sort order direction. Ascending/Descending. + nullable: true + enum: + - ASC + - DESC + - asc + - desc + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + trialPUIs: + type: array + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + items: + type: string + TrialSearchRequest: + type: object + properties: + active: + type: boolean + description: A flag to indicate if a Trial is currently active and ongoing + example: true + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + contactDbIds: + type: array + description: List of contact entities associated with this trial + items: + type: string + externalReferenceIDs: + type: array + description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ + \ Github issue number #460 \n
List of external reference IDs. Could\ + \ be a simple strings or a URIs. (use with `externalReferenceSources`\ + \ parameter)" + deprecated: true + items: + type: string + externalReferenceIds: + type: array + description: List of external reference IDs. Could be a simple strings or + a URIs. (use with `externalReferenceSources` parameter) + items: + type: string + externalReferenceSources: + type: array + description: List of identifiers for the source system or database of an + external reference (use with `externalReferenceIDs` parameter) + items: + type: string + locationDbIds: + type: array + description: The location ids to search for + items: + type: string + locationNames: + type: array + description: A human readable names to search for + items: + type: string + page: + type: integer + description: Which result page is requested. The page indexing starts at + 0 (the first page is 'page'= 0). Default is `0`. + format: int32 + example: 0 + pageSize: + type: integer + description: The size of the pages to be returned. Default is `1000`. + format: int32 + example: 1000 + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + searchDateRangeEnd: + type: string + description: "The end of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + searchDateRangeStart: + type: string + description: "The start of the overlapping search date range. `searchDateRangeStart`\ + \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ + \ of the following cases are true\n\n- `searchDateRangeStart` is before\ + \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ + \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ + \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ + \ is before `trial.endDate`" + format: date + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + trialPUIs: + type: array + description: A permanent identifier for a trial. Could be DOI or other URI + formatted identifier. + items: + type: string + description: "A Trial represents a collection of Study objects, and the metadata\ + \ associated with that collection. A Trial could represent a multi-location\ + \ experiment, and could contain information related to publications and data\ + \ licensing." + Variable: + required: + - method + - scale + - trait + type: object + properties: + additionalInfo: + $ref: "#/components/schemas/AdditionalInfo" + commonCropName: + type: string + description: "Crop name (examples: \"Maize\", \"Wheat\")" + nullable: true + contextOfUse: + type: array + description: "Indication of how trait is routinely used. (examples: [\"\ + Trial evaluation\", \"Nursery evaluation\"])" + nullable: true + items: + type: string + defaultValue: + type: string + description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" + nullable: true + documentationURL: + type: string + description: A URL to the human readable documentation of an object + format: uri + nullable: true + externalReferences: + type: array + description: An array of external reference ids. These are references to + this piece of data in an external system. Could be a simple string or + a URI. + nullable: true + items: + $ref: "#/components/schemas/ExternalReference" + growthStage: + type: string + description: "Growth stage at which measurement is made (examples: \"flowering\"\ + )" + nullable: true + institution: + type: string + description: Name of institution submitting the variable + nullable: true + language: + type: string + description: 2 letter ISO 639-1 code for the language of submission of the + variable. + nullable: true + method: + $ref: "#/components/schemas/Method" + ontologyReference: + nullable: true + allOf: + - $ref: "#/components/schemas/OntologyReference" + scale: + $ref: "#/components/schemas/Scale" + scientist: + type: string + description: Name of scientist submitting the variable. + nullable: true + status: + type: string + description: "Variable status. (examples: \"recommended\", \"obsolete\"\ + , \"legacy\", etc.)" + nullable: true + submissionTimestamp: + type: string + description: Timestamp when the Variable was added (ISO 8601) + format: date-time + nullable: true + synonyms: + type: array + description: Other variable names + nullable: true + items: + type: string + trait: + $ref: "#/components/schemas/Trait" + description: "A unique combination of Trait, Method, and Scale to define a clear\ + \ context for an Observation." + VariableBaseClassParameters: + type: object + properties: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + dataTypes: + type: array + description: List of scale data types to filter search results + items: + $ref: "#/components/schemas/TraitDataType" + methodDbIds: + type: array + description: List of methods to filter search results + items: + type: string + methodNames: + type: array + description: |- + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + items: + type: string + methodPUIs: + type: array + description: "The Permanent Unique Identifier of a Method, usually in the\ + \ form of a URI" + items: + type: string + ontologyDbIds: + type: array + description: List of ontology IDs to search for + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + scaleDbIds: + type: array + description: The unique identifier for a Scale + items: + type: string + scaleNames: + type: array + description: |- + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + items: + type: string + scalePUIs: + type: array + description: "The Permanent Unique Identifier of a Scale, usually in the\ + \ form of a URI" + items: + type: string + studyDbId: + type: array + description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ + \ number #483 \n
The unique ID of a studies to filter on" + deprecated: true + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + traitAttributePUIs: + type: array + description: |- + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + items: + type: string + traitAttributes: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the attribute is the observed feature (or characteristic) of the entity\ + \ e.g., for \"grain colour\", attribute = \"colour\"" + items: + type: string + traitClasses: + type: array + description: List of trait classes to filter search results + items: + type: string + traitDbIds: + type: array + description: The unique identifier for a Trait + items: + type: string + traitEntities: + type: array + description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ + , the entity is the part of the plant that the trait refers to e.g., for\ + \ \"grain colour\", entity = \"grain\"" + items: + type: string + traitEntityPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait Entity, usually\ + \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ + \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ + \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " + items: + type: string + traitNames: + type: array + description: |- + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + items: + type: string + traitPUIs: + type: array + description: "The Permanent Unique Identifier of a Trait, usually in the\ + \ form of a URI" + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + VariantRequest: + type: object + properties: + callSetDbIds: + type: array + description: "**Deprecated in v2.1** Parameter unnecessary. Github issue\ + \ number #474 \n
Only return variant calls which belong to call sets\ + \ with these IDs. If unspecified, return all variants and no variant call\ + \ objects." + nullable: true + deprecated: true + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + end: + type: integer + description: "The end of the window (0-based, exclusive) for which overlapping\ + \ variants should be returned." + format: int32 + example: 1500 + pageToken: + type: string + description: |- + The continuation token, which is used to page through large result sets. + To get the next page of results, set this parameter to the value of + `next_page_token` from the previous response. + deprecated: true + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbId: + type: string + description: |- + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + nullable: true + example: 120a2d5c + deprecated: true + referenceDbIds: + type: array + description: The unique identifier representing a genotype `Reference` + nullable: true + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype `ReferenceSet` + nullable: true + items: + type: string + start: + type: integer + description: "The beginning of the window (0-based, inclusive) for which\ + \ overlapping variants should be returned. Genomic positions are non-negative\ + \ integers less than reference length. Requests spanning the join of circular\ + \ genomes are represented as two requests one on each side of the join\ + \ (position 0)." + format: int32 + example: 100 + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantDbIds: + type: array + description: A list of IDs which uniquely identify `Variants` + nullable: true + items: + type: string + variantSetDbIds: + type: array + description: A list of IDs which uniquely identify `VariantSets` + nullable: true + items: + type: string + VariantSetRequest: + type: object + properties: + callSetDbIds: + type: array + description: The unique identifier representing a CallSet + items: + type: string + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + referenceDbIds: + type: array + description: The unique identifier representing a genotype Reference + items: + type: string + referenceSetDbIds: + type: array + description: The unique identifier representing a genotype ReferenceSet + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string + variantDbIds: + type: array + description: The unique identifier representing a Variant + items: + type: string + variantSetDbIds: + type: array + description: The unique identifier representing a VariantSet + items: + type: string + VariantSetsExtractRequest: + type: object + properties: + callSetDbIds: + type: array + description: The CallSet to search. + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + example: "~" + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + example: '|' + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + unknownString: + type: string + description: The string used as a representation for missing data. + example: "-" + variantDbIds: + type: array + description: The Variant to search. + items: + type: string + variantSetDbIds: + type: array + description: The VariantSet to search. + items: + type: string + description: Request object for extracting data subsets as new Variant Sets + basePagination: + required: + - currentPage + - pageSize + type: object + properties: + currentPage: + type: integer + description: The index number for the returned page of data. This should + always match the requested page number or the default page (0). + example: 0 + default: 0 + pageSize: + type: integer + description: "The number of data elements returned, aka the size of the\ + \ current page. If the requested page does not have enough elements to\ + \ fill a page at the requested page size, this field should indicate the\ + \ actual number of elements returned." + example: 1000 + default: 1000 + totalCount: + type: integer + description: The total number of elements that are available on the server + and match the requested query parameters. + example: 10 + totalPages: + type: integer + description: "The total number of pages of elements available on the server.\ + \ This should be calculated with the following formula. \n
totalPages\ + \ = CEILING( totalCount / requested_page_size)" + example: 1 + description: "The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Pages are zero indexed, so the first page will be page 0 (zero)." + dataFile: + required: + - fileURL + type: object + properties: + fileURL: + type: string + description: The absolute URL where the file is located + format: uri + example: https://wiki.brapi.org/examples/datafile.xlsx + fileName: + type: string + description: The name of the file + example: datafile.xlsx + fileSize: + type: integer + description: The size of the file in bytes + example: 4398 + fileDescription: + type: string + description: A human readable description of the file contents + example: This is an Excel data file + fileType: + type: string + description: The type or format of the file. Preferably MIME Type. + example: application/vnd.ms-excel + fileMD5Hash: + type: string + description: The MD5 Hash of the file contents to be used as a check sum + example: c2365e900c81a89cf74d83dab60df146 + description: A dataFile contains a URL and the relevant file metadata to represent + a file + metadata: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/basePagination" + metadataBase: + type: object + properties: + datafiles: + type: array + description: "The datafiles contains a list of file URLs and metadata. \n\ + These files contain additional information related to the returned object\ + \ and can be retrieved by a subsequent call. \nThis could be a supplementary\ + \ data file, an informational file, the uploaded file where the data originated\ + \ from, a generated file representing the whole dataset in a particular\ + \ format, or any other related file. " + example: [] + items: + $ref: "#/components/schemas/dataFile" + status: + type: array + description: "The status field contains a list of informational status messages\ + \ from the server. \nIf no status is reported, an empty list should be\ + \ returned. See Error Reporting for more information." + items: + $ref: "#/components/schemas/status" + description: "An object in the BrAPI standard response model that describes\ + \ some information about the service call being performed. This includes supplementary\ + \ data, status log messages, and pagination information." + metadataTokenPagination: + allOf: + - $ref: "#/components/schemas/metadataBase" + - type: object + properties: + pagination: + $ref: "#/components/schemas/tokenPagination" + status: + required: + - message + - messageType + type: object + properties: + message: + type: string + description: A short message concerning the status of this request/response + example: "Request accepted, response successful" + messageType: + type: string + description: The logging level for the attached message + example: INFO + enum: + - DEBUG + - ERROR + - WARNING + - INFO + description: An array of status messages to convey technical logging information + from the server to the client. + tokenPagination: + allOf: + - $ref: "#/components/schemas/basePagination" + - required: + - nextPageToken + type: object + properties: + nextPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the next page of data." + example: cb668f63 + deprecated: true + currentPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the current page of data." + example: 48bc6ac1 + deprecated: true + prevPageToken: + type: string + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The string token used to query the previous page of data." + example: 9659857e + deprecated: true + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
The pagination object is applicable only when the payload contains\ + \ a \"data\" key. It describes the pagination of the data contained in the\ + \ \"data\" array, as a way to identify which subset of data is being returned.\ + \ \n
Tokenized pages are for large data sets which can not be efficiently\ + \ broken into indexed pages. Use the nextPageToken and prevPageToken to\ + \ construct an additional query and move to the next or previous page respectively.\ + \ " + example: + currentPage: 0 + pageSize: 1000 + totalCount: 10 + totalPages: 1 + Service: + required: + - methods + - service + - versions + type: object + properties: + service: + type: string + description: The name of the available call as recorded in the documentation + example: "germplasm/{germplasmDbId}/pedigree" + contentTypes: + type: array + description: The possible content types returned by the service endpoint + example: + - application/json + items: + $ref: "#/components/schemas/ContentTypes" + dataTypes: + type: array + description: "**Deprecated in v2.1** Please use `contentTypes`. Github issue\ + \ number #443 \n
The possible data formats returned by the available\ + \ call " + example: + - application/json + deprecated: true + items: + $ref: "#/components/schemas/ContentTypes" + methods: + type: array + description: The possible HTTP Methods to be used with the available call + example: + - GET + - POST + items: + type: string + enum: + - GET + - POST + - PUT + - DELETE + versions: + type: array + description: The supported versions of a particular call + example: + - "2.0" + - "2.1" + items: + type: string + enum: + - "2.0" + - "2.1" + - "2.2" + ServerInfo: + required: + - calls + type: object + properties: + contactEmail: + type: string + description: A contact email address for this server management + example: contact@institute.org + documentationURL: + type: string + description: A URL to the human readable documentation of an object + example: institute.org/server + organizationURL: + type: string + description: The URL of the organization that manages this server and data + example: institute.org/home + organizationName: + type: string + description: The name of the organization that manages this server and data + example: The Institute + serverName: + type: string + description: The name of this server + example: The BrAPI Test Server + serverDescription: + type: string + description: A description of this server + example: |- + The BrAPI Test Server + Web Server - Apache Tomcat 7.0.32 + Database - Postgres 10 + Supported BrAPI Version - V2.0 + location: + type: string + description: "Physical location of this server (ie. City, Country)" + example: USA + calls: + type: array + description: Array of available calls on this server + items: + $ref: "#/components/schemas/Service" + responses: + "401Unauthorized": + description: Unauthorized + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization + token + ProgramCommonCropNameListResponse: + description: OK + content: + application/json: + schema: + title: ProgramCommonCropNameListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: string + "202AcceptedSearchResponse": + description: Accepted + content: + application/json: + schema: + title: 202AcceptedSearchResponse + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + type: object + properties: + searchResultsDbId: + type: string + example: 551ae08c + StudyStudyTypeListResponse: + description: OK + content: + application/json: + schema: + title: StudyStudyTypeListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: string + StudySingleResponse: + description: OK + content: + application/json: + schema: + title: StudySingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Study" + PersonListResponse: + description: OK + content: + application/json: + schema: + title: PersonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Person" + LocationListResponse: + description: OK + content: + application/json: + schema: + title: LocationListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Location" + TrialListResponse: + description: OK + content: + application/json: + schema: + title: TrialListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Trial" + "403Forbidden": + description: Forbidden + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to + perform this action + StudyObservationLevelsListResponse: + description: OK + content: + application/json: + schema: + title: StudyObservationLevelsListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: array + items: + $ref: "#/components/schemas/ObservationUnitHierarchyLevel" + ProgramListResponse: + description: OK + content: + application/json: + schema: + title: ProgramListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Program" + TrialSingleResponse: + description: OK + content: + application/json: + schema: + title: TrialSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Trial" + ListListResponse: + description: OK + content: + application/json: + schema: + title: ListListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/List" + SeasonSingleResponse: + description: OK + content: + application/json: + schema: + title: SeasonSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Season" + "400BadRequest": + description: Bad Request + content: + application/json: + schema: + type: string + example: |- + ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object + + ERROR - 2018-10-08T18:15:11Z - Invalid query parameter + + ERROR - 2018-10-08T18:15:11Z - Required parameter is missing + "404NotFound": + description: Not Found + content: + application/json: + schema: + type: string + example: ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not + found + StudyListResponse: + description: OK + content: + application/json: + schema: + title: StudyListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Study" + CallListResponse: + description: OK + content: + application/json: + schema: + title: CallListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + description: "The `data` array is part of the BrAPI standard List\ + \ Response JSON container. `data` will always contain the primary\ + \ list of objects being returned by a BrAPI endpoint. `data`\ + \ is also the only array impacted by the `metadata.pagination`\ + \ details. When the pagination parameters change, the `data`\ + \ array will reflect those changes in the JSON response." + items: + $ref: "#/components/schemas/Call" + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed + into a single occurrence (false) + nullable: true + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele + calls. + nullable: true + example: '|' + sepUnphased: + type: string + description: The string used as a separator for unphased allele + calls. + nullable: true + example: / + unknownString: + type: string + description: The string used as a representation for missing data. + nullable: true + example: "." + LocationSingleResponse: + description: OK + content: + application/json: + schema: + title: LocationSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Location" + SeasonListResponse: + description: OK + content: + application/json: + schema: + title: SeasonListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + $ref: "#/components/schemas/Season" + ListSingleResponse: + description: OK + content: + application/json: + schema: + title: ListSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/List" + PersonSingleResponse: + description: OK + content: + application/json: + schema: + title: PersonSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Person" + ProgramSingleResponse: + description: OK + content: + application/json: + schema: + title: ProgramSingleResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/Program" + parameters: + externalReferenceID: + name: externalReferenceID + in: query + description: "**Deprecated in v2.1** Please use `externalReferenceId`. Github\ + \ issue number #460 \n
An external reference ID. Could be a simple string\ + \ or a URI. (use with `externalReferenceSource` parameter)" + required: false + deprecated: true + style: form + explode: true + schema: + type: string + externalReferenceId: + name: externalReferenceId + in: query + description: An external reference ID. Could be a simple string or a URI. (use + with `externalReferenceSource` parameter) + required: false + style: form + explode: true + schema: + type: string + externalReferenceSource: + name: externalReferenceSource + in: query + description: An identifier for the source system or database of an external + reference (use with `externalReferenceId` parameter) + required: false + style: form + explode: true + schema: + type: string + acceptHeader: + name: Accept + in: header + description: "A standard HTTP request header that is used to request a specific\ + \ content type (JSON, CSV, etc) which is \"acceptable\" to the client and\ + \ should be returned by the server" + required: true + style: simple + explode: false + schema: + $ref: "#/components/schemas/ContentTypes" + example: application/json + searchResultsDbId: + name: searchResultsDbId + in: path + description: Unique identifier which references the search results + required: true + style: simple + explode: false + schema: + type: string + pageSize: + name: pageSize + in: query + description: The size of the pages to be returned. Default is `1000`. + required: false + style: form + explode: true + schema: + type: integer + example: 1000 + authorizationHeader: + name: Authorization + in: header + description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ + \ {token_string} " + required: false + style: simple + explode: false + schema: + pattern: ^Bearer .*$ + type: string + example: Bearer XXXX + pageToken: + name: pageToken + in: query + description: "**Deprecated in v2.1** Please use `page`. Github issue number\ + \ #451 \n
Used to request a specific page of data to be returned.\n
\ + \ Tokenized pages are for large data sets which can not be efficiently broken\ + \ into indexed pages. Use the nextPageToken and prevPageToken from a prior\ + \ response to construct a query and move to the next or previous page respectively. " + required: false + deprecated: true + style: form + explode: true + schema: + type: string + example: 33c27874 + page: + name: page + in: query + description: |- + Used to request a specific page of data to be returned. + + The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. + required: false + style: form + explode: true + schema: + type: integer + example: "0" + securitySchemes: + AuthorizationToken: + type: http + description: OAuth Bearer Token - A valid Bearer token to prove authorization + scheme: bearer + bearerFormat: nonce token or JWT diff --git a/Specification/Generated/brapi_generated.graphqls b/Specification/Generated/brapi_generated.graphqls index 5feaa080..71cdb6b4 100644 --- a/Specification/Generated/brapi_generated.graphqls +++ b/Specification/Generated/brapi_generated.graphqls @@ -1416,6 +1416,8 @@ type Image { "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] "The unique identifier of an image" + imageContent: String + "The unique identifier of an image" imageDbId: String "The name of the image file. Might be the same as 'imageName', but could be different." imageFileName: String @@ -1442,10 +1444,10 @@ type Image { imageWidth: Int "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc" mimeType: String + "A list of observation Ids this image is associated with, if applicable." + observationDbId: [ID] "The related observation unit identifier, if relevant." observationUnitDbIds: ID - "A list of observation Ids this image is associated with, if applicable." - observations(observationsInput: ObservationsInput, paging: PageInput): ObservationListResponse } type ImageListResponse { @@ -1755,8 +1757,6 @@ type Mutation { createObservation(observationInput: ObservationInput): Observation "Create a new ObservationUnit" createObservationUnit(observationUnitInput: ObservationUnitInput): ObservationUnit - "Create a new ObservationVariable" - createObservationVariable(commonCropName: String, observationVariableInput: ObservationVariableInput): ObservationVariable "Create a new Ontology" createOntology(ontologyInput: OntologyInput): Ontology "Create a new Person" @@ -1777,6 +1777,8 @@ type Mutation { createSeason(seasonInput: SeasonInput): Season "Create a new SeedLot" createSeedLot(seedLotInput: SeedLotInput): SeedLot + "Create a new SeedLotTransaction" + createSeedLotTransaction(seedLotTransactionInput: SeedLotTransactionInput): SeedLotTransaction "Create a new Study" createStudy(commonCropName: String, studyInput: StudyInput): Study "Create a new Trait" @@ -1807,8 +1809,6 @@ type Mutation { updateObservation(observationInput: ObservationInput): Observation "Update the details for an existing ObservationUnit" updateObservationUnit(observationUnitInput: ObservationUnitInput): ObservationUnit - "Update the details for an existing ObservationVariable" - updateObservationVariable(commonCropName: String, observationVariableInput: ObservationVariableInput): ObservationVariable "Update the details for an existing Ontology" updateOntology(ontologyInput: OntologyInput): Ontology "Update the details for an existing Person" @@ -1829,6 +1829,8 @@ type Mutation { updateSeason(seasonInput: SeasonInput): Season "Update the details for an existing SeedLot" updateSeedLot(seedLotInput: SeedLotInput): SeedLot + "Update the details for an existing SeedLotTransaction" + updateSeedLotTransaction(seedLotTransactionInput: SeedLotTransactionInput): SeedLotTransaction "Update the details for an existing Study" updateStudy(commonCropName: String, studyInput: StudyInput): Study "Update the details for an existing Trait" @@ -1870,7 +1872,7 @@ type Observation { "The ID which uniquely identifies an observation unit" observationUnitDbIds: ID "The ID which uniquely identifies an observation variable" - observationVariableDbIds: ID + observationVariable: ObservationVariable "The season for this Observation" seasonDbIds: ID "The ID which uniquely identifies a study within the given database server" @@ -1886,6 +1888,48 @@ type ObservationListResponse { page: PageInfo } +type ObservationTable { + "The 2D matrix of observation data. ObservationVariables and other metadata are the columns, ObservationUnits are the rows." + data: [[String]] + """ +

The table is REQUIRED to have the following columns

+
    +
  • observationUnitDbId - Each row is related to one Observation Unit
    • +
  • observationTimeStamp - Each row is has a time stamp for when the observation was taken
    • +
  • At least one column with an observationVariableDbId
    • +
+

The table may have any or all of the following OPTIONAL columns. Included columns are decided by the server developer

+
    +
  • observationUnitName
    • +
  • studyDbId
    • +
  • studyName
    • +
  • germplasmDbId
    • +
  • germplasmName
    • +
  • positionCoordinateX
    • +
  • positionCoordinateY
    • +
  • year
    • +
+

The table also may have any number of Observation Unit Hierarchy Level columns. For example:

+
    +
  • field
    • +
  • plot
    • +
  • sub-plot
    • +
  • plant
    • +
  • pot
    • +
  • block
    • +
  • entry
    • +
  • rep
    • +
+

The JSON representation provides a pair of extra arrays for defining the headers of the table. + The first array "headerRow" will always contain "observationUnitDbId" and any or all of the OPTIONAL column header names. + The second array "observationVariables" contains the names and DbIds for the Observation Variables represented in the table. + By appending the two arrays, you can construct the complete header row of the table.

+ """ + headerRow: [HeaderRow] + "The list of observation variables which have values recorded for them in the data matrix. Append to the 'headerRow' for complete header row of the table." + observationVariables: [ObservationVariable] +} + "A Treatment applied an Observation Unit at a given Modality/Level for a specific Factor." type ObservationTreatment { """ @@ -2045,7 +2089,7 @@ type ObservationUnitPosition { A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. """ - geoCoordinates: [GeoJSON] + geoCoordinates: GeoJSON """ The exact level and level code of an observation unit. @@ -2080,79 +2124,57 @@ type ObservationUnitPosition { positionCoordinateYType: PositionCoordinateType } +type ObservationUnitTable { + "The 2D matrix of observation data. ObservationVariables and other metadata are the columns, ObservationUnits are the rows." + data: [[String]] + """ +

The table is REQUIRED to have the following columns

+
    +
  • observationUnitDbId - Each row is related to one Observation Unit
    • +
  • At least one column with an observationVariableDbId
    • +
+

The table may have any or all of the following OPTIONAL columns. Included columns are decided by the server developer

+
    +
  • observationUnitName
    • +
  • studyDbId
    • +
  • studyName
    • +
  • germplasmDbId
    • +
  • germplasmName
    • +
  • positionCoordinateX
    • +
  • positionCoordinateY
    • +
  • year
    • +
+

The table also may have any number of Observation Unit Hierarchy Level columns. For example:

+
    +
  • field
    • +
  • plot
    • +
  • sub-plot
    • +
  • plant
    • +
  • pot
    • +
  • block
    • +
  • entry
    • +
  • rep
    • +
+

The JSON representation provides a pair of extra arrays for defining the headers of the table. + The first array "headerRow" will always contain "observationUnitDbId" and any or all of the OPTIONAL column header names. + The second array "observationVariables" contains the names and DbIds for the Observation Variables represented in the table. + By appending the two arrays, you can construct the complete header row of the table.

+ """ + headerRow: [HeaderRow] + "The list of observation variables which have values recorded for them in the data matrix. Append to the 'headerRow' for complete header row of the table." + observationVariables: [ObservationVariable] +} + type ObservationUnitsSearchResponse { data: [ObservationUnit] searchResultsDbId: String } -type ObservationVariable implements Variable { - "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." - additionalInfo: AdditionalInfo - "Crop name (examples: \"Maize\", \"Wheat\")" - commonCropName: String - "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])" - contextOfUse: [String] - "Variable default value. (examples: \"red\", \"2.3\", etc.)" - defaultValue: String - "A URL to the human readable documentation of an object" - documentationURL: String - "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." - externalReferences: [ExternalReference] - "Growth stage at which measurement is made (examples: \"flowering\")" - growthStage: String - "Name of institution submitting the variable" - institution: String - "2 letter ISO 639-1 code for the language of submission of the variable." - language: String - """ - A description of the way an Observation should be collected. -
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". - """ - methodDbIds: ID - """ - Variable unique identifier - - MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. - """ +type ObservationVariable { + "Variable unique identifier" observationVariableDbId: String - """ - Variable name (usually a short name) - - MIAPPE V1.1 (DM-84) Variable name - Name of the variable. - """ + "Variable name (usually a short name)" observationVariableName: String - "The Permanent Unique Identifier of a Observation Variable, usually in the form of a URI" - observationVariablePUI: String - """ - MIAPPE V1.1 - - (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology - - (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). - - (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). - - (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). - """ - ontologyReference: OntologyReference - """ - A Scale describes the units and acceptable values for an ObservationVariable. -
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". - """ - scaleDbIds: ID - "Name of scientist submitting the variable." - scientist: String - "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" - status: String - "Timestamp when the Variable was added (ISO 8601)" - submissionTimestamp: String - "Other variable names" - synonyms: [String] - """ - A Trait describes what property is being observed. -
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". - """ - traitDbIds: ID } type ObservationVariableListResponse { @@ -2160,11 +2182,6 @@ type ObservationVariableListResponse { page: PageInfo } -type ObservationVariablesSearchResponse { - data: [ObservationVariable] - searchResultsDbId: String -} - type ObservationsSearchResponse { data: [Observation] searchResultsDbId: String @@ -2546,12 +2563,6 @@ type Query { observationUnits(observationUnitsInput: ObservationUnitsInput, paging: PageInput): ObservationUnitListResponse "Returns ObservationUnit objects" observationUnitsSearch(observationUnitInput: ObservationUnitsInput): ObservationUnitsSearchResponse - "Returns a ObservationVariable object by id" - observationVariable(commonCropName: String, observationVariableDbId: ID): ObservationVariable - "Returns ObservationVariable objects" - observationVariables(observationVariablesInput: ObservationVariablesInput, paging: PageInput): ObservationVariableListResponse - "Returns ObservationVariable objects" - observationVariablesSearch(observationVariableInput: ObservationVariablesInput): ObservationVariablesSearchResponse "Returns Observation objects" observations(observationsInput: ObservationsInput, paging: PageInput): ObservationListResponse "Returns Observation objects" @@ -2618,6 +2629,12 @@ type Query { seasonsSearch(seasonInput: SeasonsInput): SeasonsSearchResponse "Returns a SeedLot object by id" seedLot(commonCropName: String, seedLotDbId: ID): SeedLot + "Returns a SeedLotTransaction object by id" + seedLotTransaction(commonCropName: String, seedLotTransactionDbId: ID): SeedLotTransaction + "Returns SeedLotTransaction objects" + seedLotTransactions(paging: PageInput, seedLotTransactionsInput: SeedLotTransactionsInput): SeedLotTransactionListResponse + "Returns SeedLotTransaction objects" + seedLotTransactionsSearch(seedLotTransactionInput: SeedLotTransactionsInput): SeedLotTransactionsSearchResponse "Returns SeedLot objects" seedLots(paging: PageInput, seedLotsInput: SeedLotsInput): SeedLotListResponse "Returns SeedLot objects" @@ -2949,7 +2966,7 @@ type SeedLot { "Description the storage location" storageLocation: String "The complete history of transactions for this seed lot. This includes seed increases, seed usage (planting), and trading with other breeding programs." - transactions: [SeedLotTransaction] + transactionDbId: [ID] "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)" units: String } @@ -2981,6 +2998,16 @@ type SeedLotTransaction { units: String } +type SeedLotTransactionListResponse { + data: [SeedLotTransaction] + page: PageInfo +} + +type SeedLotTransactionsSearchResponse { + data: [SeedLotTransaction] + searchResultsDbId: String +} + type SeedLotsSearchResponse { data: [SeedLot] searchResultsDbId: String @@ -3095,7 +3122,7 @@ type Study { This list is intended to be the wishlist of variables to collect in this study. It may or may not match the set of variables used in the collected observation records. """ - observationVariables(observationVariablesInput: ObservationVariablesInput, paging: PageInput): ObservationVariableListResponse + observationVariables(commonCropName: String, observationVariablesInput: ObservationVariablesInput, paging: PageInput): ObservationVariableListResponse "List of seasons over which this study was performed." seasons: [String] """ @@ -3403,6 +3430,8 @@ type VariantSet { calls(callsInput: CallsInput, paging: PageInput): CallListResponse "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." externalReferences: [ExternalReference] + "Will perform a search for `Calls` which match the search criteria in `variantSetsExtractRequest`. The results of the search will be used to create a new `VariantSet` on the server. The new `VariantSet` will be returned." + extractDbIds: ID """ The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet.
When possible, these field names and abbreviations should follow the VCF standard @@ -3600,6 +3629,28 @@ enum FileFormat { text_tsv } +"valid header fields" +enum HeaderRow { + block + entry + field + germplasmDbId + germplasmName + observationTimeStamp + observationUnitDbId + observationUnitName + plant + plot + positionCoordinateX + positionCoordinateY + pot + rep + studyDbId + studyName + sub_plot + year +} + "The type of objects that are referenced in a List" enum ListType { germplasm @@ -5265,6 +5316,8 @@ input ImageInput { "Filter by External References" externalReferences: [ExternalReferenceInput] "The unique identifier of an image" + imageContent: String + "The unique identifier of an image" imageDbId: String "The name of the image file. Might be the same as 'imageName', but could be different." imageFileName: String @@ -5969,7 +6022,7 @@ input ObservationUnitPositionInput { A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. """ - geoCoordinates: [GeoJSONInput] + geoCoordinates: GeoJSONInput """ The exact level and level code of an observation unit. @@ -6113,76 +6166,10 @@ input ObservationUnitsInput { } input ObservationVariableInput { - "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." - additionalInfo: AdditionalInfoInput - "Crop name (examples: \"Maize\", \"Wheat\")" - commonCropName: String - "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])" - contextOfUse: [String] - "Variable default value. (examples: \"red\", \"2.3\", etc.)" - defaultValue: String - "A URL to the human readable documentation of an object" - documentationURL: String - "Filter by External References" - externalReferences: [ExternalReferenceInput] - "Growth stage at which measurement is made (examples: \"flowering\")" - growthStage: String - "Name of institution submitting the variable" - institution: String - "2 letter ISO 639-1 code for the language of submission of the variable." - language: String - """ - A description of the way an Observation should be collected. -
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". - """ - method: MethodInput - """ - Variable unique identifier - - MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. - """ + "Variable unique identifier" observationVariableDbId: String - """ - Variable name (usually a short name) - - MIAPPE V1.1 (DM-84) Variable name - Name of the variable. - """ + "Variable name (usually a short name)" observationVariableName: String - "The Permanent Unique Identifier of a Observation Variable, usually in the form of a URI" - observationVariablePUI: String - "observations" - observations: [ObservationInput] - """ - MIAPPE V1.1 - - (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology - - (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). - - (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). - - (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). - """ - ontologyReference: OntologyReferenceInput - """ - A Scale describes the units and acceptable values for an ObservationVariable. -
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". - """ - scale: ScaleInput - "Name of scientist submitting the variable." - scientist: String - "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" - status: String - studies: [StudyInput] - "Timestamp when the Variable was added (ISO 8601)" - submissionTimestamp: String - "Other variable names" - synonyms: [String] - """ - A Trait describes what property is being observed. -
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". - """ - trait: TraitInput } input ObservationVariablesInput { @@ -7362,6 +7349,45 @@ input SeedLotTransactionInput { units: String } +input SeedLotTransactionsInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "Search for Cross with this unique id" + crossDbIds: [String] + "Search for Cross with this human readable name" + crossNames: [String] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "Unique id for a seed lot on this server" + seedLotDbIds: [String] + "Unique id for a Transaction that has occurred" + transactionDbIds: [String] + "Filter results to only include transactions directed to the specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The default value for this parameter is BOTH" + transactionDirection: TransactionDirection +} + input SeedLotsInput { """ The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. @@ -7978,6 +8004,8 @@ input VariantSetInput { calls: [CallInput] "Filter by External References" externalReferences: [ExternalReferenceInput] + "Will perform a search for `Calls` which match the search criteria in `variantSetsExtractRequest`. The results of the search will be used to create a new `VariantSet` on the server. The new `VariantSet` will be returned." + extract: VariantSetInput """ The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet.
When possible, these field names and abbreviations should follow the VCF standard diff --git a/Specification/Generated/brapi_generated.json b/Specification/Generated/brapi_generated.json index f14992cb..9077f266 100644 --- a/Specification/Generated/brapi_generated.json +++ b/Specification/Generated/brapi_generated.json @@ -1,8 +1,8 @@ { - "openapi" : "3.0.1", + "openapi" : "3.0.0", "info" : { "title" : "BrAPI", - "version" : "2.1" + "version" : "" }, "paths" : { "/allelematrix" : { @@ -65,7 +65,7 @@ { "name" : "dataMatrixNames", "in" : "query", - "description" : "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", "required" : false, "schema" : { "type" : "string" @@ -74,7 +74,7 @@ { "name" : "dataMatrixAbbreviations", "in" : "query", - "description" : "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "description" : "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", "required" : false, "schema" : { "type" : "string" @@ -195,9 +195,6 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" - }, - "404" : { - "$ref" : "#/components/responses/404NotFound" } } } @@ -343,6 +340,44 @@ "$ref" : "#/components/responses/403Forbidden" } } + }, + "put" : { + "tags" : [ + "Calls" + ], + "summary" : "Update the details for an existing Call", + "description" : "Update the details for an existing Call", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/Call" + } + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } } }, "/callsets" : { @@ -2385,6 +2420,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -2423,6 +2461,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -2700,45 +2741,126 @@ } } }, - "/variables" : { + "/ontologies" : { "get" : { "tags" : [ - "ObservationVariables" + "Ontologies" ], - "summary" : "Get a filtered list of ObservationVariable", - "description" : "Get a list of ObservationVariable", + "summary" : "Get a filtered list of Ontology", + "description" : "Get a list of Ontology", "parameters" : [ { - "name" : "observationVariableDbId", + "name" : "ontologyDbId", "in" : "query", - "description" : "The DbIds of Variables to search for", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationVariableName", + "name" : "ontologyName", "in" : "query", - "description" : "The names of Variables to search for", + "description" : "The human readable identifier for an ontology definition.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/OntologyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Ontologies" + ], + "summary" : "Create new Ontology", + "description" : "Add new Ontology to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/OntologyNewRequest" + } + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/OntologyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/pedigree" : { + "get" : { + "tags" : [ + "PedigreeNodes" + ], + "summary" : "Get a filtered list of PedigreeNode", + "description" : "Get a list of PedigreeNode", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationVariablePUI", + "name" : "germplasmDbId", "in" : "query", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "description" : "List of IDs which uniquely identify germplasm to search for", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "commonCropName", + "name" : "germplasmName", "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "description" : "List of human readable names to identify germplasm to search for", "required" : false, "schema" : { "type" : "string" @@ -2753,6 +2875,15 @@ "type" : "string" } }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { "name" : "trialDbId", "in" : "query", @@ -2763,111 +2894,131 @@ } }, { - "name" : "studyDbId", + "name" : "germplasmPUI", "in" : "query", - "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "description" : "List of Permanent Unique Identifiers to identify germplasm", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "ontologyDbId", + "name" : "accessionNumber", "in" : "query", - "description" : "List of ontology IDs to search for", + "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "methodDbId", + "name" : "collection", "in" : "query", - "description" : "List of methods to filter search results", + "description" : "A specific panel/collection/population name this germplasm belongs to.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "methodName", + "name" : "familyCode", "in" : "query", - "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "description" : "A familyCode representing the family this germplasm belongs to.", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "methodPUI", + "name" : "binomialName", "in" : "query", - "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "scaleDbId", + "name" : "genus", "in" : "query", - "description" : "The unique identifier for a Scale", + "description" : "List of Genus names to identify germplasm", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "scaleName", + "name" : "species", "in" : "query", - "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "description" : "List of Species names to identify germplasm", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "scalePUI", + "name" : "synonym", "in" : "query", - "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "description" : "List of alternative names or IDs used to reference this germplasm", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "traitClass", + "name" : "includeParents", "in" : "query", - "description" : "List of trait classes to filter search results", + "description" : "If this parameter is true, include the array of parents in the response", "required" : false, "schema" : { - "type" : "string" + "type" : "boolean" } }, { - "name" : "traitDbId", + "name" : "includeSiblings", "in" : "query", - "description" : "The unique identifier for a Trait", + "description" : "If this parameter is true, include the array of siblings in the response", "required" : false, "schema" : { - "type" : "string" + "type" : "boolean" } }, { - "name" : "traitName", + "name" : "includeProgeny", "in" : "query", - "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "description" : "If this parameter is true, include the array of progeny in the response", "required" : false, "schema" : { - "type" : "string" + "type" : "boolean" } }, { - "name" : "traitPUI", + "name" : "includeFullTree", "in" : "query", - "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "description" : "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", "required" : false, "schema" : { - "type" : "string" + "type" : "boolean" + } + }, + { + "name" : "pedigreeDepth", + "in" : "query", + "description" : "Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc)", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, + { + "name" : "progenyDepth", + "in" : "query", + "description" : "Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc)", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" } }, { @@ -2891,7 +3042,7 @@ ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" + "$ref" : "#/components/responses/PedigreeNodeListResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -2901,15 +3052,18 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, - "post" : { + "put" : { "tags" : [ - "ObservationVariables" + "PedigreeNodes" ], - "summary" : "Create new ObservationVariable", - "description" : "Add new ObservationVariable to database", + "summary" : "Update the details for an existing PedigreeNode", + "description" : "Update the details for an existing PedigreeNode", "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" @@ -2919,17 +3073,18 @@ "content" : { "application/json" : { "schema" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/ObservationVariableNewRequest" - } + "type" : "object", + "additionalProperties" : { + "$ref" : "#/components/schemas/PedigreeNode" + }, + "example" : "{_1={additionalInfo={}, breedingMethod={}, crossingProject={}, crossingYear=10, defaultDisplayName=5761c815, externalReferences=[{}], familyCode=42f142b0, germplasm={}, parents=[{}], pedigreeString=5e286b4b, progeny=[{}], siblings=[{}]}, _2={additionalInfo={}, breedingMethod={}, crossingProject={}, crossingYear=20, defaultDisplayName=5761c816, externalReferences=[{}], familyCode=42f142b1, germplasm={}, parents=[{}], pedigreeString=5e286b4c, progeny=[{}], siblings=[{}]}}" } } } }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" + "$ref" : "#/components/responses/PedigreeNodeListResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -2939,67 +3094,18 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } - } - }, - "/ontologies" : { - "get" : { + }, + "post" : { "tags" : [ - "Ontologies" + "PedigreeNodes" ], - "summary" : "Get a filtered list of Ontology", - "description" : "Get a list of Ontology", - "parameters" : [ - { - "name" : "ontologyDbId", - "in" : "query", - "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "ontologyName", - "in" : "query", - "description" : "The human readable identifier for an ontology definition.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "$ref" : "#/components/parameters/page" - }, - { - "$ref" : "#/components/parameters/pageSize" - }, - { - "$ref" : "#/components/parameters/authorizationHeader" - } - ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/OntologyListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ - "Ontologies" - ], - "summary" : "Create new Ontology", - "description" : "Add new Ontology to database", + "summary" : "Create new PedigreeNode", + "description" : "Add new PedigreeNode to database", "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" @@ -3011,7 +3117,7 @@ "schema" : { "type" : "array", "items" : { - "$ref" : "#/components/schemas/OntologyNewRequest" + "$ref" : "#/components/schemas/PedigreeNode" } } } @@ -3019,7 +3125,7 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/OntologyListResponse" + "$ref" : "#/components/responses/PedigreeNodeListResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -3029,17 +3135,20 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } }, - "/pedigree" : { + "/people" : { "get" : { "tags" : [ - "PedigreeNodes" + "People" ], - "summary" : "Get a filtered list of PedigreeNode", - "description" : "Get a list of PedigreeNode", + "summary" : "Get a filtered list of Person", + "description" : "Get a list of Person", "parameters" : [ { "name" : "commonCropName", @@ -3050,24 +3159,6 @@ "type" : "string" } }, - { - "name" : "germplasmDbId", - "in" : "query", - "description" : "List of IDs which uniquely identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "germplasmName", - "in" : "query", - "description" : "List of human readable names to identify germplasm to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, { "name" : "programDbId", "in" : "query", @@ -3078,151 +3169,41 @@ } }, { - "name" : "studyDbId", - "in" : "query", - "description" : "List of study identifiers to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "trialDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "germplasmPUI", - "in" : "query", - "description" : "List of Permanent Unique Identifiers to identify germplasm", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "accessionNumber", - "in" : "query", - "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "collection", - "in" : "query", - "description" : "A specific panel/collection/population name this germplasm belongs to.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "familyCode", - "in" : "query", - "description" : "A familyCode representing the family this germplasm belongs to.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "binomialName", + "name" : "firstName", "in" : "query", - "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "description" : "Persons first name", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "genus", + "name" : "lastName", "in" : "query", - "description" : "List of Genus names to identify germplasm", + "description" : "Persons last name", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "species", + "name" : "personDbId", "in" : "query", - "description" : "List of Species names to identify germplasm", + "description" : "Unique ID for this person", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "synonym", + "name" : "userID", "in" : "query", - "description" : "List of alternative names or IDs used to reference this germplasm", + "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", "required" : false, "schema" : { "type" : "string" } }, - { - "name" : "includeParents", - "in" : "query", - "description" : "If this parameter is true, include the array of parents in the response", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, - { - "name" : "includeSiblings", - "in" : "query", - "description" : "If this parameter is true, include the array of siblings in the response", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, - { - "name" : "includeProgeny", - "in" : "query", - "description" : "If this parameter is true, include the array of progeny in the response", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, - { - "name" : "includeFullTree", - "in" : "query", - "description" : "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, - { - "name" : "pedigreeDepth", - "in" : "query", - "description" : "Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc)", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, - { - "name" : "progenyDepth", - "in" : "query", - "description" : "Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc)", - "required" : false, - "schema" : { - "type" : "integer", - "format" : "int32" - } - }, { "$ref" : "#/components/parameters/externalReferenceId" }, @@ -3244,7 +3225,7 @@ ], "responses" : { "200" : { - "$ref" : "#/components/responses/PedigreeNodeListResponse" + "$ref" : "#/components/responses/PersonListResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -3259,10 +3240,10 @@ }, "post" : { "tags" : [ - "PedigreeNodes" + "People" ], - "summary" : "Create new PedigreeNode", - "description" : "Add new PedigreeNode to database", + "summary" : "Create new Person", + "description" : "Add new Person to database", "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" @@ -3274,7 +3255,7 @@ "schema" : { "type" : "array", "items" : { - "$ref" : "#/components/schemas/PedigreeNode" + "$ref" : "#/components/schemas/PersonNewRequest" } } } @@ -3282,7 +3263,7 @@ }, "responses" : { "200" : { - "$ref" : "#/components/responses/PedigreeNodeListResponse" + "$ref" : "#/components/responses/PersonListResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -3296,13 +3277,13 @@ } } }, - "/people" : { + "/plannedcrosses" : { "get" : { "tags" : [ - "People" + "Crosses" ], - "summary" : "Get a filtered list of Person", - "description" : "Get a list of Person", + "summary" : "Get a filtered list of PlannedCross", + "description" : "Get a list of PlannedCross", "parameters" : [ { "name" : "commonCropName", @@ -3323,171 +3304,36 @@ } }, { - "name" : "firstName", + "name" : "crossingProjectDbId", "in" : "query", - "description" : "Persons first name", + "description" : "Search for Crossing Projects with this unique id", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "lastName", + "name" : "crossingProjectName", "in" : "query", - "description" : "Persons last name", + "description" : "The human readable name for a crossing project", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "personDbId", + "name" : "plannedCrossDbId", "in" : "query", - "description" : "Unique ID for this person", + "description" : "Search for Planned Cross with this unique id", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "userID", + "name" : "plannedCrossName", "in" : "query", - "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "$ref" : "#/components/parameters/externalReferenceId" - }, - { - "$ref" : "#/components/parameters/externalReferenceID" - }, - { - "$ref" : "#/components/parameters/externalReferenceSource" - }, - { - "$ref" : "#/components/parameters/page" - }, - { - "$ref" : "#/components/parameters/pageSize" - }, - { - "$ref" : "#/components/parameters/authorizationHeader" - } - ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/PersonListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - }, - "post" : { - "tags" : [ - "People" - ], - "summary" : "Create new Person", - "description" : "Add new Person to database", - "parameters" : [ - { - "$ref" : "#/components/parameters/authorizationHeader" - } - ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/PersonNewRequest" - } - } - } - } - }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/PersonListResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/plannedcrosses" : { - "get" : { - "tags" : [ - "Crosses" - ], - "summary" : "Get a filtered list of PlannedCross", - "description" : "Get a list of PlannedCross", - "parameters" : [ - { - "name" : "commonCropName", - "in" : "query", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "programDbId", - "in" : "query", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "crossingProjectDbId", - "in" : "query", - "description" : "Search for Crossing Projects with this unique id", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "crossingProjectName", - "in" : "query", - "description" : "The human readable name for a crossing project", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "plannedCrossDbId", - "in" : "query", - "description" : "Search for Planned Cross with this unique id", - "required" : false, - "schema" : { - "type" : "string" - } - }, - { - "name" : "plannedCrossName", - "in" : "query", - "description" : "Search for Planned Cross with this human readable name", + "description" : "Search for Planned Cross with this human readable name", "required" : false, "schema" : { "type" : "string" @@ -3760,6 +3606,48 @@ } } }, + "put" : { + "tags" : [ + "Plates" + ], + "summary" : "Update the details for an existing Plate", + "description" : "Update the details for an existing Plate", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "additionalProperties" : { + "$ref" : "#/components/schemas/PlateNewRequest" + }, + "example" : "{_1={additionalInfo={}, externalReferences=[{}], plateBarcode=4eacf0b7, plateDbId=71ea8b72, plateFormat={}, plateName=72778960, program={}, sampleType={}, study={}, trial={}, samples=[{}]}, _2={additionalInfo={}, externalReferences=[{}], plateBarcode=4eacf0b8, plateDbId=71ea8b73, plateFormat={}, plateName=72778961, program={}, sampleType={}, study={}, trial={}, samples=[{}]}}" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + }, "post" : { "tags" : [ "Plates" @@ -4367,6 +4255,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } }, @@ -4788,13 +4679,13 @@ } } }, - "/studies" : { + "/seedlots/transactions" : { "get" : { "tags" : [ - "Studies" + "Seed Lots" ], - "summary" : "Get a filtered list of Study", - "description" : "Get a list of Study", + "summary" : "Get a filtered list of SeedLotTransaction", + "description" : "Get a list of SeedLotTransaction", "parameters" : [ { "name" : "commonCropName", @@ -4815,9 +4706,9 @@ } }, { - "name" : "locationDbId", + "name" : "germplasmName", "in" : "query", - "description" : "The location ids to search for", + "description" : "List of human readable names to identify germplasm to search for", "required" : false, "schema" : { "type" : "string" @@ -4833,111 +4724,264 @@ } }, { - "name" : "studyDbId", + "name" : "seedLotDbId", "in" : "query", - "description" : "List of study identifiers to search for", + "description" : "Unique id for a seed lot on this server", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "studyName", + "name" : "crossDbId", "in" : "query", - "description" : "List of study names to filter search results", + "description" : "Search for Cross with this unique id", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "trialDbId", + "name" : "crossName", "in" : "query", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "Search for Cross with this human readable name", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "observationVariableDbId", + "name" : "transactionDbId", "in" : "query", - "description" : "The DbIds of Variables to search for", + "description" : "Unique id for a Transaction that has occurred", "required" : false, "schema" : { "type" : "string" } }, { - "name" : "active", - "in" : "query", - "description" : "A flag to indicate if a Study is currently active and ongoing", - "required" : false, - "schema" : { - "type" : "boolean" - } - }, - { - "name" : "seasonDbId", - "in" : "query", - "description" : "The ID which uniquely identifies a season", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/externalReferenceId" }, { - "name" : "studyType", - "in" : "query", - "description" : "The type of study being performed. ex. \"Yield Trial\", etc", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/externalReferenceID" }, { - "name" : "studyCode", - "in" : "query", - "description" : "A short human readable code for a study", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/externalReferenceSource" }, { - "name" : "studyPUI", - "in" : "query", - "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", - "required" : false, - "schema" : { - "type" : "string" - } + "$ref" : "#/components/parameters/page" }, { - "name" : "sortBy", - "in" : "query", - "description" : "Name of the field to sort by.", - "required" : false, - "schema" : { - "type" : "string", - "description" : "Name of the field to sort by.", - "enum" : [ - "studyDbId", - "trialDbId", - "programDbId", - "locationDbId", - "seasonDbId", - "studyType", - "studyName", - "studyLocation", - "programName", - "germplasmDbId", - "observationVariableDbId" - ] - } + "$ref" : "#/components/parameters/pageSize" }, { - "name" : "sortOrder", + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotTransactionListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ + "Seed Lots" + ], + "summary" : "Create new SeedLotTransaction", + "description" : "Add new SeedLotTransaction to database", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/SeedLotTransactionNewRequest" + } + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotTransactionListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/studies" : { + "get" : { + "tags" : [ + "Studies" + ], + "summary" : "Get a filtered list of Study", + "description" : "Get a list of Study", + "parameters" : [ + { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "active", + "in" : "query", + "description" : "A flag to indicate if a Study is currently active and ongoing", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, + { + "name" : "seasonDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a season", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyType", + "in" : "query", + "description" : "The type of study being performed. ex. \"Yield Trial\", etc", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyCode", + "in" : "query", + "description" : "A short human readable code for a study", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyPUI", + "in" : "query", + "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "sortBy", + "in" : "query", + "description" : "Name of the field to sort by.", + "required" : false, + "schema" : { + "type" : "string", + "description" : "Name of the field to sort by.", + "enum" : [ + "studyDbId", + "trialDbId", + "programDbId", + "locationDbId", + "seasonDbId", + "studyType", + "studyName", + "studyLocation", + "programName", + "germplasmDbId", + "observationVariableDbId" + ] + } + }, + { + "name" : "sortOrder", "in" : "query", "description" : "Sort order direction. Ascending/Descending.", "required" : false, @@ -5608,13 +5652,13 @@ } } }, - "/studytypes" : { + "/commoncropnames" : { "get" : { "tags" : [ - "Studies" + "Programs" ], - "summary" : "Get the studyTypes of Study", - "description" : "List all available Study studyTypes", + "summary" : "Get the commonCropNames of Program", + "description" : "List all available Program commonCropNames", "parameters" : [ { "$ref" : "#/components/parameters/page" @@ -5628,7 +5672,7 @@ ], "responses" : { "200" : { - "$ref" : "#/components/responses/StudyStudyTypeListResponse" + "$ref" : "#/components/responses/ProgramCommonCropNameListResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -5642,30 +5686,54 @@ } } }, - "/breedingmethods/{breedingMethodDbId}" : { + "/observationlevels" : { "get" : { "tags" : [ - "Germplasm" + "Studies" ], - "summary" : "Get the details of a specific BreedingMethod", - "description" : "Get details for a BreedingMethod", + "summary" : "Get the observationLevelses of Study", + "description" : "List all available Study observationLevelses", "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } }, { - "name" : "breedingMethodDbId", - "in" : "path", - "description" : "the unique identifier for this breeding method", - "required" : true, + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, "schema" : { "type" : "string" } + }, + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" } ], "responses" : { "200" : { - "$ref" : "#/components/responses/BreedingMethodSingleResponse" + "$ref" : "#/components/responses/StudyObservationLevelsListResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -5675,17 +5743,88 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" - }, - "404" : { - "$ref" : "#/components/responses/404NotFound" } } } }, - "/callsets/{callSetDbId}" : { + "/studytypes" : { "get" : { "tags" : [ - "CallSets" + "Studies" + ], + "summary" : "Get the studyTypes of Study", + "description" : "List all available Study studyTypes", + "parameters" : [ + { + "$ref" : "#/components/parameters/page" + }, + { + "$ref" : "#/components/parameters/pageSize" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudyStudyTypeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/breedingmethods/{breedingMethodDbId}" : { + "get" : { + "tags" : [ + "Germplasm" + ], + "summary" : "Get the details of a specific BreedingMethod", + "description" : "Get details for a BreedingMethod", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "breedingMethodDbId", + "in" : "path", + "description" : "the unique identifier for this breeding method", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/BreedingMethodSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/callsets/{callSetDbId}" : { + "get" : { + "tags" : [ + "CallSets" ], "summary" : "Get the details of a specific CallSet", "description" : "Get details for a CallSet", @@ -5792,9 +5931,6 @@ "200" : { "$ref" : "#/components/responses/CallListResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -5803,6 +5939,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -5965,9 +6104,6 @@ "200" : { "$ref" : "#/components/responses/LinkageGroupListResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -5976,6 +6112,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -6368,6 +6507,56 @@ } } }, + "/images/{imageDbId}/imagecontent" : { + "put" : { + "tags" : [ + "Images" + ], + "summary" : "Update the details for an existing string", + "description" : "Update the details for an existing string", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + }, + { + "name" : "imageDbId", + "in" : "path", + "description" : "The unique identifier of an image", + "required" : true, + "schema" : { + "type" : "string" + } + } + ], + "requestBody" : { + "content" : { + "image/*" : { + "schema" : { + "type" : "string", + "format" : "binary" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, "/lists/{listDbId}" : { "get" : { "tags" : [ @@ -6716,32 +6905,39 @@ "$ref" : "#/components/responses/404NotFound" } } - } - }, - "/observationunits/{observationUnitDbId}" : { - "get" : { + }, + "put" : { "tags" : [ - "ObservationUnits" + "Observations" ], - "summary" : "Get the details of a specific ObservationUnit", - "description" : "Get details for a ObservationUnit", + "summary" : "Update the details for an existing Observation", + "description" : "Update the details for an existing Observation", "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" }, { - "name" : "observationUnitDbId", + "name" : "observationDbId", "in" : "path", - "description" : "The ID which uniquely identifies an observation unit\n\nMIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. ", + "description" : "The ID which uniquely identifies an observation", "required" : true, "schema" : { "type" : "string" } } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/ObservationNewRequest" + } + } + } + }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationUnitSingleResponse" + "$ref" : "#/components/responses/ObservationSingleResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -6758,21 +6954,21 @@ } } }, - "/variables/{observationVariableDbId}" : { + "/observationunits/{observationUnitDbId}" : { "get" : { "tags" : [ - "ObservationVariables" + "ObservationUnits" ], - "summary" : "Get the details of a specific ObservationVariable", - "description" : "Get details for a ObservationVariable", + "summary" : "Get the details of a specific ObservationUnit", + "description" : "Get details for a ObservationUnit", "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" }, { - "name" : "observationVariableDbId", + "name" : "observationUnitDbId", "in" : "path", - "description" : "Variable unique identifier\n\nMIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation.", + "description" : "The ID which uniquely identifies an observation unit\n\nMIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. ", "required" : true, "schema" : { "type" : "string" @@ -6781,7 +6977,7 @@ ], "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationVariableSingleResponse" + "$ref" : "#/components/responses/ObservationUnitSingleResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -6799,18 +6995,18 @@ }, "put" : { "tags" : [ - "ObservationVariables" + "ObservationUnits" ], - "summary" : "Update the details for an existing ObservationVariable", - "description" : "Update the details for an existing ObservationVariable", + "summary" : "Update the details for an existing ObservationUnit", + "description" : "Update the details for an existing ObservationUnit", "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" }, { - "name" : "observationVariableDbId", + "name" : "observationUnitDbId", "in" : "path", - "description" : "Variable unique identifier\n\nMIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation.", + "description" : "The ID which uniquely identifies an observation unit\n\nMIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. ", "required" : true, "schema" : { "type" : "string" @@ -6821,14 +7017,14 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/ObservationVariableNewRequest" + "$ref" : "#/components/schemas/ObservationUnitNewRequest" } } } }, "responses" : { "200" : { - "$ref" : "#/components/responses/ObservationVariableSingleResponse" + "$ref" : "#/components/responses/ObservationUnitSingleResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -7613,6 +7809,15 @@ "type" : "string" } }, + { + "name" : "transactionDbId", + "in" : "query", + "description" : "Unique id for a Transaction that has occurred", + "required" : false, + "schema" : { + "type" : "string" + } + }, { "name" : "transactionDirection", "in" : "query", @@ -7642,9 +7847,6 @@ "200" : { "$ref" : "#/components/responses/SeedLotTransactionListResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -7653,6 +7855,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -8028,9 +8233,6 @@ "200" : { "$ref" : "#/components/responses/CallListResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -8039,6 +8241,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -8153,9 +8358,6 @@ "200" : { "$ref" : "#/components/responses/CallListResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -8164,6 +8366,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -8217,9 +8422,6 @@ "200" : { "$ref" : "#/components/responses/CallSetListResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -8228,6 +8430,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -8275,9 +8480,6 @@ "200" : { "$ref" : "#/components/responses/VariantListResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -8286,17 +8488,20 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } }, - "/search/allelematrix" : { + "/delete/images" : { "post" : { "tags" : [ - "AlleleMatrix" + "Images" ], - "summary" : "Submit a search request for `AlleleMatrix`", - "description" : "Submit a search request for `AlleleMatrix`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "summary" : "Submit a delete request for `Images`", + "description" : "Submit a delete request for `Images`", "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" @@ -8306,17 +8511,14 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/AlleleMatrixSearchRequest" + "$ref" : "#/components/schemas/ImageSearchRequest" } } } }, "responses" : { "200" : { - "$ref" : "#/components/responses/AlleleMatrixSingleResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "$ref" : "#/components/responses/ImageDeleteResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -8330,13 +8532,13 @@ } } }, - "/search/calls" : { + "/delete/observations" : { "post" : { "tags" : [ - "Calls" + "Observations" ], - "summary" : "Submit a search request for `Call`", - "description" : "Submit a search request for `Call`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "summary" : "Submit a delete request for `Observations`", + "description" : "Submit a delete request for `Observations`", "parameters" : [ { "$ref" : "#/components/parameters/authorizationHeader" @@ -8346,17 +8548,14 @@ "content" : { "application/json" : { "schema" : { - "$ref" : "#/components/schemas/CallSearchRequest" + "$ref" : "#/components/schemas/ObservationSearchRequest" } } } }, "responses" : { "200" : { - "$ref" : "#/components/responses/CallListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" + "$ref" : "#/components/responses/ObservationDeleteResponse" }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -8370,27 +8569,477 @@ } } }, - "/search/callsets" : { - "post" : { + "/observations/table" : { + "get" : { "tags" : [ - "CallSets" + "Observations" ], - "summary" : "Submit a search request for `CallSet`", - "description" : "Submit a search request for `CallSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "summary" : "Get a table of `Observation` records as a CSV file.", + "description" : "Get a table of `Observation` records returned directly as CSV text.", "parameters" : [ { - "$ref" : "#/components/parameters/authorizationHeader" - } - ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/CallSetSearchRequest" - } + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" } - } - }, + }, + { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The unique id of an Observation Unit", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationLevel", + "in" : "query", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelName", + "in" : "query", + "description" : "The Observation Unit Level. Returns only the observation unit of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelOrder", + "in" : "query", + "description" : "The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelCode", + "in" : "query", + "description" : "The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelRelationshipName", + "in" : "query", + "description" : "The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. \n
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. \n
Use this parameter to identify groups of observation units that share a relationship level. \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelRelationshipOrder", + "in" : "query", + "description" : "The Observation Unit Level Order Number. \n
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelRelationshipCode", + "in" : "query", + "description" : "The Observation Unit Level Code. \n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelRelationshipDbId", + "in" : "query", + "description" : "The observationUnitDbId associated with a particular level and code.\n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationTimeStampRangeEnd", + "in" : "query", + "description" : "Timestamp range end", + "required" : false, + "schema" : { + "type" : "string", + "format" : "date-time" + } + }, + { + "name" : "observationTimeStampRangeStart", + "in" : "query", + "description" : "Timestamp range start", + "required" : false, + "schema" : { + "type" : "string", + "format" : "date-time" + } + }, + { + "name" : "seasonDbId", + "in" : "query", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/acceptHeader" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationTableResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/observationunits/table" : { + "get" : { + "tags" : [ + "ObservationUnits" + ], + "summary" : "Get a table of `ObservationUnit` records as a CSV file.", + "description" : "Get a table of `ObservationUnit` records returned directly as CSV text.", + "parameters" : [ + { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The unique id of an observation unit", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationLevel", + "in" : "query", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelName", + "in" : "query", + "description" : "The Observation Unit Level. Returns only the observation unit of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelOrder", + "in" : "query", + "description" : "The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelCode", + "in" : "query", + "description" : "The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelRelationshipName", + "in" : "query", + "description" : "The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. \n
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. \n
Use this parameter to identify groups of observation units that share a relationship level. \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelRelationshipOrder", + "in" : "query", + "description" : "The Observation Unit Level Order Number. \n
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelRelationshipCode", + "in" : "query", + "description" : "The Observation Unit Level Code. \n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "observationUnitLevelRelationshipDbId", + "in" : "query", + "description" : "The observationUnitDbId associated with a particular level and code.\n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "name" : "seasonDbId", + "in" : "query", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "required" : false, + "schema" : { + "type" : "string" + } + }, + { + "$ref" : "#/components/parameters/acceptHeader" + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitTableResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/allelematrix" : { + "post" : { + "tags" : [ + "AlleleMatrix" + ], + "summary" : "Submit a search request for `AlleleMatrix`", + "description" : "Submit a search request for `AlleleMatrix`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/alleleMatrix/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/AlleleMatrixSearchRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/AlleleMatrixSingleResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/calls" : { + "post" : { + "tags" : [ + "Calls" + ], + "summary" : "Submit a search request for `Call`", + "description" : "Submit a search request for `Call`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallSearchRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/callsets" : { + "post" : { + "tags" : [ + "CallSets" + ], + "summary" : "Submit a search request for `CallSet`", + "description" : "Submit a search request for `CallSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/CallSetSearchRequest" + } + } + } + }, "responses" : { "200" : { "$ref" : "#/components/responses/CallSetListResponse" @@ -8770,46 +9419,6 @@ } } }, - "/search/variables" : { - "post" : { - "tags" : [ - "ObservationVariables" - ], - "summary" : "Submit a search request for `ObservationVariable`", - "description" : "Submit a search request for `ObservationVariable`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "parameters" : [ - { - "$ref" : "#/components/parameters/authorizationHeader" - } - ], - "requestBody" : { - "content" : { - "application/json" : { - "schema" : { - "$ref" : "#/components/schemas/ObservationVariableSearchRequest" - } - } - } - }, - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, "/search/pedigree" : { "post" : { "tags" : [ @@ -9278,9 +9887,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9289,6 +9895,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9330,9 +9939,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9341,6 +9947,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9379,9 +9988,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9390,6 +9996,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9428,9 +10037,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9439,6 +10045,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9477,9 +10086,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9488,6 +10094,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9526,9 +10135,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9537,6 +10143,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9575,9 +10184,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9586,6 +10192,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9624,9 +10233,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9635,6 +10241,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9673,9 +10282,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9684,6 +10290,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9722,9 +10331,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9733,6 +10339,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9771,9 +10380,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9782,6 +10388,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9820,9 +10429,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9831,55 +10437,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" - } - } - } - }, - "/search/variables/{searchResultsDbId}" : { - "get" : { - "tags" : [ - "ObservationVariables" - ], - "summary" : "Submit a search request for `ObservationVariable`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "description" : "Get the results of a `ObservationVariable` search request
\nClients should submit a search request using the corresponding `POST /search/observationVariable` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", - "parameters" : [ - { - "name" : "searchResultsDbId", - "in" : "path", - "description" : "searchResultsDbId", - "required" : true, - "schema" : { - "type" : "string" - } - }, - { - "$ref" : "#/components/parameters/page" - }, - { - "$ref" : "#/components/parameters/pageSize" - }, - { - "$ref" : "#/components/parameters/authorizationHeader" - } - ], - "responses" : { - "200" : { - "$ref" : "#/components/responses/ObservationVariableListResponse" - }, - "202" : { - "$ref" : "#/components/responses/202AcceptedSearchResponse" }, "404" : { "$ref" : "#/components/responses/404NotFound" - }, - "400" : { - "$ref" : "#/components/responses/400BadRequest" - }, - "401" : { - "$ref" : "#/components/responses/401Unauthorized" - }, - "403" : { - "$ref" : "#/components/responses/403Forbidden" } } } @@ -9918,9 +10478,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9929,6 +10486,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -9967,9 +10527,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -9978,6 +10535,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -10016,9 +10576,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -10027,6 +10584,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -10065,9 +10625,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -10076,6 +10633,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -10114,9 +10674,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -10125,6 +10682,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -10163,9 +10723,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -10174,6 +10731,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -10212,9 +10772,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -10223,6 +10780,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -10261,9 +10821,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -10272,6 +10829,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -10310,9 +10870,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -10321,6 +10878,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -10362,9 +10922,6 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, - "404" : { - "$ref" : "#/components/responses/404NotFound" - }, "400" : { "$ref" : "#/components/responses/400BadRequest" }, @@ -10373,6 +10930,9 @@ }, "403" : { "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" } } } @@ -10411,8 +10971,122 @@ "202" : { "$ref" : "#/components/responses/202AcceptedSearchResponse" }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, + "404" : { + "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/variantsets/extract" : { + "post" : { + "tags" : [ + "VariantSets" + ], + "summary" : "Perform `extract` on `VariantSet`", + "description" : "Perform the `extract` action on `VariantSet`.", + "parameters" : [ + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "$ref" : "#/components/schemas/VariantSetsExtractRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + }, "404" : { "$ref" : "#/components/responses/404NotFound" + } + } + } + }, + "/serverinfo" : { + "get" : { + "tags" : [ + "Server Info" + ], + "summary" : "Get the list of implemented Calls", + "description" : "Implementation Notes\n\nHaving a consistent structure for the path string of each call is very \nimportant for teams to be able to connect and find errors. Read more on Github.\n\nHere are the rules for the path of each call that should be returned\n\nEvery word in the call path should match the documentation exactly, both in \nspelling and capitalization. Note that path strings are all lower case, but \npath parameters are camel case.\n\nEach path should start relative to \\\"/\\\" and therefore should not include \\\"/\\\"\n\nNo leading or trailing slashes (\\\"/\\\") \n\nPath parameters are wrapped in curly braces (\\\"{}\\\"). The name of the path parameter \nshould be spelled exactly as it is specified in the documentation.\n\nExamples \n\nGOOD \"call\": \"germplasm/{germplasmDbId}/pedigree\" \n\nBAD \"call\": \"germplasm/{id}/pedigree\"\n\nBAD \"call\": \"germplasm/{germplasmDBid}/pedigree\" \n\nBAD \"call\": \"brapi/v2/germplasm/{germplasmDbId}/pedigree\" \n\nBAD \"call\": \"/germplasm/{germplasmDbId}/pedigree/\" \n\nBAD \"call\": \"germplasm//pedigree\"", + "parameters" : [ + { + "name" : "contentType", + "in" : "query", + "description" : "Filter the list of endpoints based on the response content type.", + "required" : false, + "style" : "form", + "explode" : true, + "schema" : { + "$ref" : "#/components/schemas/ContentTypes" + } + }, + { + "name" : "dataType", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `contentType`. Github issue number #443\n
The data format supported by the call.", + "required" : false, + "deprecated" : true, + "style" : "form", + "explode" : true, + "schema" : { + "$ref" : "#/components/schemas/ContentTypes" + } + }, + { + "$ref" : "#/components/parameters/authorizationHeader" + } + ], + "responses" : { + "200" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ServerInfoResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ServerInfo" + } + } + } + } + } }, "400" : { "$ref" : "#/components/responses/400BadRequest" @@ -10570,16 +11244,20 @@ } }, "dataMatrixAbbreviations" : { - "type" : "string", - "description" : "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "type" : "array", + "description" : "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", "nullable" : true, - "example" : "GT,RD" + "items" : { + "type" : "string" + } }, "dataMatrixNames" : { - "type" : "string", - "description" : "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "type" : "array", + "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", "nullable" : true, - "example" : "Genotype,Read Depth" + "items" : { + "type" : "string" + } }, "dimensionCallSetPage" : { "type" : "integer", @@ -10735,16 +11413,20 @@ } }, "dataMatrixAbbreviations" : { - "type" : "string", - "description" : "`dataMatrixAbbreviations` is a comma separated list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", + "type" : "array", + "description" : "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT', 'RD' etc). This list controls which data matrices are returned in the response.", "nullable" : true, - "example" : "GT,RD" + "items" : { + "type" : "string" + } }, "dataMatrixNames" : { - "type" : "string", - "description" : "`dataMatrixNames` is a comma separated list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", + "type" : "array", + "description" : "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read Depth' etc). This list controls which data matrices are returned in the response.", "nullable" : true, - "example" : "Genotype,Read Depth" + "items" : { + "type" : "string" + } }, "expandHomozygotes" : { "type" : "boolean", @@ -10999,12 +11681,10 @@ "$ref" : "#/components/schemas/Method" }, "ontologyReference" : { - "anyOf" : [ + "nullable" : true, + "allOf" : [ { "$ref" : "#/components/schemas/OntologyReference" - }, - { - "type" : "null" } ] }, @@ -12967,7 +13647,9 @@ }, "GeoJSONGeometry" : { "type" : "object", - "nullable" : true, + "discriminator" : { + "propertyName" : "type" + }, "oneOf" : [ { "required" : [ @@ -13205,12 +13887,10 @@ "$ref" : "#/components/schemas/Method" }, "ontologyReference" : { - "anyOf" : [ + "nullable" : true, + "allOf" : [ { "$ref" : "#/components/schemas/OntologyReference" - }, - { - "type" : "null" } ] }, @@ -15015,6 +15695,30 @@ "description" : "Short description of the facility in which the study was carried out.", "nullable" : true }, + "HeaderRow" : { + "type" : "string", + "description" : "valid header fields", + "enum" : [ + "observationTimeStamp", + "observationUnitDbId", + "observationUnitName", + "studyDbId", + "studyName", + "germplasmDbId", + "germplasmName", + "positionCoordinateX", + "positionCoordinateY", + "year", + "field", + "plot", + "sub-plot", + "plant", + "pot", + "block", + "entry", + "rep" + ] + }, "Image" : { "allOf" : [ { @@ -15109,10 +15813,19 @@ "nullable" : true }, "mimeType" : { + "pattern" : "image/.*", "type" : "string", "description" : "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc", "nullable" : true }, + "observationDbIds" : { + "type" : "array", + "description" : "A list of observation Ids this image is associated with, if applicable.", + "nullable" : true, + "items" : { + "type" : "string" + } + }, "observationUnitDbId" : { "type" : "string", "nullable" : true @@ -15641,7 +16354,12 @@ } }, "listType" : { - "$ref" : "#/components/schemas/ListType" + "nullable" : true, + "allOf" : [ + { + "$ref" : "#/components/schemas/ListType" + } + ] }, "programDbIds" : { "type" : "array", @@ -15756,7 +16474,12 @@ } }, "listType" : { - "$ref" : "#/components/schemas/ListType" + "nullable" : true, + "allOf" : [ + { + "$ref" : "#/components/schemas/ListType" + } + ] }, "page" : { "type" : "integer", @@ -16614,21 +17337,19 @@ "type" : "string", "nullable" : true }, - "observationVariableDbId" : { - "type" : "string", - "nullable" : true - }, - "observationVariableName" : { - "type" : "string", - "nullable" : true + "observationVariable" : { + "nullable" : true, + "allOf" : [ + { + "$ref" : "#/components/schemas/ObservationVariable" + } + ] }, "season" : { - "anyOf" : [ + "nullable" : true, + "allOf" : [ { "$ref" : "#/components/schemas/Season" - }, - { - "type" : "null" } ] }, @@ -17047,6 +17768,68 @@ }, "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit." }, + "ObservationTable" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "description" : "The 2D matrix of observation data. ObservationVariables and other metadata are the columns, ObservationUnits are the rows.", + "items" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "headerRow" : { + "type" : "array", + "description" : "

The table is REQUIRED to have the following columns

\n
    \n
  • observationUnitDbId - Each row is related to one Observation Unit
    • \n
  • observationTimeStamp - Each row is has a time stamp for when the observation was taken
    • \n
  • At least one column with an observationVariableDbId
    • \n
\n

The table may have any or all of the following OPTIONAL columns. Included columns are decided by the server developer

\n
    \n
  • observationUnitName
    • \n
  • studyDbId
    • \n
  • studyName
    • \n
  • germplasmDbId
    • \n
  • germplasmName
    • \n
  • positionCoordinateX
    • \n
  • positionCoordinateY
    • \n
  • year
    • \n
\n

The table also may have any number of Observation Unit Hierarchy Level columns. For example:

\n
    \n
  • field
    • \n
  • plot
    • \n
  • sub-plot
    • \n
  • plant
    • \n
  • pot
    • \n
  • block
    • \n
  • entry
    • \n
  • rep
    • \n
\n

The JSON representation provides a pair of extra arrays for defining the headers of the table. \nThe first array \"headerRow\" will always contain \"observationUnitDbId\" and any or all of the OPTIONAL column header names. \nThe second array \"observationVariables\" contains the names and DbIds for the Observation Variables represented in the table. \nBy appending the two arrays, you can construct the complete header row of the table.

", + "items" : { + "type" : "string", + "description" : "valid header fields", + "enum" : [ + "observationTimeStamp", + "observationUnitDbId", + "observationUnitName", + "studyDbId", + "studyName", + "germplasmDbId", + "germplasmName", + "positionCoordinateX", + "positionCoordinateY", + "year", + "field", + "plot", + "sub-plot", + "plant", + "pot", + "block", + "entry", + "rep" + ] + } + }, + "observationVariables" : { + "type" : "array", + "description" : "The list of observation variables which have values recorded for them in the data matrix. Append to the 'headerRow' for complete header row of the table.", + "items" : { + "type" : "object", + "properties" : { + "observationVariableDbId" : { + "type" : "string", + "description" : "Variable unique identifier", + "example" : "367aa1a9" + }, + "observationVariableName" : { + "type" : "string", + "description" : "Variable name (usually a short name)", + "example" : "Plant height" + } + } + } + } + } + }, "ObservationTreatment" : { "type" : "object", "properties" : { @@ -17094,14 +17877,61 @@ "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", "nullable" : true }, - "levelOrder" : { - "type" : "integer", - "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "format" : "int32", - "nullable" : true + "levelOrder" : { + "type" : "integer", + "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "format" : "int32", + "nullable" : true + } + }, + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" " + }, + "ObservationUnitHierarchyLevelRequest" : { + "type" : "object", + "properties" : { + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } } - }, - "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" " + } }, "ObservationUnitLevel" : { "type" : "object", @@ -17260,259 +18090,50 @@ ] }, "geoCoordinates" : { - "type" : "array", - "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", - "nullable" : true, - "items" : { - "$ref" : "#/components/schemas/GeoJSON" - } - }, - "observationLevel" : { - "$ref" : "#/components/schemas/ObservationUnitLevel" - }, - "observationLevelRelationships" : { - "type" : "array", - "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", - "nullable" : true, - "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" - } - }, - "positionCoordinateX" : { - "type" : "string", - "description" : "The X position coordinate for an observation unit. Different systems may use different coordinate systems.", - "nullable" : true - }, - "positionCoordinateXType" : { - "anyOf" : [ - { - "$ref" : "#/components/schemas/PositionCoordinateType" - }, - { - "type" : "null" - } - ] - }, - "positionCoordinateY" : { - "type" : "string", - "description" : "The Y position coordinate for an observation unit. Different systems may use different coordinate systems.", - "nullable" : true - }, - "positionCoordinateYType" : { - "anyOf" : [ - { - "$ref" : "#/components/schemas/PositionCoordinateType" - }, - { - "type" : "null" - } - ] - } - }, - "description" : "All positional and layout information related to this Observation Unit", - "nullable" : true - }, - "ObservationUnitRequest" : { - "type" : "object", - "properties" : { - "commonCropNames" : { - "type" : "array", - "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", - "items" : { - "type" : "string" - } - }, - "germplasmDbIds" : { - "type" : "array", - "description" : "List of IDs which uniquely identify germplasm to search for", - "nullable" : true, - "items" : { - "type" : "string" - } - }, - "germplasmNames" : { - "type" : "array", - "description" : "List of human readable names to identify germplasm to search for", - "nullable" : true, - "items" : { - "type" : "string" - } - }, - "includeObservations" : { - "type" : "boolean", - "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", - "nullable" : true, - "example" : false - }, - "locationDbIds" : { - "type" : "array", - "description" : "The location ids to search for", - "items" : { - "type" : "string" - } - }, - "locationNames" : { - "type" : "array", - "description" : "A human readable names to search for", - "items" : { - "type" : "string" - } - }, - "observationLevelRelationships" : { - "type" : "array", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", - "nullable" : true, - "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" - } - }, - "observationLevels" : { - "type" : "array", - "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", - "nullable" : true, - "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevel" - } - }, - "observationUnitDbIds" : { - "type" : "array", - "description" : "The unique id of an observation unit", - "nullable" : true, - "items" : { - "type" : "string" - } - }, - "observationUnitLevelCodes" : { - "type" : "array", - "description" : "The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", - "items" : { - "type" : "string" - } - }, - "observationUnitLevelNames" : { - "type" : "array", - "description" : "The Observation Unit Level. Returns only the observation unit of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", - "items" : { - "type" : "string" - } - }, - "observationUnitLevelOrders" : { - "type" : "array", - "description" : "The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", - "items" : { - "type" : "string" - } - }, - "observationUnitLevelRelationshipCodes" : { - "type" : "array", - "description" : "The Observation Unit Level Code. \n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", - "items" : { - "type" : "string" - } - }, - "observationUnitLevelRelationshipDbIds" : { - "type" : "array", - "description" : "The observationUnitDbId associated with a particular level and code.\n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId \n
For more information on Observation Levels, please review the Observation Levels documentation. ", - "items" : { - "type" : "string" - } - }, - "observationUnitLevelRelationshipNames" : { - "type" : "array", - "description" : "The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. \n
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. \n
Use this parameter to identify groups of observation units that share a relationship level. \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", - "items" : { - "type" : "string" - } - }, - "observationUnitLevelRelationshipOrders" : { - "type" : "array", - "description" : "The Observation Unit Level Order Number. \n
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", - "items" : { - "type" : "string" - } - }, - "observationUnitNames" : { - "type" : "array", - "description" : "The human readable identifier for an Observation Unit", - "nullable" : true, - "items" : { - "type" : "string" - } - }, - "observationVariableDbIds" : { - "type" : "array", - "description" : "The DbIds of Variables to search for", - "items" : { - "type" : "string" - } - }, - "observationVariableNames" : { - "type" : "array", - "description" : "The names of Variables to search for", - "items" : { - "type" : "string" - } - }, - "observationVariablePUIs" : { - "type" : "array", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "items" : { - "type" : "string" - } - }, - "programDbIds" : { - "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "items" : { - "type" : "string" - } - }, - "programNames" : { - "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "items" : { - "type" : "string" - } - }, - "seasonDbIds" : { - "type" : "array", - "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", - "nullable" : true, - "items" : { - "type" : "string" - } + "$ref" : "#/components/schemas/GeoJSON" }, - "studyDbIds" : { - "type" : "array", - "description" : "List of study identifiers to search for", - "items" : { - "type" : "string" - } + "observationLevel" : { + "$ref" : "#/components/schemas/ObservationUnitLevel" }, - "studyNames" : { + "observationLevelRelationships" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", + "nullable" : true, "items" : { - "type" : "string" + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" } }, - "trialDbIds" : { - "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", - "items" : { - "type" : "string" - } + "positionCoordinateX" : { + "type" : "string", + "description" : "The X position coordinate for an observation unit. Different systems may use different coordinate systems.", + "nullable" : true }, - "trialNames" : { - "type" : "array", - "description" : "The human readable name of a trial to search for", - "items" : { - "type" : "string" - } + "positionCoordinateXType" : { + "nullable" : true, + "allOf" : [ + { + "$ref" : "#/components/schemas/PositionCoordinateType" + } + ] + }, + "positionCoordinateY" : { + "type" : "string", + "description" : "The Y position coordinate for an observation unit. Different systems may use different coordinate systems.", + "nullable" : true + }, + "positionCoordinateYType" : { + "nullable" : true, + "allOf" : [ + { + "$ref" : "#/components/schemas/PositionCoordinateType" + } + ] } - } + }, + "description" : "All positional and layout information related to this Observation Unit", + "nullable" : true }, - "ObservationUnitSearchRequest" : { + "ObservationUnitRequest" : { "type" : "object", "properties" : { "commonCropNames" : { @@ -17522,28 +18143,6 @@ "type" : "string" } }, - "externalReferenceIDs" : { - "type" : "array", - "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "deprecated" : true, - "items" : { - "type" : "string" - } - }, - "externalReferenceIds" : { - "type" : "array", - "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "items" : { - "type" : "string" - } - }, - "externalReferenceSources" : { - "type" : "array", - "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", - "items" : { - "type" : "string" - } - }, "germplasmDbIds" : { "type" : "array", "description" : "List of IDs which uniquely identify germplasm to search for", @@ -17604,235 +18203,63 @@ "type" : "string" } }, - "observationUnitNames" : { - "type" : "array", - "description" : "The human readable identifier for an Observation Unit", - "nullable" : true, - "items" : { - "type" : "string" - } - }, - "observationVariableDbIds" : { - "type" : "array", - "description" : "The DbIds of Variables to search for", - "items" : { - "type" : "string" - } - }, - "observationVariableNames" : { - "type" : "array", - "description" : "The names of Variables to search for", - "items" : { - "type" : "string" - } - }, - "observationVariablePUIs" : { - "type" : "array", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", - "items" : { - "type" : "string" - } - }, - "page" : { - "type" : "integer", - "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", - "format" : "int32", - "example" : 0 - }, - "pageSize" : { - "type" : "integer", - "description" : "The size of the pages to be returned. Default is `1000`.", - "format" : "int32", - "example" : 1000 - }, - "programDbIds" : { - "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", - "items" : { - "type" : "string" - } - }, - "programNames" : { - "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", - "items" : { - "type" : "string" - } - }, - "seasonDbIds" : { - "type" : "array", - "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", - "nullable" : true, - "items" : { - "type" : "string" - } - }, - "studyDbIds" : { - "type" : "array", - "description" : "List of study identifiers to search for", - "items" : { - "type" : "string" - } - }, - "studyNames" : { + "observationUnitLevelCodes" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "The Observation Unit Level Code. This parameter should be used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "items" : { "type" : "string" } }, - "trialDbIds" : { + "observationUnitLevelNames" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "The Observation Unit Level. Returns only the observation unit of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "items" : { "type" : "string" } }, - "trialNames" : { + "observationUnitLevelOrders" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "The Observation Unit Level Order Number. Returns only the observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "items" : { "type" : "string" } - } - }, - "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." - }, - "ObservationVariable" : { - "allOf" : [ - { - "$ref" : "#/components/schemas/ObservationVariableNewRequest" - }, - { - "required" : [ - "observationVariableDbId" - ], - "type" : "object", - "properties" : { - "observationVariableDbId" : { - "type" : "string", - "description" : "Variable unique identifier\n\nMIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation." - } - } - } - ] - }, - "ObservationVariableNewRequest" : { - "required" : [ - "method", - "observationVariableName", - "scale", - "trait" - ], - "type" : "object", - "properties" : { - "additionalInfo" : { - "$ref" : "#/components/schemas/AdditionalInfo" }, - "commonCropName" : { - "type" : "string", - "description" : "Crop name (examples: \"Maize\", \"Wheat\")", - "nullable" : true - }, - "contextOfUse" : { + "observationUnitLevelRelationshipCodes" : { "type" : "array", - "description" : "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])", - "nullable" : true, + "description" : "The Observation Unit Level Code. \n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->levelCode \n
For more information on Observation Levels, please review the Observation Levels documentation. ", "items" : { "type" : "string" - } - }, - "defaultValue" : { - "type" : "string", - "description" : "Variable default value. (examples: \"red\", \"2.3\", etc.)", - "nullable" : true - }, - "documentationURL" : { - "type" : "string", - "description" : "A URL to the human readable documentation of an object", - "format" : "uri", - "nullable" : true - }, - "externalReferences" : { - "type" : "array", - "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "nullable" : true, - "items" : { - "$ref" : "#/components/schemas/ExternalReference" - } - }, - "growthStage" : { - "type" : "string", - "description" : "Growth stage at which measurement is made (examples: \"flowering\")", - "nullable" : true - }, - "institution" : { - "type" : "string", - "description" : "Name of institution submitting the variable", - "nullable" : true - }, - "language" : { - "type" : "string", - "description" : "2 letter ISO 639-1 code for the language of submission of the variable.", - "nullable" : true - }, - "method" : { - "$ref" : "#/components/schemas/Method" - }, - "observationVariableName" : { - "type" : "string", - "description" : "Variable name (usually a short name)\n\nMIAPPE V1.1 (DM-84) Variable name - Name of the variable." - }, - "observationVariablePUI" : { - "type" : "string", - "description" : "The Permanent Unique Identifier of a Observation Variable, usually in the form of a URI", - "nullable" : true - }, - "ontologyReference" : { - "anyOf" : [ - { - "$ref" : "#/components/schemas/OntologyReference" - }, - { - "type" : "null" - } - ] - }, - "scale" : { - "$ref" : "#/components/schemas/Scale" - }, - "scientist" : { - "type" : "string", - "description" : "Name of scientist submitting the variable.", - "nullable" : true + } }, - "status" : { - "type" : "string", - "description" : "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)", - "nullable" : true + "observationUnitLevelRelationshipDbIds" : { + "type" : "array", + "description" : "The observationUnitDbId associated with a particular level and code.\n
This parameter should be used together with `observationUnitLevelName` or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } }, - "submissionTimestamp" : { - "type" : "string", - "description" : "Timestamp when the Variable was added (ISO 8601)", - "format" : "date-time", - "nullable" : true + "observationUnitLevelRelationshipNames" : { + "type" : "array", + "description" : "The Observation Unit Level Relationship is a connection that this observation unit has to another level of the hierarchy. \n
For example, if you have several observation units at a 'plot' level, they might all share a relationship to the same 'field' level. \n
Use this parameter to identify groups of observation units that share a relationship level. \n
**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } }, - "synonyms" : { + "observationUnitLevelRelationshipOrders" : { "type" : "array", - "description" : "Other variable names", + "description" : "The Observation Unit Level Order Number. \n
Returns only the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder \n
For more information on Observation Levels, please review the Observation Levels documentation. ", + "items" : { + "type" : "string" + } + }, + "observationUnitNames" : { + "type" : "array", + "description" : "The human readable identifier for an Observation Unit", "nullable" : true, "items" : { "type" : "string" } }, - "trait" : { - "$ref" : "#/components/schemas/Trait" - } - } - }, - "ObservationVariableParameters" : { - "type" : "object", - "properties" : { "observationVariableDbIds" : { "type" : "array", "description" : "The DbIds of Variables to search for", @@ -17853,10 +18280,60 @@ "items" : { "type" : "string" } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "seasonDbIds" : { + "type" : "array", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "description" : "The ID which uniquely identifies a trial to search for", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "description" : "The human readable name of a trial to search for", + "items" : { + "type" : "string" + } } } }, - "ObservationVariableRequest" : { + "ObservationUnitSearchRequest" : { "type" : "object", "properties" : { "commonCropNames" : { @@ -17866,192 +18343,285 @@ "type" : "string" } }, - "dataTypes" : { + "externalReferenceIDs" : { "type" : "array", - "description" : "List of scale data types to filter search results", + "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", + "deprecated" : true, "items" : { - "$ref" : "#/components/schemas/TraitDataType" + "type" : "string" } }, - "methodDbIds" : { + "externalReferenceIds" : { "type" : "array", - "description" : "List of methods to filter search results", + "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", "items" : { "type" : "string" } }, - "methodNames" : { + "externalReferenceSources" : { "type" : "array", - "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", "items" : { "type" : "string" } }, - "methodPUIs" : { + "germplasmDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "observationVariableDbIds" : { + "germplasmNames" : { "type" : "array", - "description" : "The DbIds of Variables to search for", + "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, "items" : { "type" : "string" } }, - "observationVariableNames" : { + "includeObservations" : { + "type" : "boolean", + "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", + "nullable" : true, + "example" : false + }, + "locationDbIds" : { "type" : "array", - "description" : "The names of Variables to search for", + "description" : "The location ids to search for", "items" : { "type" : "string" } }, - "observationVariablePUIs" : { + "locationNames" : { "type" : "array", - "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "description" : "A human readable names to search for", "items" : { "type" : "string" } }, - "ontologyDbIds" : { + "observationLevelRelationships" : { "type" : "array", - "description" : "List of ontology IDs to search for", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "nullable" : true, "items" : { - "type" : "string" + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" } }, - "programDbIds" : { + "observationLevels" : { "type" : "array", - "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "nullable" : true, "items" : { - "type" : "string" + "$ref" : "#/components/schemas/ObservationUnitLevel" } }, - "programNames" : { + "observationUnitDbIds" : { "type" : "array", - "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "description" : "The unique id of an observation unit", + "nullable" : true, "items" : { "type" : "string" } }, - "scaleDbIds" : { + "observationUnitNames" : { "type" : "array", - "description" : "The unique identifier for a Scale", + "description" : "The human readable identifier for an Observation Unit", + "nullable" : true, "items" : { "type" : "string" } }, - "scaleNames" : { + "observationVariableDbIds" : { "type" : "array", - "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "description" : "The DbIds of Variables to search for", "items" : { "type" : "string" } }, - "scalePUIs" : { + "observationVariableNames" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "description" : "The names of Variables to search for", "items" : { "type" : "string" } }, - "studyDbId" : { + "observationVariablePUIs" : { "type" : "array", - "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", - "deprecated" : true, + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", "items" : { "type" : "string" } }, - "studyDbIds" : { + "page" : { + "type" : "integer", + "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "format" : "int32", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "description" : "The size of the pages to be returned. Default is `1000`.", + "format" : "int32", + "example" : 1000 + }, + "programDbIds" : { "type" : "array", - "description" : "List of study identifiers to search for", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "studyNames" : { + "programNames" : { "type" : "array", - "description" : "List of study names to filter search results", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", "items" : { "type" : "string" } }, - "traitAttributePUIs" : { + "seasonDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "nullable" : true, "items" : { "type" : "string" } }, - "traitAttributes" : { + "studyDbIds" : { "type" : "array", - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "description" : "List of study identifiers to search for", "items" : { "type" : "string" } }, - "traitClasses" : { + "studyNames" : { "type" : "array", - "description" : "List of trait classes to filter search results", + "description" : "List of study names to filter search results", "items" : { "type" : "string" } }, - "traitDbIds" : { + "trialDbIds" : { "type" : "array", - "description" : "The unique identifier for a Trait", + "description" : "The ID which uniquely identifies a trial to search for", "items" : { "type" : "string" } }, - "traitEntities" : { + "trialNames" : { "type" : "array", - "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "description" : "The human readable name of a trial to search for", "items" : { "type" : "string" } + } + }, + "description" : "A representation of the physical entity being observed during a phenotype data collection process. Typically, this is a Plot or a Plant, but it could include things like Fields, Blocks, or Samples." + }, + "ObservationUnitTable" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "description" : "The 2D matrix of observation data. ObservationVariables and other metadata are the columns, ObservationUnits are the rows.", + "items" : { + "type" : "array", + "items" : { + "type" : "string" + } + } }, - "traitEntityPUIs" : { + "headerRow" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "description" : "

The table is REQUIRED to have the following columns

\n
    \n
  • observationUnitDbId - Each row is related to one Observation Unit
    • \n
  • At least one column with an observationVariableDbId
    • \n
\n

The table may have any or all of the following OPTIONAL columns. Included columns are decided by the server developer

\n
    \n
  • observationUnitName
    • \n
  • studyDbId
    • \n
  • studyName
    • \n
  • germplasmDbId
    • \n
  • germplasmName
    • \n
  • positionCoordinateX
    • \n
  • positionCoordinateY
    • \n
  • year
    • \n
\n

The table also may have any number of Observation Unit Hierarchy Level columns. For example:

\n
    \n
  • field
    • \n
  • plot
    • \n
  • sub-plot
    • \n
  • plant
    • \n
  • pot
    • \n
  • block
    • \n
  • entry
    • \n
  • rep
    • \n
\n

The JSON representation provides a pair of extra arrays for defining the headers of the table. \nThe first array \"headerRow\" will always contain \"observationUnitDbId\" and any or all of the OPTIONAL column header names. \nThe second array \"observationVariables\" contains the names and DbIds for the Observation Variables represented in the table. \nBy appending the two arrays, you can construct the complete header row of the table.

", "items" : { - "type" : "string" + "type" : "string", + "description" : "valid header fields", + "enum" : [ + "observationUnitDbId", + "observationUnitName", + "studyDbId", + "studyName", + "germplasmDbId", + "germplasmName", + "positionCoordinateX", + "positionCoordinateY", + "year", + "field", + "plot", + "sub-plot", + "plant", + "pot", + "block", + "entry", + "rep" + ] } }, - "traitNames" : { + "observationVariables" : { "type" : "array", - "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "description" : "The list of observation variables which have values recorded for them in the data matrix. Append to the 'headerRow' for complete header row of the table.", "items" : { - "type" : "string" + "type" : "object", + "properties" : { + "observationVariableDbId" : { + "type" : "string", + "description" : "Variable unique identifier", + "example" : "367aa1a9" + }, + "observationVariableName" : { + "type" : "string", + "description" : "Variable name (usually a short name)", + "example" : "Plant height" + } + } } + } + } + }, + "ObservationVariable" : { + "type" : "object", + "properties" : { + "observationVariableDbId" : { + "type" : "string", + "description" : "Variable unique identifier", + "example" : "367aa1a9" }, - "traitPUIs" : { + "observationVariableName" : { + "type" : "string", + "description" : "Variable name (usually a short name)", + "example" : "Plant height" + } + } + }, + "ObservationVariableParameters" : { + "type" : "object", + "properties" : { + "observationVariableDbIds" : { "type" : "array", - "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "description" : "The DbIds of Variables to search for", "items" : { "type" : "string" } }, - "trialDbIds" : { + "observationVariableNames" : { "type" : "array", - "description" : "The ID which uniquely identifies a trial to search for", + "description" : "The names of Variables to search for", "items" : { "type" : "string" } }, - "trialNames" : { + "observationVariablePUIs" : { "type" : "array", - "description" : "The human readable name of a trial to search for", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", "items" : { "type" : "string" } } } }, - "ObservationVariableSearchRequest" : { + "ObservationVariableRequest" : { "type" : "object", "properties" : { "commonCropNames" : { @@ -18068,28 +18638,6 @@ "$ref" : "#/components/schemas/TraitDataType" } }, - "externalReferenceIDs" : { - "type" : "array", - "description" : "**Deprecated in v2.1** Please use `externalReferenceIds`. Github issue number #460 \n
List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "deprecated" : true, - "items" : { - "type" : "string" - } - }, - "externalReferenceIds" : { - "type" : "array", - "description" : "List of external reference IDs. Could be a simple strings or a URIs. (use with `externalReferenceSources` parameter)", - "items" : { - "type" : "string" - } - }, - "externalReferenceSources" : { - "type" : "array", - "description" : "List of identifiers for the source system or database of an external reference (use with `externalReferenceIDs` parameter)", - "items" : { - "type" : "string" - } - }, "methodDbIds" : { "type" : "array", "description" : "List of methods to filter search results", @@ -18139,18 +18687,6 @@ "type" : "string" } }, - "page" : { - "type" : "integer", - "description" : "Which result page is requested. The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", - "format" : "int32", - "example" : 0 - }, - "pageSize" : { - "type" : "integer", - "description" : "The size of the pages to be returned. Default is `1000`.", - "format" : "int32", - "example" : 1000 - }, "programDbIds" : { "type" : "array", "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", @@ -21366,12 +21902,10 @@ "nullable" : true }, "validValues" : { - "anyOf" : [ + "nullable" : true, + "allOf" : [ { "$ref" : "#/components/schemas/ValidValues" - }, - { - "type" : "null" } ] } @@ -21652,9 +22186,26 @@ } }, "SeedLotTransaction" : { - "required" : [ - "transactionDbId" - ], + "allOf" : [ + { + "$ref" : "#/components/schemas/SeedLotTransactionNewRequest" + }, + { + "required" : [ + "transactionDbId" + ], + "type" : "object", + "properties" : { + "transactionDbId" : { + "type" : "string", + "description" : "Unique DbId for the Seed Lot Transaction" + } + }, + "description" : "The record of an event where material was moved in or out of a particular SeedLot" + } + ] + }, + "SeedLotTransactionNewRequest" : { "type" : "object", "properties" : { "additionalInfo" : { @@ -21681,10 +22232,6 @@ "type" : "string", "nullable" : true }, - "transactionDbId" : { - "type" : "string", - "description" : "Unique DbId for the Seed Lot Transaction" - }, "transactionDescription" : { "type" : "string", "description" : "A general description of this Seed Lot Transaction", @@ -21707,7 +22254,65 @@ "SeedLotTransactionRequest" : { "type" : "object", "properties" : { - "transactionDbIs" : { + "commonCropNames" : { + "type" : "array", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "items" : { + "type" : "string" + } + }, + "crossDbIds" : { + "type" : "array", + "description" : "Search for Cross with this unique id", + "items" : { + "type" : "string" + } + }, + "crossNames" : { + "type" : "array", + "description" : "Search for Cross with this human readable name", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "description" : "List of IDs which uniquely identify germplasm to search for", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "description" : "List of human readable names to identify germplasm to search for", + "nullable" : true, + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "items" : { + "type" : "string" + } + }, + "seedLotDbIds" : { + "type" : "array", + "description" : "Unique id for a seed lot on this server", + "items" : { + "type" : "string" + } + }, + "transactionDbIds" : { "type" : "array", "description" : "Unique id for a Transaction that has occurred", "items" : { @@ -23123,12 +23728,10 @@ "$ref" : "#/components/schemas/Method" }, "ontologyReference" : { - "anyOf" : [ + "nullable" : true, + "allOf" : [ { "$ref" : "#/components/schemas/OntologyReference" - }, - { - "type" : "null" } ] }, @@ -24046,6 +24649,67 @@ }, "description" : "A VariantSet is a collection of variants and variant calls intended to be analyzed together." }, + "VariantSetsExtractRequest" : { + "type" : "object", + "properties" : { + "callSetDbIds" : { + "type" : "array", + "description" : "The CallSet to search.", + "items" : { + "type" : "string" + } + }, + "expandHomozygotes" : { + "type" : "boolean", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "example" : true + }, + "sepPhased" : { + "type" : "string", + "description" : "The string used as a separator for phased allele calls.", + "example" : "~" + }, + "sepUnphased" : { + "type" : "string", + "description" : "The string used as a separator for unphased allele calls.", + "example" : "|" + }, + "studyDbIds" : { + "type" : "array", + "description" : "List of study identifiers to search for", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "description" : "List of study names to filter search results", + "items" : { + "type" : "string" + } + }, + "unknownString" : { + "type" : "string", + "description" : "The string used as a representation for missing data.", + "example" : "-" + }, + "variantDbIds" : { + "type" : "array", + "description" : "The Variant to search.", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "description" : "The VariantSet to search.", + "items" : { + "type" : "string" + } + } + }, + "description" : "Request object for extracting data subsets as new Variant Sets" + }, "basePagination" : { "required" : [ "currentPage", @@ -24234,35 +24898,128 @@ } } ] - } - }, - "responses" : { - "ObservationVariableSingleResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "title" : "ObservationVariableSingleResponse", - "required" : [ - "metadata", - "result" - ], - "type" : "object", - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "$ref" : "#/components/schemas/ObservationVariable" - } - } + }, + "Service" : { + "required" : [ + "methods", + "service", + "versions" + ], + "type" : "object", + "properties" : { + "service" : { + "type" : "string", + "description" : "The name of the available call as recorded in the documentation", + "example" : "germplasm/{germplasmDbId}/pedigree" + }, + "contentTypes" : { + "type" : "array", + "description" : "The possible content types returned by the service endpoint", + "example" : [ + "application/json" + ], + "items" : { + "$ref" : "#/components/schemas/ContentTypes" + } + }, + "dataTypes" : { + "type" : "array", + "description" : "**Deprecated in v2.1** Please use `contentTypes`. Github issue number #443 \n
The possible data formats returned by the available call ", + "example" : [ + "application/json" + ], + "deprecated" : true, + "items" : { + "$ref" : "#/components/schemas/ContentTypes" + } + }, + "methods" : { + "type" : "array", + "description" : "The possible HTTP Methods to be used with the available call", + "example" : [ + "GET", + "POST" + ], + "items" : { + "type" : "string", + "enum" : [ + "GET", + "POST", + "PUT", + "DELETE" + ] + } + }, + "versions" : { + "type" : "array", + "description" : "The supported versions of a particular call", + "example" : [ + "2.0", + "2.1" + ], + "items" : { + "type" : "string", + "enum" : [ + "2.0", + "2.1", + "2.2" + ] + } + } + } + }, + "ServerInfo" : { + "required" : [ + "calls" + ], + "type" : "object", + "properties" : { + "contactEmail" : { + "type" : "string", + "description" : "A contact email address for this server management", + "example" : "contact@institute.org" + }, + "documentationURL" : { + "type" : "string", + "description" : "A URL to the human readable documentation of an object", + "example" : "institute.org/server" + }, + "organizationURL" : { + "type" : "string", + "description" : "The URL of the organization that manages this server and data", + "example" : "institute.org/home" + }, + "organizationName" : { + "type" : "string", + "description" : "The name of the organization that manages this server and data", + "example" : "The Institute" + }, + "serverName" : { + "type" : "string", + "description" : "The name of this server", + "example" : "The BrAPI Test Server" + }, + "serverDescription" : { + "type" : "string", + "description" : "A description of this server", + "example" : "The BrAPI Test Server\nWeb Server - Apache Tomcat 7.0.32\nDatabase - Postgres 10\nSupported BrAPI Version - V2.0" + }, + "location" : { + "type" : "string", + "description" : "Physical location of this server (ie. City, Country)", + "example" : "USA" + }, + "calls" : { + "type" : "array", + "description" : "Array of available calls on this server", + "items" : { + "$ref" : "#/components/schemas/Service" } } } - }, + } + }, + "responses" : { "SeedLotSingleResponse" : { "description" : "OK", "content" : { @@ -24406,6 +25163,44 @@ } } }, + "ObservationDeleteResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ObservationDeleteResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "observationDbIds" + ], + "type" : "object", + "properties" : { + "observationDbIds" : { + "type" : "array", + "description" : "The unique ids of the Observation records which have been successfully deleted", + "items" : { + "type" : "string" + } + } + } + } + } + } + } + } + }, "MarkerPositionListResponse" : { "description" : "OK", "content" : { @@ -24732,43 +25527,6 @@ } } }, - "ObservationVariableListResponse" : { - "description" : "OK", - "content" : { - "application/json" : { - "schema" : { - "title" : "ObservationVariableListResponse", - "required" : [ - "metadata", - "result" - ], - "type" : "object", - "properties" : { - "@context" : { - "$ref" : "#/components/schemas/Context" - }, - "metadata" : { - "$ref" : "#/components/schemas/metadata" - }, - "result" : { - "required" : [ - "data" - ], - "type" : "object", - "properties" : { - "data" : { - "type" : "array", - "items" : { - "$ref" : "#/components/schemas/ObservationVariable" - } - } - } - } - } - } - } - } - }, "ReferenceSetSingleResponse" : { "description" : "OK", "content" : { @@ -25828,6 +26586,46 @@ } } }, + "StudyObservationLevelsListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "StudyObservationLevelsListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "$ref" : "#/components/schemas/ObservationUnitHierarchyLevel" + } + } + } + } + } + } + } + } + } + }, "ReferenceSetListResponse" : { "description" : "OK", "content" : { @@ -26006,6 +26804,44 @@ } } }, + "ImageDeleteResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ImageDeleteResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "imageDbIds" + ], + "type" : "object", + "properties" : { + "imageDbIds" : { + "type" : "array", + "description" : "The unique ids of the Image records which have been successfully deleted", + "items" : { + "type" : "string" + } + } + } + } + } + } + } + } + }, "404NotFound" : { "description" : "Not Found", "content" : { @@ -26257,6 +27093,43 @@ } } }, + "ProgramCommonCropNameListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ProgramCommonCropNameListResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "required" : [ + "data" + ], + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + } + } + } + } + } + }, "ImageListResponse" : { "description" : "OK", "content" : { @@ -26394,6 +27267,42 @@ } } }, + "ObservationTableResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ObservationTableResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/Observation" + } + } + } + }, + "text/csv" : { + "schema" : { + "type" : "string" + } + }, + "text/tsv" : { + "schema" : { + "type" : "string" + } + } + } + }, "BreedingMethodListResponse" : { "description" : "OK", "content" : { @@ -26494,6 +27403,42 @@ } } }, + "ObservationUnitTableResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "title" : "ObservationUnitTableResponse", + "required" : [ + "metadata", + "result" + ], + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "$ref" : "#/components/schemas/ObservationUnit" + } + } + } + }, + "text/csv" : { + "schema" : { + "type" : "string" + } + }, + "text/tsv" : { + "schema" : { + "type" : "string" + } + } + } + }, "GenomeMapListResponse" : { "description" : "OK", "content" : { diff --git a/Specification/Generated/brapi_openapi.json b/Specification/Generated/brapi_openapi.json index 18bb21be..0d19dbc7 100644 --- a/Specification/Generated/brapi_openapi.json +++ b/Specification/Generated/brapi_openapi.json @@ -7601,16 +7601,6 @@ "type" : "string" }, "style" : "form" - }, { - "description" : "Permanent unique identifier which references the search results", - "explode" : true, - "in" : "query", - "name" : "searchResultsDbId", - "required" : false, - "schema" : { - "type" : "string" - }, - "style" : "form" }, { "description" : "Timestamp range start", "explode" : true, @@ -27500,7 +27490,7 @@ }, "safetyDuplicateInstitutes" : { "items" : { - "$ref" : "#/components/schemas/GermplasmMCPD_safetyDuplicateInstitutes_inner" + "$ref" : "#/components/schemas/GermplasmMCPD_breedingInstitutes_inner" }, "nullable" : true, "type" : "array" @@ -29983,7 +29973,7 @@ "levelName" : "field" } ], "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship_1" + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" }, "nullable" : true, "type" : "array" @@ -30001,7 +29991,7 @@ "levelName" : "plot" } ], "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevel_1" + "$ref" : "#/components/schemas/ObservationUnitLevel" }, "nullable" : true, "type" : "array" @@ -30271,7 +30261,7 @@ "observations" : { "description" : "All observations attached to this observation unit. \n\nDefault for this field is null or omitted. Do NOT include data in this field unless the 'includeObservations' flag is explicitly set to True.", "items" : { - "$ref" : "#/components/schemas/Observation_1" + "$ref" : "#/components/schemas/Observation" }, "nullable" : true, "type" : "array" @@ -30566,7 +30556,7 @@ "$ref" : "#/components/schemas/GeoJSON" }, "observationLevel" : { - "$ref" : "#/components/schemas/ObservationUnitLevel_2" + "$ref" : "#/components/schemas/ObservationUnitLevel" }, "observationLevelRelationships" : { "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", @@ -30584,7 +30574,7 @@ "levelOrder" : 2 } ], "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship_1" + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" }, "nullable" : true, "type" : "array" @@ -30700,7 +30690,7 @@ "levelName" : "field" } ], "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship_1" + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" }, "nullable" : true, "type" : "array" @@ -30718,7 +30708,7 @@ "levelName" : "plot" } ], "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevel_1" + "$ref" : "#/components/schemas/ObservationUnitLevel" }, "nullable" : true, "type" : "array" @@ -33227,7 +33217,7 @@ "sourceGermplasm" : { "description" : "All known corresponding Germplasm", "items" : { - "$ref" : "#/components/schemas/Reference_sourceGermplasm_inner" + "$ref" : "#/components/schemas/PedigreeNodeDEP_siblings_inner" }, "nullable" : true, "type" : "array" @@ -33340,7 +33330,7 @@ "sourceGermplasm" : { "description" : "All known corresponding Germplasm", "items" : { - "$ref" : "#/components/schemas/ReferenceSet_sourceGermplasm_inner" + "$ref" : "#/components/schemas/PedigreeNodeDEP_siblings_inner" }, "nullable" : true, "type" : "array" @@ -35390,7 +35380,7 @@ "levelOrder" : 2 } ], "items" : { - "$ref" : "#/components/schemas/ObservationUnitHierarchyLevel_1" + "$ref" : "#/components/schemas/ObservationUnitHierarchyLevel" }, "nullable" : true, "type" : "array" @@ -35598,7 +35588,7 @@ "levelOrder" : 2 } ], "items" : { - "$ref" : "#/components/schemas/ObservationUnitHierarchyLevel_1" + "$ref" : "#/components/schemas/ObservationUnitHierarchyLevel" }, "nullable" : true, "type" : "array" @@ -37809,29 +37799,6 @@ "title" : "GeoJSON", "type" : "object" }, - "geoJSONSearchArea" : { - "description" : "A GeoJSON Polygon which describes an area to search for other GeoJSON objects. All contained Points and intersecting Polygons should be returned as search results. \n\nAll coordinates are decimal values on the WGS84 geographic coordinate reference system.", - "example" : { - "geometry" : { - "coordinates" : [ [ [ -77.456654, 42.241133 ], [ -75.414133, 41.508282 ], [ -76.506042, 42.417373 ], [ -77.456654, 42.241133 ] ] ], - "type" : "Polygon" - }, - "type" : "Feature" - }, - "properties" : { - "geometry" : { - "$ref" : "#/components/schemas/GeoJSON_Geometry" - }, - "type" : { - "default" : "Feature", - "description" : "The literal string \"Feature\"", - "example" : "Feature", - "type" : "string" - } - }, - "title" : "GeoJSONSearchArea", - "type" : "object" - }, "linearRing" : { "description" : "An array of at least four positions where the first equals the last", "example" : [ [ -77.456654, 42.241133, 494 ], [ -75.414133, 41.508282, 571 ], [ -76.506042, 42.417373, 123 ], [ -77.456654, 42.241133, 346 ] ], @@ -38351,21 +38318,6 @@ "title" : "callSetResponse", "type" : "object" }, - "commonCropNamesResponse_result" : { - "properties" : { - "data" : { - "description" : "The array of crop names available on the server", - "example" : [ "Tomatillo", "Paw Paw" ], - "items" : { - "description" : "supported crop name", - "type" : "string" - }, - "type" : "array" - } - }, - "required" : [ "data" ], - "type" : "object" - }, "commonCropNamesResponse" : { "properties" : { "@context" : { @@ -38375,7 +38327,7 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/commonCropNamesResponse_result" + "$ref" : "#/components/schemas/GermplasmAttributeCategoryListResponse_result" } }, "required" : [ "metadata", "result" ], @@ -39827,62 +39779,6 @@ }, "type" : "object" }, - "ObservationUnitLevelRelationship_1" : { - "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", - "properties" : { - "levelCode" : { - "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", - "example" : "Plot_123", - "nullable" : true, - "type" : "string" - }, - "levelName" : { - "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : "plot", - "nullable" : true, - "type" : "string" - }, - "levelOrder" : { - "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : 2, - "nullable" : true, - "type" : "integer" - }, - "observationUnitDbId" : { - "description" : "The ID which uniquely identifies an observation unit\n
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. \n
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response.", - "example" : "5ab883e9", - "nullable" : true, - "type" : "string" - } - }, - "title" : "ObservationUnitLevelRelationship", - "type" : "object" - }, - "ObservationUnitLevel_1" : { - "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", - "properties" : { - "levelCode" : { - "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", - "example" : "Plot_123", - "nullable" : true, - "type" : "string" - }, - "levelName" : { - "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : "plot", - "nullable" : true, - "type" : "string" - }, - "levelOrder" : { - "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : 2, - "nullable" : true, - "type" : "integer" - } - }, - "title" : "ObservationUnitLevel", - "type" : "object" - }, "_search_observations_post_request" : { "properties" : { "commonCropNames" : { @@ -39968,7 +39864,7 @@ "levelName" : "field" } ], "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship_1" + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" }, "nullable" : true, "type" : "array" @@ -39986,7 +39882,7 @@ "levelName" : "plot" } ], "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevel_1" + "$ref" : "#/components/schemas/ObservationUnitLevel" }, "nullable" : true, "type" : "array" @@ -40404,20 +40300,6 @@ "title" : "StudySingleResponse", "type" : "object" }, - "studyTypesResponse_result" : { - "properties" : { - "data" : { - "description" : "The list of all StudyTypes available on a given server.", - "example" : [ "Crossing Nursery", "Yield study" ], - "items" : { - "type" : "string" - }, - "type" : "array" - } - }, - "required" : [ "data" ], - "type" : "object" - }, "studyTypesResponse" : { "properties" : { "@context" : { @@ -40427,7 +40309,7 @@ "$ref" : "#/components/schemas/metadata" }, "result" : { - "$ref" : "#/components/schemas/studyTypesResponse_result" + "$ref" : "#/components/schemas/GermplasmAttributeCategoryListResponse_result" } }, "required" : [ "metadata", "result" ], @@ -41590,29 +41472,6 @@ }, "type" : "object" }, - "GermplasmMCPD_collectingInfo_collectingInstitutes_inner" : { - "properties" : { - "instituteAddress" : { - "description" : "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", - "example" : "123 Main Street, Lima, Peru, 5555", - "nullable" : true, - "type" : "string" - }, - "instituteCode" : { - "description" : "MCPD (v2.1) (COLLCODE) 4. FAO WIEWS code of the institute collecting the sample. If the holding institute has collected the material, the collecting institute code (COLLCODE) should be the same as the holding institute code (INSTCODE). Follows INSTCODE standard. Multiple values are separated by a semicolon without space.", - "example" : "PER001", - "nullable" : true, - "type" : "string" - }, - "instituteName" : { - "description" : "MCPD (v2.1) (COLLNAME) 4.1 Name of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled because the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", - "example" : "The BrAPI Institute", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, "GermplasmMCPD_collectingInfo_collectingSite" : { "description" : "Information about the location where the sample was collected", "nullable" : true, @@ -41686,7 +41545,7 @@ "collectingInstitutes" : { "description" : "Institutes which collected the sample", "items" : { - "$ref" : "#/components/schemas/GermplasmMCPD_collectingInfo_collectingInstitutes_inner" + "$ref" : "#/components/schemas/GermplasmMCPD_breedingInstitutes_inner" }, "nullable" : true, "type" : "array" @@ -41709,30 +41568,6 @@ }, "type" : "object" }, - "GermplasmMCPD_donorInfo_donorInstitute" : { - "description" : "The identifying information for the entity acting as an accession donor\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.\n
MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.", - "properties" : { - "instituteAddress" : { - "description" : "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", - "example" : "123 Main Street, Lima, Peru, 5555", - "nullable" : true, - "type" : "string" - }, - "instituteCode" : { - "description" : "MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard.", - "example" : "PER001", - "nullable" : true, - "type" : "string" - }, - "instituteName" : { - "description" : "MCPD (v2.1) (DONORNAME) 22.1 Name of the donor institute (or person). This descriptor should be used only if DONORCODE can not be filled because the FAO WIEWS code for this institute is not available.", - "example" : "The BrAPI Institute", - "nullable" : true, - "type" : "string" - } - }, - "type" : "object" - }, "GermplasmMCPD_donorInfo" : { "description" : "Information about an accession donor", "properties" : { @@ -41749,30 +41584,7 @@ "type" : "string" }, "donorInstitute" : { - "$ref" : "#/components/schemas/GermplasmMCPD_donorInfo_donorInstitute" - } - }, - "type" : "object" - }, - "GermplasmMCPD_safetyDuplicateInstitutes_inner" : { - "properties" : { - "instituteAddress" : { - "description" : "MCPD (v2.1) (COLLINSTADDRESS) 4.1.1 Address of the institute collecting the sample. This descriptor should be used only if COLLCODE can not be filled since the FAO WIEWS code for this institute is not available. Multiple values are separated by a semicolon without space.", - "example" : "123 Main Street, Lima, Peru, 5555", - "nullable" : true, - "type" : "string" - }, - "instituteCode" : { - "description" : "MCPD (v2.1) (DUPLSITE) 25. FAO WIEWS code of the institute(s) where a safety duplicate of the accession is maintained. Follows INSTCODE standard.", - "example" : "PER001", - "nullable" : true, - "type" : "string" - }, - "instituteName" : { - "description" : "MCPD (v2.1) (DUPLINSTNAME) 25.1 Name of the institute where a safety duplicate of the accession is maintained.", - "example" : "The BrAPI Institute", - "nullable" : true, - "type" : "string" + "$ref" : "#/components/schemas/GermplasmMCPD_breedingInstitutes_inner" } }, "type" : "object" @@ -41812,7 +41624,8 @@ "type" : "string" } }, - "title" : "GeoJSONSearchArea" + "title" : "GeoJSONSearchArea", + "type" : "object" }, "Observation_season" : { "nullable" : true, @@ -41861,31 +41674,6 @@ }, "type" : "object" }, - "ObservationUnitLevel_2" : { - "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", - "properties" : { - "levelCode" : { - "description" : "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", - "example" : "Plot_123", - "nullable" : true, - "type" : "string" - }, - "levelName" : { - "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : "plot", - "nullable" : true, - "type" : "string" - }, - "levelOrder" : { - "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : 2, - "nullable" : true, - "type" : "integer" - } - }, - "title" : "ObservationUnitLevel", - "type" : "object" - }, "ObservationUnit_observationUnitPosition" : { "description" : "All positional and layout information related to this Observation Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) \nor level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. \nLevels of observation must be consistent with those listed in the Study section.", "nullable" : true, @@ -41901,7 +41689,7 @@ "$ref" : "#/components/schemas/GeoJSON" }, "observationLevel" : { - "$ref" : "#/components/schemas/ObservationUnitLevel_2" + "$ref" : "#/components/schemas/ObservationUnitLevel" }, "observationLevelRelationships" : { "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", @@ -41919,7 +41707,7 @@ "levelOrder" : 2 } ], "items" : { - "$ref" : "#/components/schemas/ObservationUnitLevelRelationship_1" + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" }, "nullable" : true, "type" : "array" @@ -41953,119 +41741,6 @@ }, "type" : "object" }, - "Observation_1" : { - "description" : "A value assigned for a specific ObservationVariable when observing a specific ObservationUnit.", - "properties" : { - "additionalInfo" : { - "additionalProperties" : { - "type" : "string" - }, - "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", - "nullable" : true, - "type" : "object" - }, - "collector" : { - "description" : "The name or identifier of the entity which collected the observation", - "example" : "917d3ae0", - "nullable" : true, - "type" : "string" - }, - "externalReferences" : { - "description" : "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.", - "example" : [ { - "referenceId" : "doi:10.155454/12341234", - "referenceSource" : "DOI" - }, { - "referenceId" : "75a50e76", - "referenceSource" : "Remote Data Collection Upload Tool" - } ], - "items" : { - "$ref" : "#/components/schemas/ExternalReferences_1_inner" - }, - "nullable" : true, - "title" : "ExternalReferences", - "type" : "array" - }, - "geoCoordinates" : { - "$ref" : "#/components/schemas/GeoJSON" - }, - "germplasmDbId" : { - "description" : "The ID which uniquely identifies a germplasm", - "example" : "2408ab11", - "nullable" : true, - "type" : "string" - }, - "germplasmName" : { - "description" : "Name of the germplasm. It can be the preferred name and does not have to be unique.", - "example" : "A0000003", - "nullable" : true, - "type" : "string" - }, - "observationDbId" : { - "description" : "The ID which uniquely identifies an observation", - "example" : "ef24b615", - "type" : "string" - }, - "observationTimeStamp" : { - "description" : "The date and time when this observation was made", - "format" : "date-time", - "nullable" : true, - "type" : "string" - }, - "observationUnitDbId" : { - "description" : "The ID which uniquely identifies an observation unit", - "example" : "598111d4", - "nullable" : true, - "type" : "string" - }, - "observationUnitName" : { - "description" : "A human readable name for an observation unit", - "example" : "Plot 1", - "nullable" : true, - "type" : "string" - }, - "observationVariableDbId" : { - "description" : "The ID which uniquely identifies an observation variable", - "example" : "c403d107", - "nullable" : true, - "type" : "string" - }, - "observationVariableName" : { - "description" : "A human readable name for an observation variable", - "example" : "Plant Height in meters", - "nullable" : true, - "type" : "string" - }, - "season" : { - "$ref" : "#/components/schemas/Observation_season" - }, - "studyDbId" : { - "description" : "The ID which uniquely identifies a study within the given database server", - "example" : "ef2829db", - "nullable" : true, - "type" : "string" - }, - "uploadedBy" : { - "description" : "The name or id of the user who uploaded the observation to the database system", - "example" : "a2f7f60b", - "nullable" : true, - "type" : "string" - }, - "value" : { - "description" : "The value of the data collected as an observation", - "example" : "2.3", - "nullable" : true, - "type" : "string" - } - }, - "required" : [ "observationDbId" ], - "title" : "Observation", - "type" : "object", - "x-brapi-metadata" : { - "module" : "BrAPI-Phenotyping", - "primaryModel" : true - } - }, "ObservationUnit_treatments_inner" : { "properties" : { "factor" : { @@ -42191,36 +41866,6 @@ "required" : [ "germplasmDbId", "parentType" ], "type" : "object" }, - "Reference_sourceGermplasm_inner" : { - "properties" : { - "germplasmDbId" : { - "description" : "The ID which uniquely identifies a `Germplasm` within the given database server", - "example" : "d4076594", - "type" : "string" - }, - "germplasmName" : { - "description" : "The human readable name of a `Germplasm`", - "example" : "A0000003", - "type" : "string" - } - }, - "type" : "object" - }, - "ReferenceSet_sourceGermplasm_inner" : { - "properties" : { - "germplasmDbId" : { - "description" : "The ID which uniquely identifies a germplasm within the given database server", - "example" : "d4076594", - "type" : "string" - }, - "germplasmName" : { - "description" : "The human readable name of a germplasm", - "example" : "A0000003", - "type" : "string" - } - }, - "type" : "object" - }, "SeedLot_contentMixture_inner" : { "properties" : { "crossDbId" : { @@ -42450,25 +42095,6 @@ }, "type" : "object" }, - "ObservationUnitHierarchyLevel_1" : { - "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "properties" : { - "levelName" : { - "description" : "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : "plot", - "nullable" : true, - "type" : "string" - }, - "levelOrder" : { - "description" : "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "example" : 2, - "nullable" : true, - "type" : "integer" - } - }, - "title" : "ObservationUnitHierarchyLevel", - "type" : "object" - }, "Trial_datasetAuthorships_inner" : { "properties" : { "datasetPUI" : { diff --git a/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md index 70cab6c3..b6e0bad5 100644 --- a/Specification/Generated/brapi_openapi_comparison.md +++ b/Specification/Generated/brapi_openapi_comparison.md @@ -1,67 +1,27 @@ #### What's Deleted --- -##### `GET` /commoncropnames +##### `POST` /search/variables -##### `POST` /delete/images +##### `GET` /search/variables/{searchResultsDbId} -##### `POST` /delete/observations +##### `GET` /variables -##### `PUT` /images/{imageDbId}/imagecontent - - -##### `GET` /observationlevels - - -##### `GET` /observations/table - - -##### `GET` /observationunits/table - - -##### `GET` /seedlots/transactions - - -##### `POST` /seedlots/transactions - - -##### `GET` /serverinfo - - -##### `POST` /variantsets/extract - - -##### `PUT` /observations/{observationDbId} - - -##### `PUT` /observationunits/{observationUnitDbId} - - -##### `PUT` /calls +##### `POST` /variables -##### `PUT` /plates +##### `GET` /variables/{observationVariableDbId} -##### `PUT` /pedigree +##### `PUT` /variables/{observationVariableDbId} #### What's Changed --- -##### `POST` /search/lists - - -###### Request: - -* Changed content type : `application/json` - - * Changed property `listType` (string): - - Nullable changed: `true` -> `null` - ##### `POST` /search/locations @@ -72,153 +32,6 @@ * Changed property `coordinates` (object -> null): - Type changed: `object` -> `null` -##### `GET` /allelematrix - - -###### Return Type: - -New response : **404** - -##### `POST` /attributes - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - * Changed property `ontologyReference` (object -> null): - - Type changed: `object` -> `null` - -##### `PUT` /attributes/{attributeDbId} - - -###### Request: - -* Changed content type : `application/json` - - * Changed property `ontologyReference` (object -> null): - - Type changed: `object` -> `null` - -##### `PUT` /samples - - -###### Return Type: - -Deleted response : **404** - -##### `POST` /search/allelematrix - - -###### Request: - -* Changed content type : `application/json` - - * Changed property `dataMatrixAbbreviations` (array -> string): - - Type changed: `array` -> `string` - - * Changed property `dataMatrixNames` (array -> string): - - Type changed: `array` -> `string` - -##### `GET` /seedlots/{seedLotDbId}/transactions - - -###### Parameters: - -Deleted: `transactionDbId` in `query` - -##### `POST` /variables - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - * Changed property `ontologyReference` (object -> null): - - Type changed: `object` -> `null` - -##### `PUT` /variables/{observationVariableDbId} - - -###### Request: - -* Changed content type : `application/json` - - * Changed property `ontologyReference` (object -> null): - - Type changed: `object` -> `null` - -##### `POST` /images - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - Deleted properties: `observationDbIds` - - * Changed property `mimeType` (string): - - Pattern changed: `image/.*` -> `null` - - * Changed property `imageLocation` (object) - - * Changed property `geometry` (object): - - Discriminator property changed - -##### `PUT` /images/{imageDbId} - - -###### Request: - -* Changed content type : `application/json` - - Deleted properties: `observationDbIds` - - * Changed property `mimeType` (string): - - Pattern changed: `image/.*` -> `null` - - * Changed property `imageLocation` (object) - - * Changed property `geometry` (object): - - Discriminator property changed - -##### `POST` /locations - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - * Changed property `coordinates` (object) - - * Changed property `geometry` (object): - - Discriminator property changed - -##### `PUT` /locations/{locationDbId} - - -###### Request: - -* Changed content type : `application/json` - - * Changed property `coordinates` (object) - - * Changed property `geometry` (object): - - Discriminator property changed - -##### `PUT` /observations - - -###### Return Type: - -Deleted response : **404** - ##### `POST` /observations @@ -228,95 +41,18 @@ Deleted response : **404** Changed items (array): - * Changed property `season` (object -> null): - - Type changed: `object` -> `null` - - * Changed property `geoCoordinates` (object) - - * Changed property `geometry` (object): - - Discriminator property changed - -###### Return Type: - -Deleted response : **404** - -##### `POST` /observationunits - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - * Changed property `observationUnitPosition` (object) - - * Changed property `geoCoordinates` (object -> array): - - Type changed: `object` -> `array` - - * Changed property `positionCoordinateXType` (string -> null): - - Type changed: `string` -> `null` - - * Changed property `positionCoordinateYType` (string -> null): - - Type changed: `string` -> `null` - -##### `GET` /pedigree - - -###### Return Type: - -Deleted response : **404** - -##### `POST` /pedigree - - -###### Return Type: - -Deleted response : **404** - -##### `POST` /search/images - - -###### Request: - -* Changed content type : `application/json` - - * Changed property `imageLocation` (object) - - * Changed property `geometry` (object): - - Discriminator property changed - -##### `POST` /germplasm - - -###### Request: - -* Changed content type : `application/json` - - Changed items (array): - - * Changed property `germplasmOrigin` (array) + New properties: `observationVariable` - Changed items (array): + Deleted properties: `observationVariableDbId`, `observationVariableName` - * Changed property `coordinates` (object) - - * Changed property `geometry` (object): - - Discriminator property changed - -##### `PUT` /germplasm/{germplasmDbId} +##### `PUT` /observations/{observationDbId} ###### Request: * Changed content type : `application/json` - * Changed property `germplasmOrigin` (array) - - Changed items (array): - - * Changed property `coordinates` (object) + New properties: `observationVariable` - * Changed property `geometry` (object): - - Discriminator property changed + Deleted properties: `observationVariableDbId`, `observationVariableName` From a86e013faff7b80830b882a785db4b0985683952 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Sun, 7 Jun 2026 13:09:35 +1200 Subject: [PATCH 60/62] =?UTF-8?q?fixed=20the=20BrAPI-Core=20=E2=86=92=20Br?= =?UTF-8?q?API.yaml=20issue?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml b/generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml index f55f9428..24524f3e 100644 --- a/generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml +++ b/generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml @@ -1,6 +1,3 @@ -info: - title: BrAPI - version: '' openapi: 3.0.0 paths: /serverinfo: From 2ce3fc7db9fbd63fa8a3ff4c7ceb2510f79f560e Mon Sep 17 00:00:00 2001 From: guydavenport <6523224+guydavenport@users.noreply.github.com> Date: Sun, 7 Jun 2026 01:15:28 +0000 Subject: [PATCH 61/62] Generate specifications (manually triggered) --- Specification/Generated/BrAPI-Core.yaml | 639 +++++++++++++------ Specification/Generated/brapi_generated.json | 2 +- 2 files changed, 450 insertions(+), 191 deletions(-) diff --git a/Specification/Generated/BrAPI-Core.yaml b/Specification/Generated/BrAPI-Core.yaml index 375a628b..6879ac7b 100644 --- a/Specification/Generated/BrAPI-Core.yaml +++ b/Specification/Generated/BrAPI-Core.yaml @@ -2,74 +2,7 @@ openapi: 3.0.0 info: title: BrAPI-Core version: "2.1" -servers: -- url: / paths: - /serverinfo: - get: - tags: - - Server Info - summary: Get the list of implemented Calls - description: "Implementation Notes\n\nHaving a consistent structure for the\ - \ path string of each call is very \nimportant for teams to be able to connect\ - \ and find errors. Read more on Github.\n\nHere are the rules for the path\ - \ of each call that should be returned\n\nEvery word in the call path should\ - \ match the documentation exactly, both in \nspelling and capitalization.\ - \ Note that path strings are all lower case, but \npath parameters are camel\ - \ case.\n\nEach path should start relative to \\\"/\\\" and therefore should\ - \ not include \\\"/\\\"\n\nNo leading or trailing slashes (\\\"/\\\") \n\n\ - Path parameters are wrapped in curly braces (\\\"{}\\\"). The name of the\ - \ path parameter \nshould be spelled exactly as it is specified in the documentation.\n\ - \nExamples \n\nGOOD \"call\": \"germplasm/{germplasmDbId}/pedigree\" \n\n\ - BAD \"call\": \"germplasm/{id}/pedigree\"\n\nBAD \"call\": \"germplasm/{germplasmDBid}/pedigree\"\ - \ \n\nBAD \"call\": \"brapi/v2/germplasm/{germplasmDbId}/pedigree\" \n\n\ - BAD \"call\": \"/germplasm/{germplasmDbId}/pedigree/\" \n\nBAD \"call\"\ - : \"germplasm//pedigree\"" - parameters: - - name: contentType - in: query - description: Filter the list of endpoints based on the response content type. - required: false - style: form - explode: true - schema: - $ref: "#/components/schemas/ContentTypes" - - name: dataType - in: query - description: |- - **Deprecated in v2.1** Please use `contentType`. Github issue number #443 -
The data format supported by the call. - required: false - deprecated: true - style: form - explode: true - schema: - $ref: "#/components/schemas/ContentTypes" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - description: OK - content: - application/json: - schema: - title: ServerInfoResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/ServerInfo" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" /lists: get: tags: @@ -855,6 +788,66 @@ paths: $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + /commoncropnames: + get: + tags: + - Programs + summary: Get the commonCropNames of Program + description: List all available Program commonCropNames + parameters: + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/ProgramCommonCropNameListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" + /observationlevels: + get: + tags: + - Studies + summary: Get the observationLevelses of Study + description: List all available Study observationLevelses + parameters: + - name: studyDbId + in: query + description: List of study identifiers to search for + required: false + schema: + type: string + - name: programDbId + in: query + description: "A BrAPI Program represents the high level organization or group\ + \ who is responsible for conducting trials and studies. Things like Breeding\ + \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ + \ parameter to only return results associated with the given programs. \n\ + \nUse `GET /programs` to find the list of available programs on a server." + required: false + schema: + type: string + - name: trialDbId + in: query + description: The ID which uniquely identifies a trial to search for + required: false + schema: + type: string + - $ref: "#/components/parameters/page" + - $ref: "#/components/parameters/pageSize" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + $ref: "#/components/responses/StudyObservationLevelsListResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" /studytypes: get: tags: @@ -1510,14 +1503,14 @@ paths: $ref: "#/components/responses/ListListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/locations/{searchResultsDbId}: get: tags: @@ -1552,14 +1545,14 @@ paths: $ref: "#/components/responses/LocationListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/people/{searchResultsDbId}: get: tags: @@ -1594,14 +1587,14 @@ paths: $ref: "#/components/responses/PersonListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/programs/{searchResultsDbId}: get: tags: @@ -1636,14 +1629,14 @@ paths: $ref: "#/components/responses/ProgramListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/studies/{searchResultsDbId}: get: tags: @@ -1678,14 +1671,14 @@ paths: $ref: "#/components/responses/StudyListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" - "404": - $ref: "#/components/responses/404NotFound" "400": $ref: "#/components/responses/400BadRequest" "401": $ref: "#/components/responses/401Unauthorized" "403": $ref: "#/components/responses/403Forbidden" + "404": + $ref: "#/components/responses/404NotFound" /search/trials/{searchResultsDbId}: get: tags: @@ -1720,8 +1713,73 @@ paths: $ref: "#/components/responses/TrialListResponse" "202": $ref: "#/components/responses/202AcceptedSearchResponse" + "400": + $ref: "#/components/responses/400BadRequest" + "401": + $ref: "#/components/responses/401Unauthorized" + "403": + $ref: "#/components/responses/403Forbidden" "404": $ref: "#/components/responses/404NotFound" + /serverinfo: + get: + tags: + - Server Info + summary: Get the list of implemented Calls + description: "Implementation Notes\n\nHaving a consistent structure for the\ + \ path string of each call is very \nimportant for teams to be able to connect\ + \ and find errors. Read more on Github.\n\nHere are the rules for the path\ + \ of each call that should be returned\n\nEvery word in the call path should\ + \ match the documentation exactly, both in \nspelling and capitalization.\ + \ Note that path strings are all lower case, but \npath parameters are camel\ + \ case.\n\nEach path should start relative to \\\"/\\\" and therefore should\ + \ not include \\\"/\\\"\n\nNo leading or trailing slashes (\\\"/\\\") \n\n\ + Path parameters are wrapped in curly braces (\\\"{}\\\"). The name of the\ + \ path parameter \nshould be spelled exactly as it is specified in the documentation.\n\ + \nExamples \n\nGOOD \"call\": \"germplasm/{germplasmDbId}/pedigree\" \n\n\ + BAD \"call\": \"germplasm/{id}/pedigree\"\n\nBAD \"call\": \"germplasm/{germplasmDBid}/pedigree\"\ + \ \n\nBAD \"call\": \"brapi/v2/germplasm/{germplasmDbId}/pedigree\" \n\n\ + BAD \"call\": \"/germplasm/{germplasmDbId}/pedigree/\" \n\nBAD \"call\"\ + : \"germplasm//pedigree\"" + parameters: + - name: contentType + in: query + description: Filter the list of endpoints based on the response content type. + required: false + style: form + explode: true + schema: + $ref: "#/components/schemas/ContentTypes" + - name: dataType + in: query + description: |- + **Deprecated in v2.1** Please use `contentType`. Github issue number #443 +
The data format supported by the call. + required: false + deprecated: true + style: form + explode: true + schema: + $ref: "#/components/schemas/ContentTypes" + - $ref: "#/components/parameters/authorizationHeader" + responses: + "200": + description: OK + content: + application/json: + schema: + title: ServerInfoResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + $ref: "#/components/schemas/ServerInfo" "400": $ref: "#/components/responses/400BadRequest" "401": @@ -1730,101 +1788,6 @@ paths: $ref: "#/components/responses/403Forbidden" components: schemas: - Service: - required: - - methods - - service - - versions - type: object - properties: - service: - type: string - description: The name of the available call as recorded in the documentation - example: "germplasm/{germplasmDbId}/pedigree" - contentTypes: - type: array - description: The possible content types returned by the service endpoint - example: - - application/json - items: - $ref: "#/components/schemas/ContentTypes" - dataTypes: - type: array - description: "**Deprecated in v2.1** Please use `contentTypes`. Github issue\ - \ number #443 \n
The possible data formats returned by the available\ - \ call " - example: - - application/json - deprecated: true - items: - $ref: "#/components/schemas/ContentTypes" - methods: - type: array - description: The possible HTTP Methods to be used with the available call - example: - - GET - - POST - items: - type: string - enum: - - GET - - POST - - PUT - - DELETE - versions: - type: array - description: The supported versions of a particular call - example: - - "2.0" - - "2.1" - items: - type: string - enum: - - "2.0" - - "2.1" - - "2.2" - ServerInfo: - required: - - calls - type: object - properties: - contactEmail: - type: string - description: A contact email address for this server management - example: contact@institute.org - documentationURL: - type: string - description: A URL to the human readable documentation of an object - example: institute.org/server - organizationURL: - type: string - description: The URL of the organization that manages this server and data - example: institute.org/home - organizationName: - type: string - description: The name of the organization that manages this server and data - example: The Institute - serverName: - type: string - description: The name of this server - example: The BrAPI Test Server - serverDescription: - type: string - description: A description of this server - example: |- - The BrAPI Test Server - Web Server - Apache Tomcat 7.0.32 - Database - Postgres 10 - Supported BrAPI Version - V2.0 - location: - type: string - description: "Physical location of this server (ie. City, Country)" - example: USA - calls: - type: array - description: Array of available calls on this server - items: - $ref: "#/components/schemas/Service" AdditionalInfo: type: string additionalProperties: @@ -1865,19 +1828,21 @@ components: items: type: string dataMatrixAbbreviations: - type: string - description: "`dataMatrixAbbreviations` is a comma separated list of abbreviations\ - \ (ie 'GT', 'RD' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ + \ 'RD' etc). This list controls which data matrices are returned in the\ + \ response." nullable: true - example: "GT,RD" + items: + type: string dataMatrixNames: - type: string - description: "`dataMatrixNames` is a comma separated list of names (ie 'Genotype',\ - \ 'Read Depth' etc). This list controls which data matrices are returned\ - \ in the response." + type: array + description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ + \ Depth' etc). This list controls which data matrices are returned in\ + \ the response." nullable: true - example: "Genotype,Read Depth" + items: + type: string dimensionCallSetPage: type: integer description: The requested page number for the CallSet dimension of the @@ -2081,9 +2046,9 @@ components: method: $ref: "#/components/schemas/Method" ontologyReference: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/OntologyReference" - - type: "null" scale: $ref: "#/components/schemas/Scale" scientist: @@ -2763,7 +2728,8 @@ components: nullable: true GeoJSONGeometry: type: object - nullable: true + discriminator: + propertyName: type oneOf: - required: - coordinates @@ -3604,7 +3570,9 @@ components: items: type: string listType: - $ref: "#/components/schemas/ListType" + nullable: true + allOf: + - $ref: "#/components/schemas/ListType" programDbIds: type: array description: "A BrAPI Program represents the high level organization or\ @@ -3717,7 +3685,9 @@ components: items: type: string listType: - $ref: "#/components/schemas/ListType" + nullable: true + allOf: + - $ref: "#/components/schemas/ListType" page: type: integer description: Which result page is requested. The page indexing starts at @@ -4475,6 +4445,47 @@ components: \ associated observed variable (see observed variables). \nAlternatively,\ \ it is possible to use samples for more detailed tracing of sub-plant units,\ \ attaching the observations to them instead.\" " + ObservationUnitHierarchyLevelRequest: + type: object + properties: + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + trialDbIds: + type: array + description: The ID which uniquely identifies a trial to search for + items: + type: string + trialNames: + type: array + description: The human readable name of a trial to search for + items: + type: string ObservationUnitRequest: type: object properties: @@ -6305,7 +6316,64 @@ components: SeedLotTransactionRequest: type: object properties: - transactionDbIs: + commonCropNames: + type: array + description: "The BrAPI Common Crop Name is the simple, generalized, widely\ + \ accepted name of the organism being researched. It is most often used\ + \ in multi-crop systems where digital resources need to be divided at\ + \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ + \ of common crop names.\n\nUse this parameter to only return results associated\ + \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ + \ of available crops on a server." + items: + type: string + crossDbIds: + type: array + description: Search for Cross with this unique id + items: + type: string + crossNames: + type: array + description: Search for Cross with this human readable name + items: + type: string + germplasmDbIds: + type: array + description: List of IDs which uniquely identify germplasm to search for + nullable: true + items: + type: string + germplasmNames: + type: array + description: List of human readable names to identify germplasm to search + for + nullable: true + items: + type: string + programDbIds: + type: array + description: "A BrAPI Program represents the high level organization or\ + \ group who is responsible for conducting trials and studies. Things like\ + \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ + \ \n\nUse this parameter to only return results associated with the given\ + \ programs. \n\nUse `GET /programs` to find the list of available programs\ + \ on a server." + items: + type: string + programNames: + type: array + description: |- + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + items: + type: string + seedLotDbIds: + type: array + description: Unique id for a seed lot on this server + items: + type: string + transactionDbIds: type: array description: Unique id for a Transaction that has occurred items: @@ -7375,9 +7443,9 @@ components: method: $ref: "#/components/schemas/Method" ontologyReference: - anyOf: + nullable: true + allOf: - $ref: "#/components/schemas/OntologyReference" - - type: "null" scale: $ref: "#/components/schemas/Scale" scientist: @@ -7754,6 +7822,52 @@ components: description: The unique identifier representing a VariantSet items: type: string + VariantSetsExtractRequest: + type: object + properties: + callSetDbIds: + type: array + description: The CallSet to search. + items: + type: string + expandHomozygotes: + type: boolean + description: Should homozygotes be expanded (true) or collapsed into a single + occurrence (false) + example: true + sepPhased: + type: string + description: The string used as a separator for phased allele calls. + example: "~" + sepUnphased: + type: string + description: The string used as a separator for unphased allele calls. + example: '|' + studyDbIds: + type: array + description: List of study identifiers to search for + items: + type: string + studyNames: + type: array + description: List of study names to filter search results + items: + type: string + unknownString: + type: string + description: The string used as a representation for missing data. + example: "-" + variantDbIds: + type: array + description: The Variant to search. + items: + type: string + variantSetDbIds: + type: array + description: The VariantSet to search. + items: + type: string + description: Request object for extracting data subsets as new Variant Sets basePagination: required: - currentPage @@ -7918,6 +8032,101 @@ components: pageSize: 1000 totalCount: 10 totalPages: 1 + Service: + required: + - methods + - service + - versions + type: object + properties: + service: + type: string + description: The name of the available call as recorded in the documentation + example: "germplasm/{germplasmDbId}/pedigree" + contentTypes: + type: array + description: The possible content types returned by the service endpoint + example: + - application/json + items: + $ref: "#/components/schemas/ContentTypes" + dataTypes: + type: array + description: "**Deprecated in v2.1** Please use `contentTypes`. Github issue\ + \ number #443 \n
The possible data formats returned by the available\ + \ call " + example: + - application/json + deprecated: true + items: + $ref: "#/components/schemas/ContentTypes" + methods: + type: array + description: The possible HTTP Methods to be used with the available call + example: + - GET + - POST + items: + type: string + enum: + - GET + - POST + - PUT + - DELETE + versions: + type: array + description: The supported versions of a particular call + example: + - "2.0" + - "2.1" + items: + type: string + enum: + - "2.0" + - "2.1" + - "2.2" + ServerInfo: + required: + - calls + type: object + properties: + contactEmail: + type: string + description: A contact email address for this server management + example: contact@institute.org + documentationURL: + type: string + description: A URL to the human readable documentation of an object + example: institute.org/server + organizationURL: + type: string + description: The URL of the organization that manages this server and data + example: institute.org/home + organizationName: + type: string + description: The name of the organization that manages this server and data + example: The Institute + serverName: + type: string + description: The name of this server + example: The BrAPI Test Server + serverDescription: + type: string + description: A description of this server + example: |- + The BrAPI Test Server + Web Server - Apache Tomcat 7.0.32 + Database - Postgres 10 + Supported BrAPI Version - V2.0 + location: + type: string + description: "Physical location of this server (ie. City, Country)" + example: USA + calls: + type: array + description: Array of available calls on this server + items: + $ref: "#/components/schemas/Service" responses: "401Unauthorized": description: Unauthorized @@ -7927,6 +8136,30 @@ components: type: string example: ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token + ProgramCommonCropNameListResponse: + description: OK + content: + application/json: + schema: + title: ProgramCommonCropNameListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: string "202AcceptedSearchResponse": description: Accepted content: @@ -8066,6 +8299,32 @@ components: type: string example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action + StudyObservationLevelsListResponse: + description: OK + content: + application/json: + schema: + title: StudyObservationLevelsListResponse + required: + - metadata + - result + type: object + properties: + '@context': + $ref: "#/components/schemas/Context" + metadata: + $ref: "#/components/schemas/metadata" + result: + required: + - data + type: object + properties: + data: + type: array + items: + type: array + items: + $ref: "#/components/schemas/ObservationUnitHierarchyLevel" ProgramListResponse: description: OK content: diff --git a/Specification/Generated/brapi_generated.json b/Specification/Generated/brapi_generated.json index 9077f266..8139235e 100644 --- a/Specification/Generated/brapi_generated.json +++ b/Specification/Generated/brapi_generated.json @@ -2,7 +2,7 @@ "openapi" : "3.0.0", "info" : { "title" : "BrAPI", - "version" : "" + "version" : "2.1" }, "paths" : { "/allelematrix" : { From d66caa62a76014dcfe558da69f8fea6d64c92bd4 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Sun, 7 Jun 2026 15:00:51 +1200 Subject: [PATCH 62/62] =?UTF-8?q?fixed=20the=20BrAPI-Core=20=E2=86=92=20Br?= =?UTF-8?q?API.yaml=20issue?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- Specification/Generated/BrAPI.yaml | 8708 ---------------------------- 1 file changed, 8708 deletions(-) delete mode 100644 Specification/Generated/BrAPI.yaml diff --git a/Specification/Generated/BrAPI.yaml b/Specification/Generated/BrAPI.yaml deleted file mode 100644 index 34e38c81..00000000 --- a/Specification/Generated/BrAPI.yaml +++ /dev/null @@ -1,8708 +0,0 @@ -openapi: 3.0.0 -info: - title: BrAPI - version: "" -paths: - /lists: - get: - tags: - - Lists - summary: Get a filtered list of List - description: Get a list of List - parameters: - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: listDbId - in: query - description: An array of primary database identifiers to identify a set of - Lists - required: false - schema: - type: string - - name: listName - in: query - description: An array of human readable names to identify a set of Lists - required: false - schema: - type: string - - name: listSource - in: query - description: "An array of terms identifying lists from different sources (ie\ - \ 'USER', 'SYSTEM', etc)" - required: false - schema: - type: string - - name: listType - in: query - required: false - schema: - $ref: "#/components/schemas/ListType" - - $ref: "#/components/parameters/externalReferenceId" - - $ref: "#/components/parameters/externalReferenceID" - - $ref: "#/components/parameters/externalReferenceSource" - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/ListListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - post: - tags: - - Lists - summary: Create new List - description: Add new List to database - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - type: array - items: - $ref: "#/components/schemas/ListNewRequest" - responses: - "200": - $ref: "#/components/responses/ListListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /locations: - get: - tags: - - Locations - summary: Get a filtered list of Location - description: Get a list of Location - parameters: - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - - name: locationDbId - in: query - description: The location ids to search for - required: false - schema: - type: string - - name: locationName - in: query - description: A human readable names to search for - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: locationType - in: query - description: "The type of location this represents (ex. Breeding Location,\ - \ Storage Location, etc)" - required: false - schema: - type: string - - name: parentLocationDbId - in: query - description: "The unique identifier for a Location\n
The Parent Location\ - \ defines the encompassing location that this location belongs to. \nFor\ - \ example, an Institution might have multiple Field Stations inside it and\ - \ each Field Station might have multiple Fields." - required: false - schema: - type: string - - name: parentLocationName - in: query - description: "A human readable name for a location\n
The Parent Location\ - \ defines the encompassing location that this location belongs to. \nFor\ - \ example, an Institution might have multiple Field Stations inside it and\ - \ each Field Station might have multiple Fields." - required: false - schema: - type: string - - $ref: "#/components/parameters/externalReferenceId" - - $ref: "#/components/parameters/externalReferenceID" - - $ref: "#/components/parameters/externalReferenceSource" - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/LocationListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - post: - tags: - - Locations - summary: Create new Location - description: Add new Location to database - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - type: array - items: - $ref: "#/components/schemas/LocationNewRequest" - responses: - "200": - $ref: "#/components/responses/LocationListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /people: - get: - tags: - - People - summary: Get a filtered list of Person - description: Get a list of Person - parameters: - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: firstName - in: query - description: Persons first name - required: false - schema: - type: string - - name: lastName - in: query - description: Persons last name - required: false - schema: - type: string - - name: personDbId - in: query - description: Unique ID for this person - required: false - schema: - type: string - - name: userID - in: query - description: A systems user ID associated with this person. Different from - personDbId because you could have a person who is not a user of the system. - required: false - schema: - type: string - - $ref: "#/components/parameters/externalReferenceId" - - $ref: "#/components/parameters/externalReferenceID" - - $ref: "#/components/parameters/externalReferenceSource" - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/PersonListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - post: - tags: - - People - summary: Create new Person - description: Add new Person to database - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - type: array - items: - $ref: "#/components/schemas/PersonNewRequest" - responses: - "200": - $ref: "#/components/responses/PersonListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /programs: - get: - tags: - - Programs - summary: Get a filtered list of Program - description: Get a list of Program - parameters: - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: programName - in: query - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - required: false - schema: - type: string - - name: abbreviation - in: query - description: A list of shortened human readable names for a set of Programs - required: false - schema: - type: string - - name: programType - in: query - description: "The type of program entity this object represents\n
'STANDARD'\ - \ represents a standard, permanent breeding program\n
'PROJECT' represents\ - \ a short term project, usually with a set time limit based on funding " - required: false - schema: - type: string - description: |- - The type of program entity this object represents -
'STANDARD' represents a standard, permanent breeding program -
'PROJECT' represents a short term project, usually with a set time limit based on funding. - enum: - - STANDARD - - PROJECT - - $ref: "#/components/parameters/externalReferenceId" - - $ref: "#/components/parameters/externalReferenceID" - - $ref: "#/components/parameters/externalReferenceSource" - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/ProgramListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - post: - tags: - - Programs - summary: Create new Program - description: Add new Program to database - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - type: array - items: - $ref: "#/components/schemas/ProgramNewRequest" - responses: - "200": - $ref: "#/components/responses/ProgramListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /seasons: - get: - tags: - - Seasons - summary: Get a filtered list of Season - description: Get a list of Season - parameters: - - name: seasonDbId - in: query - description: "The unique identifier for a season. For backward compatibility\ - \ it can be a string like '2012', '1957-2004'." - required: false - schema: - type: string - - name: season - in: query - description: The term to describe a given season. Example "Spring" OR "May" - OR "Planting_Time_7". - required: false - schema: - type: string - - name: seasonName - in: query - description: The term to describe a given season. Example "Spring" OR "May" - OR "Planting_Time_7". - required: false - schema: - type: string - - name: year - in: query - description: The 4 digit year of a season. Example 2017 - required: false - schema: - type: integer - format: int32 - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/SeasonListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - post: - tags: - - Seasons - summary: Create new Season - description: Add new Season to database - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - type: array - items: - $ref: "#/components/schemas/Season" - responses: - "200": - $ref: "#/components/responses/SeasonListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /studies: - get: - tags: - - Studies - summary: Get a filtered list of Study - description: Get a list of Study - parameters: - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - - name: germplasmDbId - in: query - description: List of IDs which uniquely identify germplasm to search for - required: false - schema: - type: string - - name: locationDbId - in: query - description: The location ids to search for - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: studyDbId - in: query - description: List of study identifiers to search for - required: false - schema: - type: string - - name: studyName - in: query - description: List of study names to filter search results - required: false - schema: - type: string - - name: trialDbId - in: query - description: The ID which uniquely identifies a trial to search for - required: false - schema: - type: string - - name: observationVariableDbId - in: query - description: The DbIds of Variables to search for - required: false - schema: - type: string - - name: active - in: query - description: A flag to indicate if a Study is currently active and ongoing - required: false - schema: - type: boolean - - name: seasonDbId - in: query - description: The ID which uniquely identifies a season - required: false - schema: - type: string - - name: studyType - in: query - description: "The type of study being performed. ex. \"Yield Trial\", etc" - required: false - schema: - type: string - - name: studyCode - in: query - description: A short human readable code for a study - required: false - schema: - type: string - - name: studyPUI - in: query - description: "Permanent unique identifier associated with study data. For\ - \ example, a URI or DOI" - required: false - schema: - type: string - - name: sortBy - in: query - description: Name of the field to sort by. - required: false - schema: - type: string - description: Name of the field to sort by. - enum: - - studyDbId - - trialDbId - - programDbId - - locationDbId - - seasonDbId - - studyType - - studyName - - studyLocation - - programName - - germplasmDbId - - observationVariableDbId - - name: sortOrder - in: query - description: Sort order direction. Ascending/Descending. - required: false - schema: - type: string - description: Sort order direction. Ascending/Descending. - enum: - - ASC - - DESC - - asc - - desc - - $ref: "#/components/parameters/externalReferenceId" - - $ref: "#/components/parameters/externalReferenceID" - - $ref: "#/components/parameters/externalReferenceSource" - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/StudyListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - post: - tags: - - Studies - summary: Create new Study - description: Add new Study to database - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - type: array - items: - $ref: "#/components/schemas/StudyNewRequest" - responses: - "200": - $ref: "#/components/responses/StudyListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /trials: - get: - tags: - - Trials - summary: Get a filtered list of Trial - description: Get a list of Trial - parameters: - - name: commonCropName - in: query - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at a\ - \ high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common\ - \ crop names.\n\nUse this parameter to only return results associated with\ - \ the given crops. \n\nUse `GET /commoncropnames` to find the list of available\ - \ crops on a server." - required: false - schema: - type: string - - name: locationDbId - in: query - description: The location ids to search for - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: studyDbId - in: query - description: List of study identifiers to search for - required: false - schema: - type: string - - name: trialDbId - in: query - description: The ID which uniquely identifies a trial to search for - required: false - schema: - type: string - - name: trialName - in: query - description: The human readable name of a trial to search for - required: false - schema: - type: string - - name: active - in: query - description: A flag to indicate if a Trial is currently active and ongoing - required: false - schema: - type: boolean - - name: contactDbId - in: query - description: List of contact entities associated with this trial - required: false - schema: - type: string - - name: searchDateRangeStart - in: query - description: "The start of the overlapping search date range. `searchDateRangeStart`\ - \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of\ - \ the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate`\ - \ AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before\ - \ `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n\ - - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is before `trial.endDate`" - required: false - schema: - type: string - format: date - - name: searchDateRangeEnd - in: query - description: "The end of the overlapping search date range. `searchDateRangeStart`\ - \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of\ - \ the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate`\ - \ AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before\ - \ `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n\ - - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is before `trial.endDate`" - required: false - schema: - type: string - format: date - - name: trialPUI - in: query - description: A permanent identifier for a trial. Could be DOI or other URI - formatted identifier. - required: false - schema: - type: string - - name: sortBy - in: query - description: Name of the field to sort by. - required: false - schema: - type: string - description: Name of the field to sort by. - enum: - - trialDbId - - trialName - - programDbId - - programName - - locationDbId - - startDate - - endDate - - name: sortOrder - in: query - description: Sort order direction. Ascending/Descending. - required: false - schema: - type: string - description: Sort order direction. Ascending/Descending. - enum: - - ASC - - DESC - - asc - - desc - - $ref: "#/components/parameters/externalReferenceId" - - $ref: "#/components/parameters/externalReferenceID" - - $ref: "#/components/parameters/externalReferenceSource" - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/TrialListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - post: - tags: - - Trials - summary: Create new Trial - description: Add new Trial to database - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - type: array - items: - $ref: "#/components/schemas/TrialNewRequest" - responses: - "200": - $ref: "#/components/responses/TrialListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /commoncropnames: - get: - tags: - - Programs - summary: Get the commonCropNames of Program - description: List all available Program commonCropNames - parameters: - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/ProgramCommonCropNameListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /observationlevels: - get: - tags: - - Studies - summary: Get the observationLevelses of Study - description: List all available Study observationLevelses - parameters: - - name: studyDbId - in: query - description: List of study identifiers to search for - required: false - schema: - type: string - - name: programDbId - in: query - description: "A BrAPI Program represents the high level organization or group\ - \ who is responsible for conducting trials and studies. Things like Breeding\ - \ Programs and Funded Projects are considered BrAPI Programs. \n\nUse this\ - \ parameter to only return results associated with the given programs. \n\ - \nUse `GET /programs` to find the list of available programs on a server." - required: false - schema: - type: string - - name: trialDbId - in: query - description: The ID which uniquely identifies a trial to search for - required: false - schema: - type: string - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/StudyObservationLevelsListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /studytypes: - get: - tags: - - Studies - summary: Get the studyTypes of Study - description: List all available Study studyTypes - parameters: - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/StudyStudyTypeListResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /lists/{listDbId}: - get: - tags: - - Lists - summary: Get the details of a specific List - description: Get details for a List - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: listDbId - in: path - description: The unique identifier for a List - required: true - schema: - type: string - responses: - "200": - $ref: "#/components/responses/ListSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - put: - tags: - - Lists - summary: Update the details for an existing List - description: Update the details for an existing List - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: listDbId - in: path - description: The unique identifier for a List - required: true - schema: - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ListNewRequest" - responses: - "200": - $ref: "#/components/responses/ListSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /lists/{listDbId}/data: - post: - tags: - - Lists - summary: Create new string - description: Add new string to database - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: listDbId - in: path - description: The unique identifier for a List - required: true - schema: - type: string - requestBody: - content: - application/json: - schema: - type: string - responses: - "200": - $ref: "#/components/responses/ListSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /locations/{locationDbId}: - get: - tags: - - Locations - summary: Get the details of a specific Location - description: Get details for a Location - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: locationDbId - in: path - description: The unique identifier for a Location - required: true - schema: - type: string - responses: - "200": - $ref: "#/components/responses/LocationSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - put: - tags: - - Locations - summary: Update the details for an existing Location - description: Update the details for an existing Location - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: locationDbId - in: path - description: The unique identifier for a Location - required: true - schema: - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/LocationNewRequest" - responses: - "200": - $ref: "#/components/responses/LocationSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /people/{personDbId}: - get: - tags: - - People - summary: Get the details of a specific Person - description: Get details for a Person - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: personDbId - in: path - description: Unique ID for a person - required: true - schema: - type: string - responses: - "200": - $ref: "#/components/responses/PersonSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - put: - tags: - - People - summary: Update the details for an existing Person - description: Update the details for an existing Person - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: personDbId - in: path - description: Unique ID for a person - required: true - schema: - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/PersonNewRequest" - responses: - "200": - $ref: "#/components/responses/PersonSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /programs/{programDbId}: - get: - tags: - - Programs - summary: Get the details of a specific Program - description: Get details for a Program - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: programDbId - in: path - description: The ID which uniquely identifies the program - required: true - schema: - type: string - responses: - "200": - $ref: "#/components/responses/ProgramSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - put: - tags: - - Programs - summary: Update the details for an existing Program - description: Update the details for an existing Program - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: programDbId - in: path - description: The ID which uniquely identifies the program - required: true - schema: - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ProgramNewRequest" - responses: - "200": - $ref: "#/components/responses/ProgramSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /seasons/{seasonDbId}: - get: - tags: - - Seasons - summary: Get the details of a specific Season - description: Get details for a Season - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: seasonDbId - in: path - description: "The ID which uniquely identifies a season. For backward compatibility\ - \ it can be a string like '2012', '1957-2004'" - required: true - schema: - type: string - responses: - "200": - $ref: "#/components/responses/SeasonSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - put: - tags: - - Seasons - summary: Update the details for an existing Season - description: Update the details for an existing Season - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: seasonDbId - in: path - description: "The ID which uniquely identifies a season. For backward compatibility\ - \ it can be a string like '2012', '1957-2004'" - required: true - schema: - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/Season" - responses: - "200": - $ref: "#/components/responses/SeasonSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /studies/{studyDbId}: - get: - tags: - - Studies - summary: Get the details of a specific Study - description: Get details for a Study - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: studyDbId - in: path - description: |- - The ID which uniquely identifies a study within the given database server - - MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. - required: true - schema: - type: string - responses: - "200": - $ref: "#/components/responses/StudySingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - put: - tags: - - Studies - summary: Update the details for an existing Study - description: Update the details for an existing Study - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: studyDbId - in: path - description: |- - The ID which uniquely identifies a study within the given database server - - MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. - required: true - schema: - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/StudyNewRequest" - responses: - "200": - $ref: "#/components/responses/StudySingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /trials/{trialDbId}: - get: - tags: - - Trials - summary: Get the details of a specific Trial - description: Get details for a Trial - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: trialDbId - in: path - description: |- - The ID which uniquely identifies a trial - - MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. - required: true - schema: - type: string - responses: - "200": - $ref: "#/components/responses/TrialSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - put: - tags: - - Trials - summary: Update the details for an existing Trial - description: Update the details for an existing Trial - parameters: - - $ref: "#/components/parameters/authorizationHeader" - - name: trialDbId - in: path - description: |- - The ID which uniquely identifies a trial - - MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. - required: true - schema: - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/TrialNewRequest" - responses: - "200": - $ref: "#/components/responses/TrialSingleResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /search/lists: - post: - tags: - - Lists - summary: Submit a search request for `List` - description: "Submit a search request for `List`
\nSearch requests allow\ - \ a client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.\ - \
\nReview the Search Services documentation for additional implementation details." - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ListSearchRequest" - responses: - "200": - $ref: "#/components/responses/ListListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /search/locations: - post: - tags: - - Locations - summary: Submit a search request for `Location` - description: "Submit a search request for `Location`
\nSearch requests allow\ - \ a client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/location/{searchResultsDbId}` to retrieve the results of the\ - \ search.
\nReview the Search Services documentation for additional implementation details." - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/LocationSearchRequest" - responses: - "200": - $ref: "#/components/responses/LocationListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /search/people: - post: - tags: - - People - summary: Submit a search request for `Person` - description: "Submit a search request for `Person`
\nSearch requests allow\ - \ a client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/person/{searchResultsDbId}` to retrieve the results of the\ - \ search.
\nReview the Search Services documentation for additional implementation details." - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/PersonSearchRequest" - responses: - "200": - $ref: "#/components/responses/PersonListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /search/programs: - post: - tags: - - Programs - summary: Submit a search request for `Program` - description: "Submit a search request for `Program`
\nSearch requests allow\ - \ a client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/program/{searchResultsDbId}` to retrieve the results of the\ - \ search.
\nReview the Search Services documentation for additional implementation details." - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ProgramSearchRequest" - responses: - "200": - $ref: "#/components/responses/ProgramListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /search/studies: - post: - tags: - - Studies - summary: Submit a search request for `Study` - description: "Submit a search request for `Study`
\nSearch requests allow\ - \ a client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.\ - \
\nReview the Search Services documentation for additional implementation details." - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/StudySearchRequest" - responses: - "200": - $ref: "#/components/responses/StudyListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /search/trials: - post: - tags: - - Trials - summary: Submit a search request for `Trial` - description: "Submit a search request for `Trial`
\nSearch requests allow\ - \ a client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.\ - \
\nReview the Search Services documentation for additional implementation details." - parameters: - - $ref: "#/components/parameters/authorizationHeader" - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/TrialSearchRequest" - responses: - "200": - $ref: "#/components/responses/TrialListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - /search/lists/{searchResultsDbId}: - get: - tags: - - Lists - summary: "Submit a search request for `List`
\nSearch requests allow a client\ - \ to send a complex query for data. However, the server may not respond with\ - \ the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.\ - \
\nReview the Search Services documentation for additional implementation details." - description: "Get the results of a `List` search request
\nClients should\ - \ submit a search request using the corresponding `POST /search/list` endpoint.\n\ - Search requests allow a client to send a complex query for data. However,\ - \ the server may not respond with the search results immediately. \nIf a server\ - \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ - \ \nUse this endpoint to retrieve the results of the search.
\nReview\ - \ the Search Services documentation for additional implementation details." - parameters: - - name: searchResultsDbId - in: path - description: searchResultsDbId - required: true - schema: - type: string - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/ListListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /search/locations/{searchResultsDbId}: - get: - tags: - - Locations - summary: "Submit a search request for `Location`
\nSearch requests allow\ - \ a client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/location/{searchResultsDbId}` to retrieve the results of the\ - \ search.
\nReview the Search Services documentation for additional implementation details." - description: "Get the results of a `Location` search request
\nClients\ - \ should submit a search request using the corresponding `POST /search/location`\ - \ endpoint.\nSearch requests allow a client to send a complex query for data.\ - \ However, the server may not respond with the search results immediately.\ - \ \nIf a server needs more time to process the request, it might respond with\ - \ a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the\ - \ search.
\nReview the Search Services documentation for additional implementation details." - parameters: - - name: searchResultsDbId - in: path - description: searchResultsDbId - required: true - schema: - type: string - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/LocationListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /search/people/{searchResultsDbId}: - get: - tags: - - People - summary: "Submit a search request for `Person`
\nSearch requests allow a\ - \ client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/person/{searchResultsDbId}` to retrieve the results of the\ - \ search.
\nReview the Search Services documentation for additional implementation details." - description: "Get the results of a `Person` search request
\nClients should\ - \ submit a search request using the corresponding `POST /search/person` endpoint.\n\ - Search requests allow a client to send a complex query for data. However,\ - \ the server may not respond with the search results immediately. \nIf a server\ - \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ - \ \nUse this endpoint to retrieve the results of the search.
\nReview\ - \ the Search Services documentation for additional implementation details." - parameters: - - name: searchResultsDbId - in: path - description: searchResultsDbId - required: true - schema: - type: string - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/PersonListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /search/programs/{searchResultsDbId}: - get: - tags: - - Programs - summary: "Submit a search request for `Program`
\nSearch requests allow\ - \ a client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/program/{searchResultsDbId}` to retrieve the results of the\ - \ search.
\nReview the Search Services documentation for additional implementation details." - description: "Get the results of a `Program` search request
\nClients should\ - \ submit a search request using the corresponding `POST /search/program` endpoint.\n\ - Search requests allow a client to send a complex query for data. However,\ - \ the server may not respond with the search results immediately. \nIf a server\ - \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ - \ \nUse this endpoint to retrieve the results of the search.
\nReview\ - \ the Search Services documentation for additional implementation details." - parameters: - - name: searchResultsDbId - in: path - description: searchResultsDbId - required: true - schema: - type: string - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/ProgramListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /search/studies/{searchResultsDbId}: - get: - tags: - - Studies - summary: "Submit a search request for `Study`
\nSearch requests allow a\ - \ client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.\ - \
\nReview the Search Services documentation for additional implementation details." - description: "Get the results of a `Study` search request
\nClients should\ - \ submit a search request using the corresponding `POST /search/study` endpoint.\n\ - Search requests allow a client to send a complex query for data. However,\ - \ the server may not respond with the search results immediately. \nIf a server\ - \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ - \ \nUse this endpoint to retrieve the results of the search.
\nReview\ - \ the Search Services documentation for additional implementation details." - parameters: - - name: searchResultsDbId - in: path - description: searchResultsDbId - required: true - schema: - type: string - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/StudyListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /search/trials/{searchResultsDbId}: - get: - tags: - - Trials - summary: "Submit a search request for `Trial`
\nSearch requests allow a\ - \ client to send a complex query for data. However, the server may not respond\ - \ with the search results immediately. \nIf a server needs more time to process\ - \ the request, it might respond with a `searchResultsDbId`. \nUse the corresponding\ - \ `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.\ - \
\nReview the Search Services documentation for additional implementation details." - description: "Get the results of a `Trial` search request
\nClients should\ - \ submit a search request using the corresponding `POST /search/trial` endpoint.\n\ - Search requests allow a client to send a complex query for data. However,\ - \ the server may not respond with the search results immediately. \nIf a server\ - \ needs more time to process the request, it might respond with a `searchResultsDbId`.\ - \ \nUse this endpoint to retrieve the results of the search.
\nReview\ - \ the Search Services documentation for additional implementation details." - parameters: - - name: searchResultsDbId - in: path - description: searchResultsDbId - required: true - schema: - type: string - - $ref: "#/components/parameters/page" - - $ref: "#/components/parameters/pageSize" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - $ref: "#/components/responses/TrialListResponse" - "202": - $ref: "#/components/responses/202AcceptedSearchResponse" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" - "404": - $ref: "#/components/responses/404NotFound" - /serverinfo: - get: - tags: - - Server Info - summary: Get the list of implemented Calls - description: "Implementation Notes\n\nHaving a consistent structure for the\ - \ path string of each call is very \nimportant for teams to be able to connect\ - \ and find errors. Read more on Github.\n\nHere are the rules for the path\ - \ of each call that should be returned\n\nEvery word in the call path should\ - \ match the documentation exactly, both in \nspelling and capitalization.\ - \ Note that path strings are all lower case, but \npath parameters are camel\ - \ case.\n\nEach path should start relative to \\\"/\\\" and therefore should\ - \ not include \\\"/\\\"\n\nNo leading or trailing slashes (\\\"/\\\") \n\n\ - Path parameters are wrapped in curly braces (\\\"{}\\\"). The name of the\ - \ path parameter \nshould be spelled exactly as it is specified in the documentation.\n\ - \nExamples \n\nGOOD \"call\": \"germplasm/{germplasmDbId}/pedigree\" \n\n\ - BAD \"call\": \"germplasm/{id}/pedigree\"\n\nBAD \"call\": \"germplasm/{germplasmDBid}/pedigree\"\ - \ \n\nBAD \"call\": \"brapi/v2/germplasm/{germplasmDbId}/pedigree\" \n\n\ - BAD \"call\": \"/germplasm/{germplasmDbId}/pedigree/\" \n\nBAD \"call\"\ - : \"germplasm//pedigree\"" - parameters: - - name: contentType - in: query - description: Filter the list of endpoints based on the response content type. - required: false - style: form - explode: true - schema: - $ref: "#/components/schemas/ContentTypes" - - name: dataType - in: query - description: |- - **Deprecated in v2.1** Please use `contentType`. Github issue number #443 -
The data format supported by the call. - required: false - deprecated: true - style: form - explode: true - schema: - $ref: "#/components/schemas/ContentTypes" - - $ref: "#/components/parameters/authorizationHeader" - responses: - "200": - description: OK - content: - application/json: - schema: - title: ServerInfoResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/ServerInfo" - "400": - $ref: "#/components/responses/400BadRequest" - "401": - $ref: "#/components/responses/401Unauthorized" - "403": - $ref: "#/components/responses/403Forbidden" -components: - schemas: - AdditionalInfo: - type: string - additionalProperties: - description: A free space containing any additional information related to - a particular object. - description: "A free space containing any additional information related to\ - \ a particular object. A data source may provide any JSON object, unrestricted\ - \ by the BrAPI specification." - nullable: true - AlleleMatrixPagination: - type: object - properties: - dimension: - type: string - description: the dimension of the matrix being paginated - example: VARIANTS - enum: - - CALLSETS - - VARIANTS - page: - type: integer - description: the requested page number (zero indexed) - format: int32 - example: 0 - pageSize: - type: integer - description: the maximum number of elements per page in this dimension of - the matrix - format: int32 - example: 500 - AlleleMatrixRequest: - type: object - properties: - callSetDbIds: - type: array - description: A list of IDs which uniquely identify `CallSets` within the - given database server - items: - type: string - dataMatrixAbbreviations: - type: array - description: "`dataMatrixAbbreviations` is a list of abbreviations (ie 'GT',\ - \ 'RD' etc). This list controls which data matrices are returned in the\ - \ response." - nullable: true - items: - type: string - dataMatrixNames: - type: array - description: "`dataMatrixNames` is a list of names (ie 'Genotype', 'Read\ - \ Depth' etc). This list controls which data matrices are returned in\ - \ the response." - nullable: true - items: - type: string - dimensionCallSetPage: - type: integer - description: The requested page number for the CallSet dimension of the - matrix - format: int32 - nullable: true - dimensionCallSetPageSize: - type: integer - description: The requested page size for the CallSet dimension of the matrix - format: int32 - nullable: true - dimensionVariantPage: - type: integer - description: The requested page number for the Variant dimension of the - matrix - format: int32 - nullable: true - dimensionVariantPageSize: - type: integer - description: The requested page size for the Variant dimension of the matrix - format: int32 - nullable: true - expandHomozygotes: - type: boolean - description: Should homozygotes be expanded (true) or collapsed into a single - occurrence (false) - nullable: true - example: true - germplasmDbIds: - type: array - description: A list of IDs which uniquely identify `Germplasm` within the - given database server - nullable: true - items: - type: string - germplasmNames: - type: array - description: A list of human readable `Germplasm` names - nullable: true - items: - type: string - germplasmPUIs: - type: array - description: A list of permanent unique identifiers associated with `Germplasm` - nullable: true - items: - type: string - pagination: - type: array - description: Pagination for the matrix - nullable: true - items: - type: object - properties: - dimension: - type: string - description: the dimension of the matrix being paginated - example: VARIANTS - enum: - - CALLSETS - - VARIANTS - page: - type: integer - description: the requested page number (zero indexed) - format: int32 - example: 0 - pageSize: - type: integer - description: the maximum number of elements per page in this dimension - of the matrix - format: int32 - example: 500 - positionRanges: - type: array - description: "The postion range to search\n
\nUses the format \":-\"\ - \ where is the chromosome name, is \nthe starting position\ - \ of the range, and is the ending position of the range" - nullable: true - items: - type: string - preview: - type: boolean - description: "Default Value = false\n
\nIf 'preview' is set to true,\ - \ then the server should only return the lists of 'callSetDbIds', \n'variantDbIds',\ - \ and 'variantSetDbIds'. The server should not return any matrix data.\ - \ This\nis intended to be a preview and give the client a sense of how\ - \ large the matrix returned will be\n
\nIf 'preview' is set to false\ - \ or not set (default), then the server should return all the matrix\n\ - data as requested." - example: true - default: false - sampleDbIds: - type: array - description: A list of IDs which uniquely identify `Samples` within the - given database server - nullable: true - items: - type: string - sepPhased: - type: string - description: The string used as a separator for phased allele calls. - nullable: true - example: '|' - sepUnphased: - type: string - description: The string used as a separator for unphased allele calls. - nullable: true - example: / - unknownString: - type: string - description: The string used as a representation for missing data. - nullable: true - example: "." - variantDbIds: - type: array - description: A list of IDs which uniquely identify `Variants` within the - given database server - nullable: true - items: - type: string - variantSetDbIds: - type: array - description: A list of IDs which uniquely identify `VariantSets` within - the given database server - nullable: true - items: - type: string - Attribute: - required: - - attributeName - - method - - scale - - trait - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - attributeCategory: - type: string - description: General category for the attribute. very similar to Trait class. - example: Morphological - attributeDbId: - type: string - description: The ID which uniquely identifies this attribute within the - given database server - attributeDescription: - type: string - description: A human readable description of this attribute - example: Height of the plant measured in meters by a tape - attributeName: - type: string - description: A human readable name for this attribute - example: Plant Height 1 - attributePUI: - type: string - description: "The Permanent Unique Identifier of an Attribute, usually in\ - \ the form of a URI" - example: http://my-traits.com/trait/CO_123:0008012 - commonCropName: - type: string - description: "Crop name (examples: \"Maize\", \"Wheat\")" - nullable: true - contextOfUse: - type: array - description: "Indication of how trait is routinely used. (examples: [\"\ - Trial evaluation\", \"Nursery evaluation\"])" - nullable: true - items: - type: string - defaultValue: - type: string - description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" - nullable: true - documentationURL: - type: string - description: A URL to the human readable documentation of an object - format: uri - nullable: true - externalReferences: - type: array - description: An array of external reference ids. These are references to - this piece of data in an external system. Could be a simple string or - a URI. - nullable: true - items: - $ref: "#/components/schemas/ExternalReference" - growthStage: - type: string - description: "Growth stage at which measurement is made (examples: \"flowering\"\ - )" - nullable: true - institution: - type: string - description: Name of institution submitting the variable - nullable: true - language: - type: string - description: 2 letter ISO 639-1 code for the language of submission of the - variable. - nullable: true - method: - $ref: "#/components/schemas/Method" - ontologyReference: - nullable: true - allOf: - - $ref: "#/components/schemas/OntologyReference" - scale: - $ref: "#/components/schemas/Scale" - scientist: - type: string - description: Name of scientist submitting the variable. - nullable: true - status: - type: string - description: "Variable status. (examples: \"recommended\", \"obsolete\"\ - , \"legacy\", etc.)" - nullable: true - submissionTimestamp: - type: string - description: Timestamp when the Variable was added (ISO 8601) - format: date-time - nullable: true - synonyms: - type: array - description: Other variable names - nullable: true - items: - type: string - trait: - $ref: "#/components/schemas/Trait" - CallRequest: - type: object - properties: - callSetDbIds: - type: array - description: A list of IDs which uniquely identify `CallSets` within the - given database server - nullable: true - items: - type: string - expandHomozygotes: - type: boolean - description: Should homozygotes be expanded (true) or collapsed into a single - occurrence (false) - nullable: true - example: true - pageToken: - type: string - description: |- - The continuation token, which is used to page through large result sets. - To get the next page of results, set this parameter to the value of - `next_page_token` from the previous response. - deprecated: true - sepPhased: - type: string - description: The string used as a separator for phased allele calls. - nullable: true - example: '|' - sepUnphased: - type: string - description: The string used as a separator for unphased allele calls. - nullable: true - example: / - unknownString: - type: string - description: The string used as a representation for missing data. - nullable: true - example: "." - variantDbIds: - type: array - description: A list of IDs which uniquely identify `Variant` within the - given database server - nullable: true - items: - type: string - variantSetDbIds: - type: array - description: A list of IDs which uniquely identify `VariantSets` within - the given database server - nullable: true - items: - type: string - CallSetRequest: - type: object - properties: - callSetDbIds: - type: array - description: A list of IDs which uniquely identify `CallSets` within the - given database server - nullable: true - items: - type: string - callSetNames: - type: array - description: A list of human readable names associated with `CallSets` - nullable: true - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - sampleDbIds: - type: array - description: A list of IDs which uniquely identify `Samples` within the - given database server - nullable: true - items: - type: string - sampleNames: - type: array - description: A list of human readable names associated with `Samples` - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - variantSetDbIds: - type: array - description: A list of IDs which uniquely identify `VariantSets` within - the given database server - nullable: true - items: - type: string - CommonCropNamesParameters: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - Contact: - required: - - contactDbId - type: object - properties: - contactDbId: - type: string - description: |- - The ID which uniquely identifies this contact - - MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. - email: - type: string - description: |- - The contacts email address - - MIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person. - nullable: true - instituteName: - type: string - description: |- - The name of the institution which this contact is part of - - MIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to - nullable: true - name: - type: string - description: |- - The full name of this contact person - - MIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications) - nullable: true - orcid: - type: string - description: |- - The Open Researcher and Contributor ID for this contact person (orcid.org) - - MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. - nullable: true - type: - type: string - description: |- - The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.) - - MIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation - nullable: true - description: A persons contact information - ContentTypes: - type: string - enum: - - application/json - - text/csv - - text/tsv - - application/flapjack - Context: - title: context - type: array - description: "The JSON-LD Context is used to provide JSON-LD definitions to\ - \ each field in a JSON object. By providing an array of context file urls,\ - \ a BrAPI response object becomes JSON-LD compatible. \n\nFor more information,\ - \ see https://w3c.github.io/json-ld-syntax/#the-context" - example: - - https://brapi.org/jsonld/context/metadata.jsonld - items: - type: string - format: uri - CrossRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - crossDbIds: - type: array - description: Search for Cross with this unique id - items: - type: string - crossNames: - type: array - description: Search for Cross with this human readable name - items: - type: string - crossingProjectDbIds: - type: array - description: Search for Crossing Projects with this unique id - items: - type: string - crossingProjectNames: - type: array - description: The human readable name for a crossing project - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - CrossStatus: - type: string - enum: - - TODO - - DONE - - SKIPPED - CrossingProjectRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - crossingProjectDbIds: - type: array - description: Search for Crossing Projects with this unique id - items: - type: string - crossingProjectNames: - type: array - description: The human readable name for a crossing project - items: - type: string - includePotentialParents: - type: boolean - description: "If the parameter 'includePotentialParents' is false, the array\ - \ 'potentialParents' should be empty, null, or excluded from the response\ - \ object." - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - DataLink: - type: object - properties: - dataFormat: - type: string - description: |- - The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy) - - MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. - nullable: true - description: - type: string - description: |- - The general description of this data link - - MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. - nullable: true - fileFormat: - type: string - description: |- - The MIME type of the file (ie text/csv, application/excel, application/zip). - - MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. - nullable: true - name: - type: string - description: |- - The name of the external data link - - MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. - nullable: true - provenance: - type: string - description: "The description of the origin or ownership of this linked\ - \ data. Could be a formal reference to software, method, or workflow." - nullable: true - scientificType: - type: string - description: "The general type of data. For example- Genotyping, Phenotyping\ - \ raw data, Phenotyping reduced data, Environmental, etc" - nullable: true - url: - type: string - description: |- - URL describing the location of this data file to view or download - - MIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission. - format: uri - nullable: true - version: - type: string - description: "The version number for this data \n\nMIAPPE V1.1 (DM-39) Data\ - \ file version - The version of the dataset (the actual data)." - nullable: true - description: "A link to extra data files associated with this study. Extra data\ - \ could include notes, images, and reference data." - DatasetAuthorships: - type: object - properties: - datasetPUI: - type: string - description: The DOI or other permanent unique identifier for this published - dataset - nullable: true - license: - type: string - description: MIAPPE V1.1 (DM-7) License - License for the reuse of the data - associated with this investigation. The Creative Commons licenses cover - most use cases and are recommended. - nullable: true - publicReleaseDate: - type: string - description: MIAPPE V1.1 (DM-6) Public release date - Date of first public - release of the dataset presently being described. - nullable: true - submissionDate: - type: string - description: MIAPPE V1.1 (DM-5) Submission date - Date of submission of - the dataset presently being described to a host repository. - nullable: true - description: License and citation information for the data in this trial - Dimension: - type: string - description: the dimension of the matrix being paginated - enum: - - CALLSETS - - VARIANTS - EnvironmentParameter: - required: - - description - - parameterName - type: object - properties: - description: - type: string - description: Human-readable value of the environment parameter (defined - above) constant within the experiment - parameterName: - type: string - description: "Name of the environment parameter constant within the experiment\n\ - \nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment\ - \ parameter constant within the experiment. " - parameterPUI: - type: string - description: URI pointing to an ontology class for the parameter - nullable: true - unit: - type: string - description: Unit of the value for this parameter - nullable: true - unitPUI: - type: string - description: URI pointing to an ontology class for the unit - nullable: true - value: - type: string - description: |- - Numerical or categorical value - - MIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment. - nullable: true - valuePUI: - type: string - description: URI pointing to an ontology class for the parameter value - nullable: true - description: "Environmental parameters that were kept constant throughout the\ - \ study and did not change between observation units. \n\nMIAPPE V1.1 (DM-57)\ - \ Environment - Environmental parameters that were kept constant throughout\ - \ the study and did not change between observation units or assays. Environment\ - \ characteristics that vary over time, i.e. environmental variables, should\ - \ be recorded as Observed Variables (see below)." - EventRequest: - type: object - properties: - dateRangeEnd: - type: string - description: Filter based on an Event start date. - format: date-time - dateRangeStart: - type: string - description: Filter based on an Event start date. - format: date-time - eventDbIds: - type: array - description: Filter based on an Event DbId. - items: - type: string - eventTypes: - type: array - description: Filter based on an Event Type - items: - type: string - observationUnitDbIds: - type: array - description: The ID which uniquely identifies an observation unit. - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - ExperimentalDesign: - type: object - properties: - PUI: - type: string - description: "MIAPPE V1.1 (DM-23) Type of experimental design - Type of\ - \ experimental design of the study, in the form of an accession number\ - \ from the Crop Ontology." - nullable: true - description: - type: string - description: "MIAPPE V1.1 (DM-22) Description of the experimental design\ - \ - Short description of the experimental design, possibly including statistical\ - \ design. In specific cases, e.g. legacy datasets or data computed from\ - \ several studies, the experimental design can be \"unknown\"/\"NA\",\ - \ \"aggregated/reduced data\", or simply 'none'." - nullable: true - description: The experimental and statistical design full description plus a - category PUI taken from crop research ontology or agronomy ontology - nullable: true - ExternalReference: - type: object - properties: - referenceID: - type: string - description: "**Deprecated in v2.1** Please use `referenceId`. Github issue\ - \ number #460
The external reference ID. Could be a simple string\ - \ or a URI." - nullable: true - deprecated: true - referenceId: - type: string - description: The external reference ID. Could be a simple string or a URI. - referenceSource: - type: string - description: An identifier for the source system or database of this reference - ExternalReferencesParameters: - type: object - properties: - externalReferenceIDs: - type: array - description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ - \ Github issue number #460 \n
List of external reference IDs. Could\ - \ be a simple strings or a URIs. (use with `externalReferenceSources`\ - \ parameter)" - deprecated: true - items: - type: string - externalReferenceIds: - type: array - description: List of external reference IDs. Could be a simple strings or - a URIs. (use with `externalReferenceSources` parameter) - items: - type: string - externalReferenceSources: - type: array - description: List of identifiers for the source system or database of an - external reference (use with `externalReferenceIDs` parameter) - items: - type: string - GenomeMapRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - mapDbIds: - type: array - description: The ID which uniquely identifies a `GenomeMap` - items: - type: string - mapPUIs: - type: array - description: The DOI or other permanent identifier for a `GenomeMap` - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - scientificName: - type: array - description: "Full scientific binomial format name. This includes Genus,\ - \ Species, and Sub-species" - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - types: - type: array - description: "The type of map, usually \"Genetic\" or \"Physical\"" - items: - type: string - GeoJSON: - type: object - properties: - geometry: - $ref: "#/components/schemas/GeoJSONGeometry" - type: - type: string - description: The literal string "Feature" - example: Feature - default: Feature - description: |- - One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. - - Copied from RFC 7946 Section 3.1.1 - - A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. - nullable: true - GeoJSONGeometry: - type: object - discriminator: - propertyName: type - oneOf: - - required: - - coordinates - - type - type: object - properties: - coordinates: - type: array - description: A single position - items: - type: number - type: - type: string - description: The literal string "Point" - default: Point - description: |- - Copied from RFC 7946 Section 3.1.1 - - A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. - - required: - - coordinates - - type - type: object - properties: - coordinates: - type: array - description: An array of linear rings - items: - type: array - items: - type: array - items: - type: number - type: - type: string - description: The literal string "Polygon" - default: Polygon - description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ - \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ - \ The first two elements are longitude and latitude, or\neasting and northing,\ - \ precisely in that order and using decimal numbers. Altitude or elevation\ - \ MAY be included as an optional third element." - GeoJSONPoint: - required: - - coordinates - - type - type: object - properties: - coordinates: - type: array - description: A single position - items: - type: number - type: - type: string - description: The literal string "Point" - default: Point - description: |- - Copied from RFC 7946 Section 3.1.1 - - A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or - easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. - GeoJSONPolygon: - required: - - coordinates - - type - type: object - properties: - coordinates: - type: array - description: An array of linear rings - items: - type: array - items: - type: array - items: - type: number - type: - type: string - description: The literal string "Polygon" - default: Polygon - description: "An array of Linear Rings. Each Linear Ring is an array of Points.\ - \ \n\nA Point is an array of numbers. There MUST be two or more elements.\ - \ The first two elements are longitude and latitude, or\neasting and northing,\ - \ precisely in that order and using decimal numbers. Altitude or elevation\ - \ MAY be included as an optional third element." - GeoJSONSearchArea: - type: object - properties: - geometry: - $ref: "#/components/schemas/GeoJSONGeometry" - type: - type: string - description: The literal string "Feature" - example: Feature - default: Feature - GermplasmAttributeRequest: - type: object - properties: - attributeCategories: - type: array - description: General category for the attribute. very similar to Trait class. - nullable: true - items: - type: string - attributeDbIds: - type: array - description: List of Germplasm Attribute IDs to search for - nullable: true - items: - type: string - attributeNames: - type: array - description: List of human readable Germplasm Attribute names to search - for - nullable: true - items: - type: string - attributePUIs: - type: array - description: "The Permanent Unique Identifier of an Attribute, usually in\ - \ the form of a URI" - nullable: true - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - dataTypes: - type: array - description: List of scale data types to filter search results - items: - $ref: "#/components/schemas/TraitDataType" - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - methodDbIds: - type: array - description: List of methods to filter search results - items: - type: string - methodNames: - type: array - description: |- - Human readable name for the method -
MIAPPE V1.1 (DM-88) Method Name of the method of observation - items: - type: string - methodPUIs: - type: array - description: "The Permanent Unique Identifier of a Method, usually in the\ - \ form of a URI" - items: - type: string - ontologyDbIds: - type: array - description: List of ontology IDs to search for - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - scaleDbIds: - type: array - description: The unique identifier for a Scale - items: - type: string - scaleNames: - type: array - description: |- - Name of the scale -
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable - items: - type: string - scalePUIs: - type: array - description: "The Permanent Unique Identifier of a Scale, usually in the\ - \ form of a URI" - items: - type: string - studyDbId: - type: array - description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ - \ number #483 \n
The unique ID of a studies to filter on" - deprecated: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - traitAttributePUIs: - type: array - description: |- - The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI -
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" - items: - type: string - traitAttributes: - type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the attribute is the observed feature (or characteristic) of the entity\ - \ e.g., for \"grain colour\", attribute = \"colour\"" - items: - type: string - traitClasses: - type: array - description: List of trait classes to filter search results - items: - type: string - traitDbIds: - type: array - description: The unique identifier for a Trait - items: - type: string - traitEntities: - type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the entity is the part of the plant that the trait refers to e.g., for\ - \ \"grain colour\", entity = \"grain\"" - items: - type: string - traitEntityPUIs: - type: array - description: "The Permanent Unique Identifier of a Trait Entity, usually\ - \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ - \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ - \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " - items: - type: string - traitNames: - type: array - description: |- - The human readable name of a trait -
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation - items: - type: string - traitPUIs: - type: array - description: "The Permanent Unique Identifier of a Trait, usually in the\ - \ form of a URI" - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - GermplasmAttributeValueRequest: - type: object - properties: - attributeDbIds: - type: array - description: List of Germplasm Attribute IDs to search for - nullable: true - items: - type: string - attributeNames: - type: array - description: List of human readable Germplasm Attribute names to search - for - nullable: true - items: - type: string - attributeValueDbIds: - type: array - description: List of Germplasm Attribute Value IDs to search for - nullable: true - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - dataTypes: - type: array - description: List of scale data types to filter search results - nullable: true - items: - $ref: "#/components/schemas/TraitDataType" - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - methodDbIds: - type: array - description: List of methods to filter search results - nullable: true - items: - type: string - ontologyDbIds: - type: array - description: List of ontology IDs to search for - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - scaleDbIds: - type: array - description: List of scales to filter search results - nullable: true - items: - type: string - traitClasses: - type: array - description: List of trait classes to filter search results - nullable: true - items: - type: string - traitDbIds: - type: array - description: List of trait unique ID to filter search results - nullable: true - items: - type: string - GermplasmParameters: - type: object - properties: - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - GermplasmRequest: - type: object - properties: - accessionNumbers: - type: array - description: |- - A collection of unique identifiers for materials or germplasm within a genebank - - MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). - nullable: true - items: - type: string - binomialNames: - type: array - description: List of the full binomial name (scientific name) to identify - a germplasm - nullable: true - items: - type: string - collections: - type: array - description: A specific panel/collection/population name this germplasm - belongs to. - nullable: true - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - familyCodes: - type: array - description: A familyCode representing the family this germplasm belongs - to. - nullable: true - items: - type: string - genus: - type: array - description: List of Genus names to identify germplasm - nullable: true - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - germplasmPUIs: - type: array - description: List of Permanent Unique Identifiers to identify germplasm - nullable: true - items: - type: string - instituteCodes: - type: array - description: "The code for the institute that maintains the material. \n\ -
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ - \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ - \ country code of the country where the institute is located plus a number\ - \ (e.g. PER001). The current set of institute codes is available from\ - \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ - \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ - \ rules (v)\"." - nullable: true - items: - type: string - parentDbIds: - type: array - description: Search for Germplasm with these parents - nullable: true - items: - type: string - progenyDbIds: - type: array - description: Search for Germplasm with these children - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - species: - type: array - description: List of Species names to identify germplasm - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - synonyms: - type: array - description: List of alternative names or IDs used to reference this germplasm - nullable: true - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - GrowthFacility: - type: object - properties: - PUI: - type: string - description: "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth\ - \ facility in which the study was carried out, in the form of an accession\ - \ number from the Crop Ontology." - description: - type: string - description: MIAPPE V1.1 (DM-26) Description of growth facility - Short - description of the facility in which the study was carried out. - nullable: true - description: Short description of the facility in which the study was carried - out. - nullable: true - ImageRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - descriptiveOntologyTerms: - type: array - description: "A list of terms to formally describe the image to search for.\ - \ Each item could be a simple Tag, an Ontology reference Id, or a full\ - \ ontology URL." - items: - type: string - imageDbIds: - type: array - description: A list of image Ids to search for - items: - type: string - imageFileNames: - type: array - description: Image file names to search for. - items: - type: string - imageFileSizeMax: - type: integer - description: A maximum image file size to search for. - format: int32 - example: 20000000 - imageFileSizeMin: - type: integer - description: A minimum image file size to search for. - format: int32 - example: 1000 - imageHeightMax: - type: integer - description: A maximum image height to search for. - format: int32 - example: 1080 - imageHeightMin: - type: integer - description: A minimum image height to search for. - format: int32 - example: 720 - imageLocation: - $ref: "#/components/schemas/GeoJSONSearchArea" - imageNames: - type: array - description: Human readable names to search for. - items: - type: string - imageTimeStampRangeEnd: - type: string - description: The latest timestamp to search for. - format: date-time - imageTimeStampRangeStart: - type: string - description: The earliest timestamp to search for. - format: date-time - imageWidthMax: - type: integer - description: A maximum image width to search for. - format: int32 - example: 1920 - imageWidthMin: - type: integer - description: A minimum image width to search for. - format: int32 - example: 1280 - mimeTypes: - type: array - description: A set of image file types to search for. - items: - type: string - observationDbIds: - type: array - description: A list of observation Ids this image is associated with to - search for - items: - type: string - observationUnitDbIds: - type: array - description: A set of observation unit identifiers to search for. - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - LastUpdate: - type: object - properties: - timestamp: - type: string - description: The timestamp of the update. - format: date-time - nullable: true - version: - type: string - description: The version of the update. - nullable: true - description: The date and time when this study was last modified - nullable: true - List: - allOf: - - $ref: "#/components/schemas/ListNewRequest" - - required: - - listDbId - type: object - properties: - listDbId: - type: string - description: The unique identifier for a List - description: "A List represents a collection of other BrAPI data objects.\ - \ Typically these are custom lists generated by a user to keep track of\ - \ interesting data. For example, a user might build a List of Germplasm\ - \ that they have manually marked for further study." - ListNewRequest: - required: - - listName - - listType - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - data: - type: array - description: The array of DbIds of the BrAPI objects contained in a List - nullable: true - items: - type: string - dateCreated: - type: string - description: Timestamp when the entity was first created - format: date-time - nullable: true - dateModified: - type: string - description: Timestamp when the entity was last updated - format: date-time - nullable: true - externalReferences: - type: array - description: An array of external reference ids. These are references to - this piece of data in an external system. Could be a simple string or - a URI. - nullable: true - items: - $ref: "#/components/schemas/ExternalReference" - listDescription: - type: string - description: Description of a List - nullable: true - listName: - type: string - description: Human readable name of a List - listOwnerName: - type: string - description: Human readable name of a List Owner. (usually a user or person) - nullable: true - listOwnerPersonDbId: - type: string - listSize: - type: integer - description: The number of elements in a List - format: int32 - nullable: true - listSource: - type: string - description: The description of where a List originated from - nullable: true - listType: - $ref: "#/components/schemas/ListType" - description: "A List represents a collection of other BrAPI data objects. Typically\ - \ these are custom lists generated by a user to keep track of interesting\ - \ data. For example, a user might build a List of Germplasm that they have\ - \ manually marked for further study." - ListRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - dateCreatedRangeEnd: - type: string - description: Define the end for an interval of time and only include Lists - that are created within this interval. - format: date-time - nullable: true - dateCreatedRangeStart: - type: string - description: Define the beginning for an interval of time and only include - Lists that are created within this interval. - format: date-time - nullable: true - dateModifiedRangeEnd: - type: string - description: Define the end for an interval of time and only include Lists - that are modified within this interval. - format: date-time - nullable: true - dateModifiedRangeStart: - type: string - description: Define the beginning for an interval of time and only include - Lists that are modified within this interval. - format: date-time - nullable: true - listDbIds: - type: array - description: An array of primary database identifiers to identify a set - of Lists - nullable: true - items: - type: string - listNames: - type: array - description: An array of human readable names to identify a set of Lists - nullable: true - items: - type: string - listOwnerNames: - type: array - description: An array of names for the people or entities who are responsible - for a set of Lists - nullable: true - items: - type: string - listOwnerPersonDbIds: - type: array - description: An array of primary database identifiers to identify people - or entities who are responsible for a set of Lists - nullable: true - items: - type: string - listSources: - type: array - description: "An array of terms identifying lists from different sources\ - \ (ie 'USER', 'SYSTEM', etc)" - nullable: true - items: - type: string - listType: - nullable: true - allOf: - - $ref: "#/components/schemas/ListType" - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - ListSearchRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - dateCreatedRangeEnd: - type: string - description: Define the end for an interval of time and only include Lists - that are created within this interval. - format: date-time - nullable: true - dateCreatedRangeStart: - type: string - description: Define the beginning for an interval of time and only include - Lists that are created within this interval. - format: date-time - nullable: true - dateModifiedRangeEnd: - type: string - description: Define the end for an interval of time and only include Lists - that are modified within this interval. - format: date-time - nullable: true - dateModifiedRangeStart: - type: string - description: Define the beginning for an interval of time and only include - Lists that are modified within this interval. - format: date-time - nullable: true - externalReferenceIDs: - type: array - description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ - \ Github issue number #460 \n
List of external reference IDs. Could\ - \ be a simple strings or a URIs. (use with `externalReferenceSources`\ - \ parameter)" - deprecated: true - items: - type: string - externalReferenceIds: - type: array - description: List of external reference IDs. Could be a simple strings or - a URIs. (use with `externalReferenceSources` parameter) - items: - type: string - externalReferenceSources: - type: array - description: List of identifiers for the source system or database of an - external reference (use with `externalReferenceIDs` parameter) - items: - type: string - listDbIds: - type: array - description: An array of primary database identifiers to identify a set - of Lists - nullable: true - items: - type: string - listNames: - type: array - description: An array of human readable names to identify a set of Lists - nullable: true - items: - type: string - listOwnerNames: - type: array - description: An array of names for the people or entities who are responsible - for a set of Lists - nullable: true - items: - type: string - listOwnerPersonDbIds: - type: array - description: An array of primary database identifiers to identify people - or entities who are responsible for a set of Lists - nullable: true - items: - type: string - listSources: - type: array - description: "An array of terms identifying lists from different sources\ - \ (ie 'USER', 'SYSTEM', etc)" - nullable: true - items: - type: string - listType: - nullable: true - allOf: - - $ref: "#/components/schemas/ListType" - page: - type: integer - description: Which result page is requested. The page indexing starts at - 0 (the first page is 'page'= 0). Default is `0`. - format: int32 - example: 0 - pageSize: - type: integer - description: The size of the pages to be returned. Default is `1000`. - format: int32 - example: 1000 - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - description: "A List represents a collection of other BrAPI data objects. Typically\ - \ these are custom lists generated by a user to keep track of interesting\ - \ data. For example, a user might build a List of Germplasm that they have\ - \ manually marked for further study." - ListType: - type: string - description: The type of objects that are referenced in a List - enum: - - germplasm - - markers - - variants - - programs - - trials - - studies - - observationUnits - - observations - - observationVariables - - samples - Location: - allOf: - - $ref: "#/components/schemas/LocationNewRequest" - - required: - - locationDbId - type: object - properties: - locationDbId: - type: string - description: The unique identifier for a Location - description: "A geographic Location on earth. This is usually used to describe\ - \ the general area where an experiment took place. For example, a natural\ - \ site, an experimental field, a greenhouse, a phenotyping facility, etc." - LocationNewRequest: - required: - - locationName - type: object - properties: - abbreviation: - type: string - description: A shortened version of the human readable name for a Location - nullable: true - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - coordinateDescription: - type: string - description: "Describes the precision and landmarks of the coordinate values\ - \ used for a Location. (ex. the site, the nearest town, a 10 kilometers\ - \ radius circle, +/- 20 meters, etc)" - nullable: true - coordinateUncertainty: - type: string - description: Uncertainty associated with the coordinates in meters. Leave - the value empty if the uncertainty is unknown. - nullable: true - coordinates: - $ref: "#/components/schemas/GeoJSON" - countryCode: - type: string - description: |- - [ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec -
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.' - nullable: true - countryName: - type: string - description: |- - The full name of the country where a Location is located -
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code. - nullable: true - documentationURL: - type: string - description: A URL to the human readable documentation of an object - format: uri - nullable: true - environmentType: - type: string - description: "Describes the general type of environment of a Location. (ex.\ - \ forest, field, nursery, etc)" - nullable: true - exposure: - type: string - description: Describes the level of protection/exposure for things like - sun light and wind at a particular Location - nullable: true - externalReferences: - type: array - description: An array of external reference ids. These are references to - this piece of data in an external system. Could be a simple string or - a URI. - nullable: true - items: - $ref: "#/components/schemas/ExternalReference" - instituteAddress: - type: string - description: |- - The street address of the institute at a particular Location -
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. - nullable: true - instituteName: - type: string - description: |- - The full name of the institute at a particular Location -
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. - nullable: true - locationName: - type: string - description: |- - A human readable name for a Location -
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place. - locationType: - type: string - description: "A short description of a type of Location (ex. Field Station,\ - \ Breeding Location, Storage Location, etc)" - nullable: true - parentLocationDbId: - type: string - nullable: true - parentLocationName: - type: string - nullable: true - siteStatus: - type: string - description: "Description of the accessibility of the location (ex. Public,\ - \ Private)" - nullable: true - slope: - type: string - description: Describes the approximate slope (height/distance) of a Location. - nullable: true - topography: - type: string - description: "Describes the topography of the land at a Location. (ex. Plateau,\ - \ Cirque, Hill, Valley, etc)" - nullable: true - description: "A geographic Location on earth. This is usually used to describe\ - \ the general area where an experiment took place. For example, a natural\ - \ site, an experimental field, a greenhouse, a phenotyping facility, etc." - LocationParameters: - type: object - properties: - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - LocationRequest: - type: object - properties: - abbreviations: - type: array - description: A list of shortened human readable names for a set of Locations - nullable: true - items: - type: string - altitudeMax: - type: number - description: The maximum altitude to search for - nullable: true - example: 200 - altitudeMin: - type: number - description: The minimum altitude to search for - nullable: true - example: 20 - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - coordinates: - anyOf: - - $ref: "#/components/schemas/GeoJSONSearchArea" - - type: "null" - countryCodes: - type: array - description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ - \ spec" - nullable: true - items: - type: string - countryNames: - type: array - description: The full name of the country to search for - nullable: true - items: - type: string - instituteAddresses: - type: array - description: The street address of the institute to search for - nullable: true - items: - type: string - instituteNames: - type: array - description: The name of the institute to search for - nullable: true - items: - type: string - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - locationTypes: - type: array - description: "The type of location this represents (ex. Breeding Location,\ - \ Storage Location, etc)" - nullable: true - items: - type: string - parentLocationDbIds: - type: array - description: "The unique identifier for a Location\n
The Parent Location\ - \ defines the encompassing location that this location belongs to. \n\ - For example, an Institution might have multiple Field Stations inside\ - \ it and each Field Station might have multiple Fields." - nullable: true - items: - type: string - parentLocationNames: - type: array - description: "A human readable name for a location\n
The Parent Location\ - \ defines the encompassing location that this location belongs to. \n\ - For example, an Institution might have multiple Field Stations inside\ - \ it and each Field Station might have multiple Fields." - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - LocationSearchRequest: - type: object - properties: - abbreviations: - type: array - description: A list of shortened human readable names for a set of Locations - nullable: true - items: - type: string - altitudeMax: - type: number - description: The maximum altitude to search for - nullable: true - example: 200 - altitudeMin: - type: number - description: The minimum altitude to search for - nullable: true - example: 20 - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - coordinates: - anyOf: - - $ref: "#/components/schemas/GeoJSONSearchArea" - - type: "null" - countryCodes: - type: array - description: "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3)\ - \ spec" - nullable: true - items: - type: string - countryNames: - type: array - description: The full name of the country to search for - nullable: true - items: - type: string - externalReferenceIDs: - type: array - description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ - \ Github issue number #460 \n
List of external reference IDs. Could\ - \ be a simple strings or a URIs. (use with `externalReferenceSources`\ - \ parameter)" - deprecated: true - items: - type: string - externalReferenceIds: - type: array - description: List of external reference IDs. Could be a simple strings or - a URIs. (use with `externalReferenceSources` parameter) - items: - type: string - externalReferenceSources: - type: array - description: List of identifiers for the source system or database of an - external reference (use with `externalReferenceIDs` parameter) - items: - type: string - instituteAddresses: - type: array - description: The street address of the institute to search for - nullable: true - items: - type: string - instituteNames: - type: array - description: The name of the institute to search for - nullable: true - items: - type: string - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - locationTypes: - type: array - description: "The type of location this represents (ex. Breeding Location,\ - \ Storage Location, etc)" - nullable: true - items: - type: string - page: - type: integer - description: Which result page is requested. The page indexing starts at - 0 (the first page is 'page'= 0). Default is `0`. - format: int32 - example: 0 - pageSize: - type: integer - description: The size of the pages to be returned. Default is `1000`. - format: int32 - example: 1000 - parentLocationDbIds: - type: array - description: "The unique identifier for a Location\n
The Parent Location\ - \ defines the encompassing location that this location belongs to. \n\ - For example, an Institution might have multiple Field Stations inside\ - \ it and each Field Station might have multiple Fields." - nullable: true - items: - type: string - parentLocationNames: - type: array - description: "A human readable name for a location\n
The Parent Location\ - \ defines the encompassing location that this location belongs to. \n\ - For example, an Institution might have multiple Field Stations inside\ - \ it and each Field Station might have multiple Fields." - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - description: "A geographic Location on earth. This is usually used to describe\ - \ the general area where an experiment took place. For example, a natural\ - \ site, an experimental field, a greenhouse, a phenotyping facility, etc." - MarkerPositionRequest: - type: object - properties: - linkageGroupNames: - type: array - description: A list of Uniquely Identifiable linkage group names - nullable: true - items: - type: string - mapDbIds: - type: array - description: A list of IDs which uniquely identify `GenomeMaps` within the - given database server - nullable: true - items: - type: string - maxPosition: - type: integer - description: The maximum position of markers in a given map - format: int32 - nullable: true - example: 4000 - minPosition: - type: integer - description: The minimum position of markers in a given map - format: int32 - nullable: true - example: 250 - variantDbIds: - type: array - description: A list of IDs which uniquely identify `Variants` within the - given database server - nullable: true - items: - type: string - MethodRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - methodDbIds: - type: array - description: The unique identifier for a method. - items: - type: string - observationVariableDbIds: - type: array - description: The unique identifier for an observation variable. - items: - type: string - ontologyDbIds: - type: array - description: "The unique identifier for an ontology definition. Use this\ - \ parameter to filter results based on a specific ontology \n\n Use `GET\ - \ /ontologies` to find the list of available ontologies on a server." - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - ObservationRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - observationDbIds: - type: array - description: The unique id of an Observation - nullable: true - items: - type: string - observationLevelRelationships: - type: array - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships - nullable: true - items: - $ref: "#/components/schemas/ObservationUnitLevelRelationship" - observationLevels: - type: array - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel - nullable: true - items: - $ref: "#/components/schemas/ObservationUnitLevel" - observationTimeStampRangeEnd: - type: string - description: Timestamp range end - format: date-time - nullable: true - observationTimeStampRangeStart: - type: string - description: Timestamp range start - format: date-time - nullable: true - observationUnitDbIds: - type: array - description: The unique id of an Observation Unit - nullable: true - items: - type: string - observationUnitLevelCodes: - type: array - description: "The Observation Unit Level Code. This parameter should be\ - \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ - \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelNames: - type: array - description: "The Observation Unit Level. Returns only the observation unit\ - \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ - \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ - \ plot, sub-plot, plant, pot, sample** \n
For more information on\ - \ Observation Levels, please review the Observation Levels documentation. " - items: - type: string - observationUnitLevelOrders: - type: array - description: "The Observation Unit Level Order Number. Returns only the\ - \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipCodes: - type: array - description: "The Observation Unit Level Code. \n
This parameter should\ - \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ - \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipDbIds: - type: array - description: "The observationUnitDbId associated with a particular level\ - \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ - \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipNames: - type: array - description: "The Observation Unit Level Relationship is a connection that\ - \ this observation unit has to another level of the hierarchy. \n
For\ - \ example, if you have several observation units at a 'plot' level, they\ - \ might all share a relationship to the same 'field' level. \n
Use\ - \ this parameter to identify groups of observation units that share a\ - \ relationship level. \n
**Standard Level Names: study, field, entry,\ - \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ - \ more information on Observation Levels, please review the Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipOrders: - type: array - description: "The Observation Unit Level Order Number. \n
Returns only\ - \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - seasonDbIds: - type: array - description: "The year or Phenotyping campaign of a multi-annual study (trees,\ - \ grape, ...)" - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - ObservationUnitHierarchyLevel: - type: object - properties: - levelName: - type: string - description: "A name for this level \n\n**Standard Level Names: study, field,\ - \ entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\ - \nFor more information on Observation Levels, please review the Observation Levels documentation. " - nullable: true - levelOrder: - type: integer - description: "`levelOrder` defines where that level exists in the hierarchy\ - \ of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy\ - \ (ie field -> 1) and higher numbers are at the bottom of the hierarchy\ - \ (ie plant -> 9). \n\nFor more information on Observation Levels, please\ - \ review the Observation Levels documentation. " - format: int32 - nullable: true - description: "The exact level and level code of an observation unit. \n\nFor\ - \ more information on Observation Levels, please review the Observation\ - \ Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"\ - Type of observation unit in textual form, usually one of the following: study,\ - \ block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit\ - \ types is possible but not recommended. \nThe observation unit type can not\ - \ be used to indicate sub-plant levels. However, observations can still be\ - \ made on the sub-plant level, as long as the details are indicated in the\ - \ associated observed variable (see observed variables). \nAlternatively,\ - \ it is possible to use samples for more detailed tracing of sub-plant units,\ - \ attaching the observations to them instead.\" " - ObservationUnitHierarchyLevelRequest: - type: object - properties: - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - ObservationUnitRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - includeObservations: - type: boolean - description: "Use this parameter to include a list of observations embedded\ - \ in each ObservationUnit object. \n\nCAUTION - Use this parameter at\ - \ your own risk. It may return large, unpaginated lists of observation\ - \ data. Only set this value to True if you are sure you need to." - nullable: true - example: false - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - observationLevelRelationships: - type: array - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships - nullable: true - items: - $ref: "#/components/schemas/ObservationUnitLevelRelationship" - observationLevels: - type: array - description: Searches for values in ObservationUnit->observationUnitPosition->observationLevel - nullable: true - items: - $ref: "#/components/schemas/ObservationUnitLevel" - observationUnitDbIds: - type: array - description: The unique id of an observation unit - nullable: true - items: - type: string - observationUnitLevelCodes: - type: array - description: "The Observation Unit Level Code. This parameter should be\ - \ used together with `observationUnitLevelName` \nor `observationUnitLevelOrder`.\ - \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelNames: - type: array - description: "The Observation Unit Level. Returns only the observation unit\ - \ of the specified Level. \n
References ObservationUnit->observationUnitPosition->observationLevel->levelName\ - \ \n
**Standard Level Names: study, field, entry, rep, block, sub-block,\ - \ plot, sub-plot, plant, pot, sample** \n
For more information on\ - \ Observation Levels, please review the Observation Levels documentation. " - items: - type: string - observationUnitLevelOrders: - type: array - description: "The Observation Unit Level Order Number. Returns only the\ - \ observation unit of the specified Level. \nReferences ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipCodes: - type: array - description: "The Observation Unit Level Code. \n
This parameter should\ - \ be used together with `observationUnitLevelName` or `observationUnitLevelOrder`.\ - \ References ObservationUnit->observationUnitPosition->observationLevel->levelCode\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipDbIds: - type: array - description: "The observationUnitDbId associated with a particular level\ - \ and code.\n
This parameter should be used together with `observationUnitLevelName`\ - \ or `observationUnitLevelOrder`. References ObservationUnit->observationUnitPosition->observationLevel->observationUnitDbId\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipNames: - type: array - description: "The Observation Unit Level Relationship is a connection that\ - \ this observation unit has to another level of the hierarchy. \n
For\ - \ example, if you have several observation units at a 'plot' level, they\ - \ might all share a relationship to the same 'field' level. \n
Use\ - \ this parameter to identify groups of observation units that share a\ - \ relationship level. \n
**Standard Level Names: study, field, entry,\ - \ rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n
For\ - \ more information on Observation Levels, please review the Observation Levels documentation. " - items: - type: string - observationUnitLevelRelationshipOrders: - type: array - description: "The Observation Unit Level Order Number. \n
Returns only\ - \ the observation unit of the specified Level. References ObservationUnit->observationUnitPosition->observationLevel->levelOrder\ - \ \n
For more information on Observation Levels, please review the\ - \ Observation Levels documentation. " - items: - type: string - observationUnitNames: - type: array - description: The human readable identifier for an Observation Unit - nullable: true - items: - type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - seasonDbIds: - type: array - description: "The year or Phenotyping campaign of a multi-annual study (trees,\ - \ grape, ...)" - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - ObservationVariableParameters: - type: object - properties: - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string - ObservationVariableRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - dataTypes: - type: array - description: List of scale data types to filter search results - items: - $ref: "#/components/schemas/TraitDataType" - methodDbIds: - type: array - description: List of methods to filter search results - items: - type: string - methodNames: - type: array - description: |- - Human readable name for the method -
MIAPPE V1.1 (DM-88) Method Name of the method of observation - items: - type: string - methodPUIs: - type: array - description: "The Permanent Unique Identifier of a Method, usually in the\ - \ form of a URI" - items: - type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string - ontologyDbIds: - type: array - description: List of ontology IDs to search for - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - scaleDbIds: - type: array - description: The unique identifier for a Scale - items: - type: string - scaleNames: - type: array - description: |- - Name of the scale -
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable - items: - type: string - scalePUIs: - type: array - description: "The Permanent Unique Identifier of a Scale, usually in the\ - \ form of a URI" - items: - type: string - studyDbId: - type: array - description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ - \ number #483 \n
The unique ID of a studies to filter on" - deprecated: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - traitAttributePUIs: - type: array - description: |- - The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI -
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" - items: - type: string - traitAttributes: - type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the attribute is the observed feature (or characteristic) of the entity\ - \ e.g., for \"grain colour\", attribute = \"colour\"" - items: - type: string - traitClasses: - type: array - description: List of trait classes to filter search results - items: - type: string - traitDbIds: - type: array - description: The unique identifier for a Trait - items: - type: string - traitEntities: - type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the entity is the part of the plant that the trait refers to e.g., for\ - \ \"grain colour\", entity = \"grain\"" - items: - type: string - traitEntityPUIs: - type: array - description: "The Permanent Unique Identifier of a Trait Entity, usually\ - \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ - \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ - \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " - items: - type: string - traitNames: - type: array - description: |- - The human readable name of a trait -
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation - items: - type: string - traitPUIs: - type: array - description: "The Permanent Unique Identifier of a Trait, usually in the\ - \ form of a URI" - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - OntologyParameters: - type: object - properties: - ontologyDbIds: - type: array - description: "The unique identifier for an ontology definition. Use this\ - \ parameter to filter results based on a specific ontology \n\n Use `GET\ - \ /ontologies` to find the list of available ontologies on a server." - items: - type: string - OntologyRequest: - type: object - properties: - ontologyDbIds: - type: array - description: "The unique identifier for an ontology definition. Use this\ - \ parameter to filter results based on a specific ontology \n\n Use `GET\ - \ /ontologies` to find the list of available ontologies on a server." - items: - type: string - ontologyNames: - type: array - description: The human readable identifier for an ontology definition. - items: - type: string - OntologyTerm: - type: object - properties: - term: - type: string - description: Ontology term - the label of the ontology term the termId is - pointing to. - nullable: true - termURI: - type: string - description: Ontology term identifier - the CURIE for an ontology term. - It differs from the standard GA4GH schema's :ref:`id ` in that it is a - CURIE pointing to an information resource outside of the scope of the - schema or its resource implementation. - nullable: true - description: A pointer to an ontology used by a genomic reference - PagingParameters: - type: object - properties: - page: - type: integer - description: Which result page is requested. The page indexing starts at - 0 (the first page is 'page'= 0). Default is `0`. - format: int32 - example: 0 - pageSize: - type: integer - description: The size of the pages to be returned. Default is `1000`. - format: int32 - example: 1000 - PedigreeNodeRequest: - type: object - properties: - accessionNumbers: - type: array - description: |- - A collection of unique identifiers for materials or germplasm within a genebank - - MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). - nullable: true - items: - type: string - binomialNames: - type: array - description: List of the full binomial name (scientific name) to identify - a germplasm - nullable: true - items: - type: string - collections: - type: array - description: A specific panel/collection/population name this germplasm - belongs to. - nullable: true - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - familyCodes: - type: array - description: A familyCode representing the family this germplasm belongs - to. - nullable: true - items: - type: string - genus: - type: array - description: List of Genus names to identify germplasm - nullable: true - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - germplasmPUIs: - type: array - description: List of Permanent Unique Identifiers to identify germplasm - nullable: true - items: - type: string - includeFullTree: - type: boolean - description: "If this parameter is true, recursively include ALL of the\ - \ nodes available in this pedigree tree" - nullable: true - example: true - includeParents: - type: boolean - description: "If this parameter is true, include the array of parents in\ - \ the response" - nullable: true - example: true - includeProgeny: - type: boolean - description: "If this parameter is true, include the array of progeny in\ - \ the response" - nullable: true - example: true - includeSiblings: - type: boolean - description: "If this parameter is true, include the array of siblings in\ - \ the response" - nullable: true - example: true - instituteCodes: - type: array - description: "The code for the institute that maintains the material. \n\ -
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where\ - \ the accession is maintained. The codes consist of the 3-letter ISO 3166\ - \ country code of the country where the institute is located plus a number\ - \ (e.g. PER001). The current set of institute codes is available from\ - \ http://www.fao.org/wiews. For those institutes not yet having an FAO\ - \ Code, or for those with \"obsolete\" codes, see \"Common formatting\ - \ rules (v)\"." - nullable: true - items: - type: string - pedigreeDepth: - type: integer - description: "Recursively include this number of levels up the tree in the\ - \ response (parents, grand-parents, great-grand-parents, etc)" - format: int32 - example: 3 - progenyDepth: - type: integer - description: "Recursively include this number of levels down the tree in\ - \ the response (children, grand-children, great-grand-children, etc)" - format: int32 - example: 3 - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - species: - type: array - description: List of Species names to identify germplasm - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - synonyms: - type: array - description: List of alternative names or IDs used to reference this germplasm - nullable: true - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - Person: - allOf: - - $ref: "#/components/schemas/PersonNewRequest" - - required: - - personDbId - type: object - properties: - personDbId: - type: string - description: Unique ID for a person - description: "A generic object used to maintain the metadata needed to describe\ - \ a human. The Person might be a software user, a field technician, or a\ - \ primary contact for a Program." - PersonNewRequest: - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - description: - type: string - description: description of this person - nullable: true - emailAddress: - type: string - description: email address for this person - nullable: true - externalReferences: - type: array - description: An array of external reference ids. These are references to - this piece of data in an external system. Could be a simple string or - a URI. - nullable: true - items: - $ref: "#/components/schemas/ExternalReference" - firstName: - type: string - description: Persons first name - nullable: true - lastName: - type: string - description: Persons last name - nullable: true - mailingAddress: - type: string - description: physical address of this person - nullable: true - middleName: - type: string - description: Persons middle name - nullable: true - phoneNumber: - type: string - description: phone number of this person - nullable: true - userID: - type: string - description: A systems user ID associated with this person. Different from - personDbId because you could have a person who is not a user of the system. - nullable: true - description: "A generic object used to maintain the metadata needed to describe\ - \ a human. The Person might be a software user, a field technician, or a primary\ - \ contact for a Program." - PersonRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - emailAddresses: - type: array - description: email address for this person - nullable: true - items: - type: string - firstNames: - type: array - description: Persons first name - nullable: true - items: - type: string - lastNames: - type: array - description: Persons last name - nullable: true - items: - type: string - mailingAddresses: - type: array - description: physical address of this person - nullable: true - items: - type: string - middleNames: - type: array - description: Persons middle name - nullable: true - items: - type: string - personDbIds: - type: array - description: Unique ID for this person - nullable: true - items: - type: string - phoneNumbers: - type: array - description: phone number of this person - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - userIDs: - type: array - description: A systems user ID associated with this person. Different from - personDbId because you could have a person who is not a user of the system. - nullable: true - items: - type: string - PersonSearchRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - emailAddresses: - type: array - description: email address for this person - nullable: true - items: - type: string - externalReferenceIDs: - type: array - description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ - \ Github issue number #460 \n
List of external reference IDs. Could\ - \ be a simple strings or a URIs. (use with `externalReferenceSources`\ - \ parameter)" - deprecated: true - items: - type: string - externalReferenceIds: - type: array - description: List of external reference IDs. Could be a simple strings or - a URIs. (use with `externalReferenceSources` parameter) - items: - type: string - externalReferenceSources: - type: array - description: List of identifiers for the source system or database of an - external reference (use with `externalReferenceIDs` parameter) - items: - type: string - firstNames: - type: array - description: Persons first name - nullable: true - items: - type: string - lastNames: - type: array - description: Persons last name - nullable: true - items: - type: string - mailingAddresses: - type: array - description: physical address of this person - nullable: true - items: - type: string - middleNames: - type: array - description: Persons middle name - nullable: true - items: - type: string - page: - type: integer - description: Which result page is requested. The page indexing starts at - 0 (the first page is 'page'= 0). Default is `0`. - format: int32 - example: 0 - pageSize: - type: integer - description: The size of the pages to be returned. Default is `1000`. - format: int32 - example: 1000 - personDbIds: - type: array - description: Unique ID for this person - nullable: true - items: - type: string - phoneNumbers: - type: array - description: phone number of this person - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - userIDs: - type: array - description: A systems user ID associated with this person. Different from - personDbId because you could have a person who is not a user of the system. - nullable: true - items: - type: string - description: "A generic object used to maintain the metadata needed to describe\ - \ a human. The Person might be a software user, a field technician, or a primary\ - \ contact for a Program." - PlannedCrossRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - crossingProjectDbIds: - type: array - description: Search for Crossing Projects with this unique id - items: - type: string - crossingProjectNames: - type: array - description: The human readable name for a crossing project - items: - type: string - plannedCrossDbIds: - type: array - description: Search for Planned Cross with this unique id - items: - type: string - plannedCrossNames: - type: array - description: Search for Planned Cross with this human readable name - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - statuses: - type: array - description: "The status of this planned cross. Is it waiting to be performed\ - \ ('TODO'), has it been completed successfully ('DONE'), or has it not\ - \ been done on purpose ('SKIPPED')." - items: - type: string - enum: - - TODO - - DONE - - SKIPPED - PlateRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - observationUnitDbIds: - type: array - description: The ID which uniquely identifies an observation unit - nullable: true - items: - type: string - plateBarcodes: - type: array - description: A unique identifier physically attached to the plate - nullable: true - items: - type: string - plateDbIds: - type: array - description: The ID which uniquely identifies a plate of samples - nullable: true - items: - type: string - plateNames: - type: array - description: The human readable name of a plate of samples - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - sampleDbIds: - type: array - description: The ID which uniquely identifies a sample - nullable: true - items: - type: string - sampleGroupDbIds: - type: array - description: The unique identifier for a group of related Samples - nullable: true - items: - type: string - sampleNames: - type: array - description: The human readable name of the sample - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - Program: - allOf: - - $ref: "#/components/schemas/ProgramNewRequest" - - required: - - programDbId - type: object - properties: - programDbId: - type: string - description: The ID which uniquely identifies the program - description: A BrAPI Program represents the high level organization or group - who is responsible for conducting trials and studies. Things like Breeding - Programs and Funded Projects are considered BrAPI Programs. A Program can - contain multiple Trials. A Trial can contain multiple Studies. - ProgramNewRequest: - required: - - programName - type: object - properties: - abbreviation: - type: string - description: A shortened version of the human readable name for a Program - nullable: true - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - description: Common name for the crop which this program is for - nullable: true - documentationURL: - type: string - description: A URL to the human readable documentation of an object - format: uri - nullable: true - externalReferences: - type: array - description: An array of external reference ids. These are references to - this piece of data in an external system. Could be a simple string or - a URI. - nullable: true - items: - $ref: "#/components/schemas/ExternalReference" - fundingInformation: - type: string - description: Information describing the grant or funding source for this - program - nullable: true - leadPersonDbId: - type: string - nullable: true - leadPersonName: - type: string - nullable: true - objective: - type: string - description: The primary objective of the program - nullable: true - programName: - type: string - description: Human readable name of the program - programType: - type: string - description: "The type of program entity this object represents\n
'STANDARD'\ - \ represents a standard, permanent breeding program\n
'PROJECT' represents\ - \ a short term project, usually with a set time limit based on funding\ - \ " - enum: - - STANDARD - - PROJECT - description: A BrAPI Program represents the high level organization or group - who is responsible for conducting trials and studies. Things like Breeding - Programs and Funded Projects are considered BrAPI Programs. A Program can - contain multiple Trials. A Trial can contain multiple Studies. - ProgramParameters: - type: object - properties: - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - ProgramRequest: - type: object - properties: - abbreviations: - type: array - description: A list of shortened human readable names for a set of Programs - nullable: true - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - leadPersonDbIds: - type: array - description: The person DbIds of the program leader to search for - nullable: true - items: - type: string - leadPersonNames: - type: array - description: The names of the program leader to search for - nullable: true - items: - type: string - objectives: - type: array - description: A program objective to search for - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - programTypes: - type: array - description: "The type of program entity this object represents\n
'STANDARD'\ - \ represents a standard, permanent breeding program\n
'PROJECT' represents\ - \ a short term project, usually with a set time limit based on funding " - nullable: true - items: - type: string - description: |- - The type of program entity this object represents -
'STANDARD' represents a standard, permanent breeding program -
'PROJECT' represents a short term project, usually with a set time limit based on funding. - enum: - - STANDARD - - PROJECT - ProgramSearchRequest: - type: object - properties: - abbreviations: - type: array - description: A list of shortened human readable names for a set of Programs - nullable: true - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - externalReferenceIDs: - type: array - description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ - \ Github issue number #460 \n
List of external reference IDs. Could\ - \ be a simple strings or a URIs. (use with `externalReferenceSources`\ - \ parameter)" - deprecated: true - items: - type: string - externalReferenceIds: - type: array - description: List of external reference IDs. Could be a simple strings or - a URIs. (use with `externalReferenceSources` parameter) - items: - type: string - externalReferenceSources: - type: array - description: List of identifiers for the source system or database of an - external reference (use with `externalReferenceIDs` parameter) - items: - type: string - leadPersonDbIds: - type: array - description: The person DbIds of the program leader to search for - nullable: true - items: - type: string - leadPersonNames: - type: array - description: The names of the program leader to search for - nullable: true - items: - type: string - objectives: - type: array - description: A program objective to search for - nullable: true - items: - type: string - page: - type: integer - description: Which result page is requested. The page indexing starts at - 0 (the first page is 'page'= 0). Default is `0`. - format: int32 - example: 0 - pageSize: - type: integer - description: The size of the pages to be returned. Default is `1000`. - format: int32 - example: 1000 - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - programTypes: - type: array - description: "The type of program entity this object represents\n
'STANDARD'\ - \ represents a standard, permanent breeding program\n
'PROJECT' represents\ - \ a short term project, usually with a set time limit based on funding " - nullable: true - items: - type: string - description: |- - The type of program entity this object represents -
'STANDARD' represents a standard, permanent breeding program -
'PROJECT' represents a short term project, usually with a set time limit based on funding. - enum: - - STANDARD - - PROJECT - description: A BrAPI Program represents the high level organization or group - who is responsible for conducting trials and studies. Things like Breeding - Programs and Funded Projects are considered BrAPI Programs. A Program can - contain multiple Trials. A Trial can contain multiple Studies. - ProgramType: - type: string - description: "The type of program entity this object represents\n
'STANDARD'\ - \ represents a standard, permanent breeding program\n
'PROJECT' represents\ - \ a short term project, usually with a set time limit based on funding " - enum: - - STANDARD - - PROJECT - Publication: - type: object - properties: - publicationPUI: - type: string - description: The permanent unique identifier of the publication. - nullable: true - publicationReference: - type: string - description: The publication reference. - nullable: true - description: MIAPPE V1.1 (DM-9) Associated publication - An identifier for a - literature publication where the investigation is described. Use of DOIs is - recommended. - ReferenceBasesRequest: - type: object - properties: - end: - type: integer - description: "The end position (0-based, exclusive) of this query. Defaults\ - \ to the length of this `Reference`." - format: int32 - pageToken: - type: string - description: |- - The continuation token, which is used to page through large result sets. - To get the next page of results, set this parameter to the value of - `next_page_token` from the previous response. - start: - type: integer - description: |- - The start position (0-based) of this query. Defaults to 0. - Genomic positions are non-negative integers less than reference length. - Requests spanning the join of circular genomes are represented as - two requests one on each side of the join (position 0). - format: int32 - ReferenceRequest: - type: object - properties: - accessions: - type: array - description: "If specified, return the references for which the `accession`\ - \ matches this string (case-sensitive, exact match)." - nullable: true - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - isDerived: - type: boolean - description: "A sequence X is said to be derived from source sequence Y,\ - \ if X and Y are of the same length and the per-base sequence divergence\ - \ at A/C/G/T bases is sufficiently small. Two sequences derived from the\ - \ same official sequence share the same coordinates and annotations, and\ - \ can be replaced with the official sequence for certain use cases." - format: boolean - nullable: true - maxLength: - type: integer - description: The minimum length of this `References` sequence. - format: int32 - example: 90000 - md5checksums: - type: array - description: "If specified, return the references for which the `md5checksum`\ - \ matches this string (case-sensitive, exact match)." - nullable: true - items: - type: string - minLength: - type: integer - description: The minimum length of this `References` sequence. - format: int32 - example: 4000 - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - referenceDbIds: - type: array - description: A list of IDs which uniquely identify `References` within the - given database server - nullable: true - items: - type: string - referenceSetDbIds: - type: array - description: A list of IDs which uniquely identify `ReferenceSets` within - the given database server - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - ReferenceSetRequest: - type: object - properties: - accessions: - type: array - description: "If set, return the reference sets for which the `accession`\ - \ matches this string (case-sensitive, exact match)." - nullable: true - items: - type: string - assemblyPUIs: - type: array - description: "If set, return the reference sets for which the `assemblyId`\ - \ matches this string (case-sensitive, exact match)." - nullable: true - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - md5checksums: - type: array - description: "If set, return the reference sets for which the `md5checksum`\ - \ matches this string (case-sensitive, exact match)." - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - referenceSetDbIds: - type: array - description: The `ReferenceSets` to search. - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - SampleRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - observationUnitDbIds: - type: array - description: The ID which uniquely identifies an `ObservationUnit` - nullable: true - items: - type: string - plateDbIds: - type: array - description: The ID which uniquely identifies a `Plate` of `Samples` - nullable: true - items: - type: string - plateNames: - type: array - description: The human readable name of a `Plate` of `Samples` - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - sampleDbIds: - type: array - description: The ID which uniquely identifies a `Sample` - nullable: true - items: - type: string - sampleGroupDbIds: - type: array - description: The unique identifier for a group of related `Samples` - nullable: true - items: - type: string - sampleNames: - type: array - description: The human readable name of the `Sample` - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - ScaleRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - observationVariableDbIds: - type: array - description: The unique identifier for an observation variable. - items: - type: string - ontologyDbIds: - type: array - description: "The unique identifier for an ontology definition. Use this\ - \ parameter to filter results based on a specific ontology \n\n Use `GET\ - \ /ontologies` to find the list of available ontologies on a server." - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - scaleDbIds: - type: array - description: The unique identifier for a scale. - items: - type: string - Season: - required: - - seasonDbId - type: object - properties: - seasonDbId: - type: string - description: "The ID which uniquely identifies a season. For backward compatibility\ - \ it can be a string like '2012', '1957-2004'" - seasonName: - type: string - description: "Name of the season. ex. 'Spring', 'Q2', 'Season A', etc." - nullable: true - year: - type: integer - description: The 4 digit year of the season. - format: int32 - nullable: true - description: "A Season defines a period in time. A Season is made of two parts;\ - \ (1) the primary year and (2) a term which defines a segment of the year.\ - \ This term could be a traditional season, like \"Spring\" or \"Summer\",\ - \ or this term could be a month, like \"May\" or \"June\", or this could be\ - \ an arbitrary season name which is meaningful to the breeding Program like\ - \ \"PlantingTime_3\" or \"Season E\"." - SeasonRequest: - type: object - properties: - seasonDbIds: - type: array - description: "The unique identifier for a season. For backward compatibility\ - \ it can be a string like '2012', '1957-2004'." - items: - type: string - seasonNames: - type: array - description: The term to describe a given season. Example "Spring" OR "May" - OR "Planting_Time_7". - items: - type: string - seasons: - type: array - description: The term to describe a given season. Example "Spring" OR "May" - OR "Planting_Time_7". - items: - type: string - years: - type: array - description: The 4 digit year of a season. Example 2017 - items: - type: integer - format: int32 - SeedLotRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - crossDbIds: - type: array - description: Search for Cross with this unique id - items: - type: string - crossNames: - type: array - description: Search for Cross with this human readable name - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - seedLotDbIds: - type: array - description: Unique id for a seed lot on this server - items: - type: string - SeedLotTransactionRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - crossDbIds: - type: array - description: Search for Cross with this unique id - items: - type: string - crossNames: - type: array - description: Search for Cross with this human readable name - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - seedLotDbIds: - type: array - description: Unique id for a seed lot on this server - items: - type: string - transactionDbIds: - type: array - description: Unique id for a Transaction that has occurred - items: - type: string - transactionDirection: - type: string - description: "Filter results to only include transactions directed to the\ - \ specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both\ - \ (BOTH). The default value for this parameter is BOTH" - nullable: true - enum: - - TO - - FROM - - BOTH - SortBy: - type: string - description: Name of the field to sort by. - enum: - - trialDbId - - trialName - - programDbId - - programName - - locationDbId - - startDate - - endDate - SortOrder: - type: string - description: Sort order direction. Ascending/Descending. - enum: - - ASC - - DESC - - asc - - desc - Study: - allOf: - - $ref: "#/components/schemas/StudyNewRequest" - - required: - - studyDbId - type: object - properties: - studyDbId: - type: string - description: |- - The ID which uniquely identifies a study within the given database server - - MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. - description: A Study represents an experiment that has taken place at a single - location. The Study contains metadata about the parameters and design of - the experiment. It can also be used to group results and data sets generated - from the experiment. A Trial can represent a collection of one or more Studies. - StudyNewRequest: - required: - - studyName - type: object - properties: - active: - type: boolean - description: A flag to indicate if a Study is currently active and ongoing - nullable: true - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - description: Common name for the crop associated with this study - nullable: true - contacts: - type: array - description: List of contact entities associated with this study - nullable: true - items: - $ref: "#/components/schemas/Contact" - culturalPractices: - type: string - description: MIAPPE V1.1 (DM-28) Cultural practices - General description - of the cultural practices of the study. - nullable: true - dataLinks: - type: array - description: "List of links to extra data files associated with this study.\ - \ Extra data could include notes, images, and reference data." - nullable: true - items: - $ref: "#/components/schemas/DataLink" - documentationURL: - type: string - description: A URL to the human readable documentation of an object - format: uri - nullable: true - endDate: - type: string - description: |- - The date the study ends - - MIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended - format: date-time - nullable: true - environmentParameters: - type: array - description: |- - Environmental parameters that were kept constant throughout the study and did not change between observation units. - - MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). - nullable: true - items: - $ref: "#/components/schemas/EnvironmentParameter" - experimentalDesign: - $ref: "#/components/schemas/ExperimentalDesign" - externalReferences: - type: array - description: An array of external reference ids. These are references to - this piece of data in an external system. Could be a simple string or - a URI. - nullable: true - items: - $ref: "#/components/schemas/ExternalReference" - growthFacility: - $ref: "#/components/schemas/GrowthFacility" - lastUpdate: - $ref: "#/components/schemas/LastUpdate" - license: - type: string - description: The usage license associated with the study data - nullable: true - locationDbId: - type: string - nullable: true - locationName: - type: string - nullable: true - observationLevels: - type: array - description: "Observation levels indicate the granularity level at which\ - \ the measurements are taken. `levelName` \ndefines the level, `levelOrder`\ - \ defines where that level exists in the hierarchy of levels. \n`levelOrder`s\ - \ lower numbers are at the top of the hierarchy (ie field > 0) and higher\ - \ numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard\ - \ Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot,\ - \ plant, pot, sample** \n\nFor more information on Observation Levels,\ - \ please review the Observation Levels documentation. " - nullable: true - items: - $ref: "#/components/schemas/ObservationUnitHierarchyLevel" - observationUnitsDescription: - type: string - description: MIAPPE V1.1 (DM-25) Observation unit description - General - description of the observation units in the study. - nullable: true - observationVariableDbIds: - type: array - description: "The list of Observation Variables being used in this study.\ - \ \n\nThis list is intended to be the wishlist of variables to collect\ - \ in this study. It may or may not match the set of variables used in\ - \ the collected observation records. " - items: - type: string - seasons: - type: array - description: List of seasons over which this study was performed. - nullable: true - items: - type: string - startDate: - type: string - description: |- - The date this study started - - MIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started - format: date-time - nullable: true - studyCode: - type: string - description: A short human readable code for a study - nullable: true - studyDescription: - type: string - description: |- - The description of this study - - MIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study - studyName: - type: string - description: |- - The human readable name for a study - - MIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study - nullable: true - studyPUI: - type: string - description: "A permanent unique identifier associated with this study data.\ - \ For example, a URI or DOI" - nullable: true - studyType: - type: string - description: "The type of study being performed. ex. \"Yield Trial\", etc" - nullable: true - trialDbId: - type: string - trialName: - type: string - description: A Study represents an experiment that has taken place at a single - location. The Study contains metadata about the parameters and design of the - experiment. It can also be used to group results and data sets generated from - the experiment. A Trial can represent a collection of one or more Studies. - StudyParameters: - type: object - properties: - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - StudyRequest: - type: object - properties: - active: - type: boolean - description: A flag to indicate if a Study is currently active and ongoing - nullable: true - example: true - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - seasonDbIds: - type: array - description: The ID which uniquely identifies a season - nullable: true - items: - type: string - sortBy: - type: string - description: Name of the field to sort by. - nullable: true - enum: - - studyDbId - - trialDbId - - programDbId - - locationDbId - - seasonDbId - - studyType - - studyName - - studyLocation - - programName - - germplasmDbId - - observationVariableDbId - sortOrder: - type: string - description: Sort order direction. Ascending/Descending. - nullable: true - enum: - - ASC - - DESC - - asc - - desc - studyCodes: - type: array - description: A short human readable code for a study - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - studyPUIs: - type: array - description: "Permanent unique identifier associated with study data. For\ - \ example, a URI or DOI" - nullable: true - items: - type: string - studyTypes: - type: array - description: "The type of study being performed. ex. \"Yield Trial\", etc" - nullable: true - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - StudySearchRequest: - type: object - properties: - active: - type: boolean - description: A flag to indicate if a Study is currently active and ongoing - nullable: true - example: true - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - externalReferenceIDs: - type: array - description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ - \ Github issue number #460 \n
List of external reference IDs. Could\ - \ be a simple strings or a URIs. (use with `externalReferenceSources`\ - \ parameter)" - deprecated: true - items: - type: string - externalReferenceIds: - type: array - description: List of external reference IDs. Could be a simple strings or - a URIs. (use with `externalReferenceSources` parameter) - items: - type: string - externalReferenceSources: - type: array - description: List of identifiers for the source system or database of an - external reference (use with `externalReferenceIDs` parameter) - items: - type: string - germplasmDbIds: - type: array - description: List of IDs which uniquely identify germplasm to search for - nullable: true - items: - type: string - germplasmNames: - type: array - description: List of human readable names to identify germplasm to search - for - nullable: true - items: - type: string - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - observationVariableDbIds: - type: array - description: The DbIds of Variables to search for - items: - type: string - observationVariableNames: - type: array - description: The names of Variables to search for - items: - type: string - observationVariablePUIs: - type: array - description: "The Permanent Unique Identifier of an Observation Variable,\ - \ usually in the form of a URI" - items: - type: string - page: - type: integer - description: Which result page is requested. The page indexing starts at - 0 (the first page is 'page'= 0). Default is `0`. - format: int32 - example: 0 - pageSize: - type: integer - description: The size of the pages to be returned. Default is `1000`. - format: int32 - example: 1000 - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - seasonDbIds: - type: array - description: The ID which uniquely identifies a season - nullable: true - items: - type: string - sortBy: - type: string - description: Name of the field to sort by. - nullable: true - enum: - - studyDbId - - trialDbId - - programDbId - - locationDbId - - seasonDbId - - studyType - - studyName - - studyLocation - - programName - - germplasmDbId - - observationVariableDbId - sortOrder: - type: string - description: Sort order direction. Ascending/Descending. - nullable: true - enum: - - ASC - - DESC - - asc - - desc - studyCodes: - type: array - description: A short human readable code for a study - nullable: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - studyPUIs: - type: array - description: "Permanent unique identifier associated with study data. For\ - \ example, a URI or DOI" - nullable: true - items: - type: string - studyTypes: - type: array - description: "The type of study being performed. ex. \"Yield Trial\", etc" - nullable: true - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - description: A Study represents an experiment that has taken place at a single - location. The Study contains metadata about the parameters and design of the - experiment. It can also be used to group results and data sets generated from - the experiment. A Trial can represent a collection of one or more Studies. - TokenPagingParameters: - type: object - properties: - page: - type: integer - description: Which result page is requested. The page indexing starts at - 0 (the first page is 'page'= 0). Default is `0`. - format: int32 - example: 0 - pageSize: - type: integer - description: The size of the pages to be returned. Default is `1000`. - format: int32 - example: 1000 - pageToken: - type: string - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
Used to request a specific page of data to be returned.\n\ -
Tokenized pages are for large data sets which can not be efficiently\ - \ broken into indexed pages. Use the nextPageToken and prevPageToken from\ - \ a prior response to construct a query and move to the next or previous\ - \ page respectively. " - example: 33c27874 - deprecated: true - TraitDataType: - type: string - description: |- -

Class of the scale, entries can be

-

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

-

"Date" - The date class is for events expressed in a time format, See ISO 8601

-

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

-

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

-

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

-

"Ordinal" - Ordinal scales are scales composed of ordered categories

-

"Text" - A free text is used to express the trait.

- enum: - - Code - - Date - - Duration - - Nominal - - Numerical - - Ordinal - - Text - TraitRequest: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - observationVariableDbIds: - type: array - description: The unique identifier for an observation variable. - items: - type: string - ontologyDbIds: - type: array - description: "The unique identifier for an ontology definition. Use this\ - \ parameter to filter results based on a specific ontology \n\n Use `GET\ - \ /ontologies` to find the list of available ontologies on a server." - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - traitDbIds: - type: array - description: The unique identifier for a trait. - items: - type: string - TransactionDirection: - type: string - description: "Filter results to only include transactions directed to the specific\ - \ Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The\ - \ default value for this parameter is BOTH" - enum: - - TO - - FROM - - BOTH - Trial: - allOf: - - $ref: "#/components/schemas/TrialNewRequest" - - required: - - trialDbId - type: object - properties: - trialDbId: - type: string - description: |- - The ID which uniquely identifies a trial - - MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. - description: "A Trial represents a collection of Study objects, and the metadata\ - \ associated with that collection. A Trial could represent a multi-location\ - \ experiment, and could contain information related to publications and\ - \ data licensing." - TrialNewRequest: - required: - - trialName - type: object - properties: - active: - type: boolean - description: A flag to indicate if a Trial is currently active and ongoing - nullable: true - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - description: Common name for the crop associated with this trial - nullable: true - contacts: - type: array - description: List of contact entities associated with this trial - nullable: true - items: - $ref: "#/components/schemas/Contact" - datasetAuthorships: - type: array - description: License and citation information for the data in this trial - nullable: true - items: - $ref: "#/components/schemas/DatasetAuthorships" - documentationURL: - type: string - description: A URL to the human readable documentation of an object - format: uri - nullable: true - endDate: - type: string - description: The date this trial ends - nullable: true - externalReferences: - type: array - description: An array of external reference ids. These are references to - this piece of data in an external system. Could be a simple string or - a URI. - nullable: true - items: - $ref: "#/components/schemas/ExternalReference" - programDbId: - type: string - nullable: true - programName: - type: string - nullable: true - publications: - type: array - description: MIAPPE V1.1 (DM-9) Associated publication - An identifier for - a literature publication where the investigation is described. Use of - DOIs is recommended. - nullable: true - items: - $ref: "#/components/schemas/Publication" - startDate: - type: string - description: The date this trial started - nullable: true - trialDescription: - type: string - description: |- - The human readable description of a trial - - MIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail. - nullable: true - trialName: - type: string - description: |- - The human readable name of a trial - - MIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation. - trialPUI: - type: string - description: A permanent identifier for a trial. Could be DOI or other URI - formatted identifier. - nullable: true - description: "A Trial represents a collection of Study objects, and the metadata\ - \ associated with that collection. A Trial could represent a multi-location\ - \ experiment, and could contain information related to publications and data\ - \ licensing." - TrialParameters: - type: object - properties: - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - TrialRequest: - type: object - properties: - active: - type: boolean - description: A flag to indicate if a Trial is currently active and ongoing - example: true - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - contactDbIds: - type: array - description: List of contact entities associated with this trial - items: - type: string - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - searchDateRangeEnd: - type: string - description: "The end of the overlapping search date range. `searchDateRangeStart`\ - \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ - \ of the following cases are true\n\n- `searchDateRangeStart` is before\ - \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ - \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ - \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is before `trial.endDate`" - format: date - searchDateRangeStart: - type: string - description: "The start of the overlapping search date range. `searchDateRangeStart`\ - \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ - \ of the following cases are true\n\n- `searchDateRangeStart` is before\ - \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ - \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ - \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is before `trial.endDate`" - format: date - sortBy: - type: string - description: Name of the field to sort by. - nullable: true - enum: - - trialDbId - - trialName - - programDbId - - programName - - locationDbId - - startDate - - endDate - sortOrder: - type: string - description: Sort order direction. Ascending/Descending. - nullable: true - enum: - - ASC - - DESC - - asc - - desc - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - trialPUIs: - type: array - description: A permanent identifier for a trial. Could be DOI or other URI - formatted identifier. - items: - type: string - TrialSearchRequest: - type: object - properties: - active: - type: boolean - description: A flag to indicate if a Trial is currently active and ongoing - example: true - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - contactDbIds: - type: array - description: List of contact entities associated with this trial - items: - type: string - externalReferenceIDs: - type: array - description: "**Deprecated in v2.1** Please use `externalReferenceIds`.\ - \ Github issue number #460 \n
List of external reference IDs. Could\ - \ be a simple strings or a URIs. (use with `externalReferenceSources`\ - \ parameter)" - deprecated: true - items: - type: string - externalReferenceIds: - type: array - description: List of external reference IDs. Could be a simple strings or - a URIs. (use with `externalReferenceSources` parameter) - items: - type: string - externalReferenceSources: - type: array - description: List of identifiers for the source system or database of an - external reference (use with `externalReferenceIDs` parameter) - items: - type: string - locationDbIds: - type: array - description: The location ids to search for - items: - type: string - locationNames: - type: array - description: A human readable names to search for - items: - type: string - page: - type: integer - description: Which result page is requested. The page indexing starts at - 0 (the first page is 'page'= 0). Default is `0`. - format: int32 - example: 0 - pageSize: - type: integer - description: The size of the pages to be returned. Default is `1000`. - format: int32 - example: 1000 - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - searchDateRangeEnd: - type: string - description: "The end of the overlapping search date range. `searchDateRangeStart`\ - \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ - \ of the following cases are true\n\n- `searchDateRangeStart` is before\ - \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ - \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ - \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is before `trial.endDate`" - format: date - searchDateRangeStart: - type: string - description: "The start of the overlapping search date range. `searchDateRangeStart`\ - \ must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any\ - \ of the following cases are true\n\n- `searchDateRangeStart` is before\ - \ `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart`\ - \ is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\ - \n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart`\ - \ is before `trial.endDate`" - format: date - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - trialPUIs: - type: array - description: A permanent identifier for a trial. Could be DOI or other URI - formatted identifier. - items: - type: string - description: "A Trial represents a collection of Study objects, and the metadata\ - \ associated with that collection. A Trial could represent a multi-location\ - \ experiment, and could contain information related to publications and data\ - \ licensing." - Variable: - required: - - method - - scale - - trait - type: object - properties: - additionalInfo: - $ref: "#/components/schemas/AdditionalInfo" - commonCropName: - type: string - description: "Crop name (examples: \"Maize\", \"Wheat\")" - nullable: true - contextOfUse: - type: array - description: "Indication of how trait is routinely used. (examples: [\"\ - Trial evaluation\", \"Nursery evaluation\"])" - nullable: true - items: - type: string - defaultValue: - type: string - description: "Variable default value. (examples: \"red\", \"2.3\", etc.)" - nullable: true - documentationURL: - type: string - description: A URL to the human readable documentation of an object - format: uri - nullable: true - externalReferences: - type: array - description: An array of external reference ids. These are references to - this piece of data in an external system. Could be a simple string or - a URI. - nullable: true - items: - $ref: "#/components/schemas/ExternalReference" - growthStage: - type: string - description: "Growth stage at which measurement is made (examples: \"flowering\"\ - )" - nullable: true - institution: - type: string - description: Name of institution submitting the variable - nullable: true - language: - type: string - description: 2 letter ISO 639-1 code for the language of submission of the - variable. - nullable: true - method: - $ref: "#/components/schemas/Method" - ontologyReference: - nullable: true - allOf: - - $ref: "#/components/schemas/OntologyReference" - scale: - $ref: "#/components/schemas/Scale" - scientist: - type: string - description: Name of scientist submitting the variable. - nullable: true - status: - type: string - description: "Variable status. (examples: \"recommended\", \"obsolete\"\ - , \"legacy\", etc.)" - nullable: true - submissionTimestamp: - type: string - description: Timestamp when the Variable was added (ISO 8601) - format: date-time - nullable: true - synonyms: - type: array - description: Other variable names - nullable: true - items: - type: string - trait: - $ref: "#/components/schemas/Trait" - description: "A unique combination of Trait, Method, and Scale to define a clear\ - \ context for an Observation." - VariableBaseClassParameters: - type: object - properties: - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - dataTypes: - type: array - description: List of scale data types to filter search results - items: - $ref: "#/components/schemas/TraitDataType" - methodDbIds: - type: array - description: List of methods to filter search results - items: - type: string - methodNames: - type: array - description: |- - Human readable name for the method -
MIAPPE V1.1 (DM-88) Method Name of the method of observation - items: - type: string - methodPUIs: - type: array - description: "The Permanent Unique Identifier of a Method, usually in the\ - \ form of a URI" - items: - type: string - ontologyDbIds: - type: array - description: List of ontology IDs to search for - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - scaleDbIds: - type: array - description: The unique identifier for a Scale - items: - type: string - scaleNames: - type: array - description: |- - Name of the scale -
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable - items: - type: string - scalePUIs: - type: array - description: "The Permanent Unique Identifier of a Scale, usually in the\ - \ form of a URI" - items: - type: string - studyDbId: - type: array - description: "**Deprecated in v2.1** Please use `studyDbIds`. Github issue\ - \ number #483 \n
The unique ID of a studies to filter on" - deprecated: true - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - traitAttributePUIs: - type: array - description: |- - The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI -
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" - items: - type: string - traitAttributes: - type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the attribute is the observed feature (or characteristic) of the entity\ - \ e.g., for \"grain colour\", attribute = \"colour\"" - items: - type: string - traitClasses: - type: array - description: List of trait classes to filter search results - items: - type: string - traitDbIds: - type: array - description: The unique identifier for a Trait - items: - type: string - traitEntities: - type: array - description: "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\"\ - , the entity is the part of the plant that the trait refers to e.g., for\ - \ \"grain colour\", entity = \"grain\"" - items: - type: string - traitEntityPUIs: - type: array - description: "The Permanent Unique Identifier of a Trait Entity, usually\ - \ in the form of a URI\n
A trait can be decomposed as \"Trait\" =\ - \ \"Entity\" + \"Attribute\", the entity is the part of the plant that\ - \ the trait refers to e.g., for \"grain colour\", entity = \"grain\" " - items: - type: string - traitNames: - type: array - description: |- - The human readable name of a trait -
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation - items: - type: string - traitPUIs: - type: array - description: "The Permanent Unique Identifier of a Trait, usually in the\ - \ form of a URI" - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - VariantRequest: - type: object - properties: - callSetDbIds: - type: array - description: "**Deprecated in v2.1** Parameter unnecessary. Github issue\ - \ number #474 \n
Only return variant calls which belong to call sets\ - \ with these IDs. If unspecified, return all variants and no variant call\ - \ objects." - nullable: true - deprecated: true - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - end: - type: integer - description: "The end of the window (0-based, exclusive) for which overlapping\ - \ variants should be returned." - format: int32 - example: 1500 - pageToken: - type: string - description: |- - The continuation token, which is used to page through large result sets. - To get the next page of results, set this parameter to the value of - `next_page_token` from the previous response. - deprecated: true - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - referenceDbId: - type: string - description: |- - **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 -
Only return variants on this reference. - nullable: true - example: 120a2d5c - deprecated: true - referenceDbIds: - type: array - description: The unique identifier representing a genotype `Reference` - nullable: true - items: - type: string - referenceSetDbIds: - type: array - description: The unique identifier representing a genotype `ReferenceSet` - nullable: true - items: - type: string - start: - type: integer - description: "The beginning of the window (0-based, inclusive) for which\ - \ overlapping variants should be returned. Genomic positions are non-negative\ - \ integers less than reference length. Requests spanning the join of circular\ - \ genomes are represented as two requests one on each side of the join\ - \ (position 0)." - format: int32 - example: 100 - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - variantDbIds: - type: array - description: A list of IDs which uniquely identify `Variants` - nullable: true - items: - type: string - variantSetDbIds: - type: array - description: A list of IDs which uniquely identify `VariantSets` - nullable: true - items: - type: string - VariantSetRequest: - type: object - properties: - callSetDbIds: - type: array - description: The unique identifier representing a CallSet - items: - type: string - commonCropNames: - type: array - description: "The BrAPI Common Crop Name is the simple, generalized, widely\ - \ accepted name of the organism being researched. It is most often used\ - \ in multi-crop systems where digital resources need to be divided at\ - \ a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples\ - \ of common crop names.\n\nUse this parameter to only return results associated\ - \ with the given crops. \n\nUse `GET /commoncropnames` to find the list\ - \ of available crops on a server." - items: - type: string - programDbIds: - type: array - description: "A BrAPI Program represents the high level organization or\ - \ group who is responsible for conducting trials and studies. Things like\ - \ Breeding Programs and Funded Projects are considered BrAPI Programs.\ - \ \n\nUse this parameter to only return results associated with the given\ - \ programs. \n\nUse `GET /programs` to find the list of available programs\ - \ on a server." - items: - type: string - programNames: - type: array - description: |- - Use this parameter to only return results associated with the given program names. Program names are not required to be unique. - - Use `GET /programs` to find the list of available programs on a server. - items: - type: string - referenceDbIds: - type: array - description: The unique identifier representing a genotype Reference - items: - type: string - referenceSetDbIds: - type: array - description: The unique identifier representing a genotype ReferenceSet - items: - type: string - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - trialDbIds: - type: array - description: The ID which uniquely identifies a trial to search for - items: - type: string - trialNames: - type: array - description: The human readable name of a trial to search for - items: - type: string - variantDbIds: - type: array - description: The unique identifier representing a Variant - items: - type: string - variantSetDbIds: - type: array - description: The unique identifier representing a VariantSet - items: - type: string - VariantSetsExtractRequest: - type: object - properties: - callSetDbIds: - type: array - description: The CallSet to search. - items: - type: string - expandHomozygotes: - type: boolean - description: Should homozygotes be expanded (true) or collapsed into a single - occurrence (false) - example: true - sepPhased: - type: string - description: The string used as a separator for phased allele calls. - example: "~" - sepUnphased: - type: string - description: The string used as a separator for unphased allele calls. - example: '|' - studyDbIds: - type: array - description: List of study identifiers to search for - items: - type: string - studyNames: - type: array - description: List of study names to filter search results - items: - type: string - unknownString: - type: string - description: The string used as a representation for missing data. - example: "-" - variantDbIds: - type: array - description: The Variant to search. - items: - type: string - variantSetDbIds: - type: array - description: The VariantSet to search. - items: - type: string - description: Request object for extracting data subsets as new Variant Sets - basePagination: - required: - - currentPage - - pageSize - type: object - properties: - currentPage: - type: integer - description: The index number for the returned page of data. This should - always match the requested page number or the default page (0). - example: 0 - default: 0 - pageSize: - type: integer - description: "The number of data elements returned, aka the size of the\ - \ current page. If the requested page does not have enough elements to\ - \ fill a page at the requested page size, this field should indicate the\ - \ actual number of elements returned." - example: 1000 - default: 1000 - totalCount: - type: integer - description: The total number of elements that are available on the server - and match the requested query parameters. - example: 10 - totalPages: - type: integer - description: "The total number of pages of elements available on the server.\ - \ This should be calculated with the following formula. \n
totalPages\ - \ = CEILING( totalCount / requested_page_size)" - example: 1 - description: "The pagination object is applicable only when the payload contains\ - \ a \"data\" key. It describes the pagination of the data contained in the\ - \ \"data\" array, as a way to identify which subset of data is being returned.\ - \ \n
Pages are zero indexed, so the first page will be page 0 (zero)." - dataFile: - required: - - fileURL - type: object - properties: - fileURL: - type: string - description: The absolute URL where the file is located - format: uri - example: https://wiki.brapi.org/examples/datafile.xlsx - fileName: - type: string - description: The name of the file - example: datafile.xlsx - fileSize: - type: integer - description: The size of the file in bytes - example: 4398 - fileDescription: - type: string - description: A human readable description of the file contents - example: This is an Excel data file - fileType: - type: string - description: The type or format of the file. Preferably MIME Type. - example: application/vnd.ms-excel - fileMD5Hash: - type: string - description: The MD5 Hash of the file contents to be used as a check sum - example: c2365e900c81a89cf74d83dab60df146 - description: A dataFile contains a URL and the relevant file metadata to represent - a file - metadata: - allOf: - - $ref: "#/components/schemas/metadataBase" - - type: object - properties: - pagination: - $ref: "#/components/schemas/basePagination" - metadataBase: - type: object - properties: - datafiles: - type: array - description: "The datafiles contains a list of file URLs and metadata. \n\ - These files contain additional information related to the returned object\ - \ and can be retrieved by a subsequent call. \nThis could be a supplementary\ - \ data file, an informational file, the uploaded file where the data originated\ - \ from, a generated file representing the whole dataset in a particular\ - \ format, or any other related file. " - example: [] - items: - $ref: "#/components/schemas/dataFile" - status: - type: array - description: "The status field contains a list of informational status messages\ - \ from the server. \nIf no status is reported, an empty list should be\ - \ returned. See Error Reporting for more information." - items: - $ref: "#/components/schemas/status" - description: "An object in the BrAPI standard response model that describes\ - \ some information about the service call being performed. This includes supplementary\ - \ data, status log messages, and pagination information." - metadataTokenPagination: - allOf: - - $ref: "#/components/schemas/metadataBase" - - type: object - properties: - pagination: - $ref: "#/components/schemas/tokenPagination" - status: - required: - - message - - messageType - type: object - properties: - message: - type: string - description: A short message concerning the status of this request/response - example: "Request accepted, response successful" - messageType: - type: string - description: The logging level for the attached message - example: INFO - enum: - - DEBUG - - ERROR - - WARNING - - INFO - description: An array of status messages to convey technical logging information - from the server to the client. - tokenPagination: - allOf: - - $ref: "#/components/schemas/basePagination" - - required: - - nextPageToken - type: object - properties: - nextPageToken: - type: string - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The string token used to query the next page of data." - example: cb668f63 - deprecated: true - currentPageToken: - type: string - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The string token used to query the current page of data." - example: 48bc6ac1 - deprecated: true - prevPageToken: - type: string - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The string token used to query the previous page of data." - example: 9659857e - deprecated: true - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
The pagination object is applicable only when the payload contains\ - \ a \"data\" key. It describes the pagination of the data contained in the\ - \ \"data\" array, as a way to identify which subset of data is being returned.\ - \ \n
Tokenized pages are for large data sets which can not be efficiently\ - \ broken into indexed pages. Use the nextPageToken and prevPageToken to\ - \ construct an additional query and move to the next or previous page respectively.\ - \ " - example: - currentPage: 0 - pageSize: 1000 - totalCount: 10 - totalPages: 1 - Service: - required: - - methods - - service - - versions - type: object - properties: - service: - type: string - description: The name of the available call as recorded in the documentation - example: "germplasm/{germplasmDbId}/pedigree" - contentTypes: - type: array - description: The possible content types returned by the service endpoint - example: - - application/json - items: - $ref: "#/components/schemas/ContentTypes" - dataTypes: - type: array - description: "**Deprecated in v2.1** Please use `contentTypes`. Github issue\ - \ number #443 \n
The possible data formats returned by the available\ - \ call " - example: - - application/json - deprecated: true - items: - $ref: "#/components/schemas/ContentTypes" - methods: - type: array - description: The possible HTTP Methods to be used with the available call - example: - - GET - - POST - items: - type: string - enum: - - GET - - POST - - PUT - - DELETE - versions: - type: array - description: The supported versions of a particular call - example: - - "2.0" - - "2.1" - items: - type: string - enum: - - "2.0" - - "2.1" - - "2.2" - ServerInfo: - required: - - calls - type: object - properties: - contactEmail: - type: string - description: A contact email address for this server management - example: contact@institute.org - documentationURL: - type: string - description: A URL to the human readable documentation of an object - example: institute.org/server - organizationURL: - type: string - description: The URL of the organization that manages this server and data - example: institute.org/home - organizationName: - type: string - description: The name of the organization that manages this server and data - example: The Institute - serverName: - type: string - description: The name of this server - example: The BrAPI Test Server - serverDescription: - type: string - description: A description of this server - example: |- - The BrAPI Test Server - Web Server - Apache Tomcat 7.0.32 - Database - Postgres 10 - Supported BrAPI Version - V2.0 - location: - type: string - description: "Physical location of this server (ie. City, Country)" - example: USA - calls: - type: array - description: Array of available calls on this server - items: - $ref: "#/components/schemas/Service" - responses: - "401Unauthorized": - description: Unauthorized - content: - application/json: - schema: - type: string - example: ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization - token - ProgramCommonCropNameListResponse: - description: OK - content: - application/json: - schema: - title: ProgramCommonCropNameListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - type: string - "202AcceptedSearchResponse": - description: Accepted - content: - application/json: - schema: - title: 202AcceptedSearchResponse - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - type: object - properties: - searchResultsDbId: - type: string - example: 551ae08c - StudyStudyTypeListResponse: - description: OK - content: - application/json: - schema: - title: StudyStudyTypeListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - type: string - StudySingleResponse: - description: OK - content: - application/json: - schema: - title: StudySingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/Study" - PersonListResponse: - description: OK - content: - application/json: - schema: - title: PersonListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Person" - LocationListResponse: - description: OK - content: - application/json: - schema: - title: LocationListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Location" - TrialListResponse: - description: OK - content: - application/json: - schema: - title: TrialListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Trial" - "403Forbidden": - description: Forbidden - content: - application/json: - schema: - type: string - example: ERROR - 2018-10-08T18:15:11Z - User does not have permission to - perform this action - StudyObservationLevelsListResponse: - description: OK - content: - application/json: - schema: - title: StudyObservationLevelsListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - type: array - items: - $ref: "#/components/schemas/ObservationUnitHierarchyLevel" - ProgramListResponse: - description: OK - content: - application/json: - schema: - title: ProgramListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Program" - TrialSingleResponse: - description: OK - content: - application/json: - schema: - title: TrialSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/Trial" - ListListResponse: - description: OK - content: - application/json: - schema: - title: ListListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/List" - SeasonSingleResponse: - description: OK - content: - application/json: - schema: - title: SeasonSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/Season" - "400BadRequest": - description: Bad Request - content: - application/json: - schema: - type: string - example: |- - ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object - - ERROR - 2018-10-08T18:15:11Z - Invalid query parameter - - ERROR - 2018-10-08T18:15:11Z - Required parameter is missing - "404NotFound": - description: Not Found - content: - application/json: - schema: - type: string - example: ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not - found - StudyListResponse: - description: OK - content: - application/json: - schema: - title: StudyListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Study" - CallListResponse: - description: OK - content: - application/json: - schema: - title: CallListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - description: "The `data` array is part of the BrAPI standard List\ - \ Response JSON container. `data` will always contain the primary\ - \ list of objects being returned by a BrAPI endpoint. `data`\ - \ is also the only array impacted by the `metadata.pagination`\ - \ details. When the pagination parameters change, the `data`\ - \ array will reflect those changes in the JSON response." - items: - $ref: "#/components/schemas/Call" - expandHomozygotes: - type: boolean - description: Should homozygotes be expanded (true) or collapsed - into a single occurrence (false) - nullable: true - example: true - sepPhased: - type: string - description: The string used as a separator for phased allele - calls. - nullable: true - example: '|' - sepUnphased: - type: string - description: The string used as a separator for unphased allele - calls. - nullable: true - example: / - unknownString: - type: string - description: The string used as a representation for missing data. - nullable: true - example: "." - LocationSingleResponse: - description: OK - content: - application/json: - schema: - title: LocationSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/Location" - SeasonListResponse: - description: OK - content: - application/json: - schema: - title: SeasonListResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - required: - - data - type: object - properties: - data: - type: array - items: - $ref: "#/components/schemas/Season" - ListSingleResponse: - description: OK - content: - application/json: - schema: - title: ListSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/List" - PersonSingleResponse: - description: OK - content: - application/json: - schema: - title: PersonSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/Person" - ProgramSingleResponse: - description: OK - content: - application/json: - schema: - title: ProgramSingleResponse - required: - - metadata - - result - type: object - properties: - '@context': - $ref: "#/components/schemas/Context" - metadata: - $ref: "#/components/schemas/metadata" - result: - $ref: "#/components/schemas/Program" - parameters: - externalReferenceID: - name: externalReferenceID - in: query - description: "**Deprecated in v2.1** Please use `externalReferenceId`. Github\ - \ issue number #460 \n
An external reference ID. Could be a simple string\ - \ or a URI. (use with `externalReferenceSource` parameter)" - required: false - deprecated: true - style: form - explode: true - schema: - type: string - externalReferenceId: - name: externalReferenceId - in: query - description: An external reference ID. Could be a simple string or a URI. (use - with `externalReferenceSource` parameter) - required: false - style: form - explode: true - schema: - type: string - externalReferenceSource: - name: externalReferenceSource - in: query - description: An identifier for the source system or database of an external - reference (use with `externalReferenceId` parameter) - required: false - style: form - explode: true - schema: - type: string - acceptHeader: - name: Accept - in: header - description: "A standard HTTP request header that is used to request a specific\ - \ content type (JSON, CSV, etc) which is \"acceptable\" to the client and\ - \ should be returned by the server" - required: true - style: simple - explode: false - schema: - $ref: "#/components/schemas/ContentTypes" - example: application/json - searchResultsDbId: - name: searchResultsDbId - in: path - description: Unique identifier which references the search results - required: true - style: simple - explode: false - schema: - type: string - pageSize: - name: pageSize - in: query - description: The size of the pages to be returned. Default is `1000`. - required: false - style: form - explode: true - schema: - type: integer - example: 1000 - authorizationHeader: - name: Authorization - in: header - description: "HTTP HEADER - Token used for Authorization \n\n Bearer\ - \ {token_string} " - required: false - style: simple - explode: false - schema: - pattern: ^Bearer .*$ - type: string - example: Bearer XXXX - pageToken: - name: pageToken - in: query - description: "**Deprecated in v2.1** Please use `page`. Github issue number\ - \ #451 \n
Used to request a specific page of data to be returned.\n
\ - \ Tokenized pages are for large data sets which can not be efficiently broken\ - \ into indexed pages. Use the nextPageToken and prevPageToken from a prior\ - \ response to construct a query and move to the next or previous page respectively. " - required: false - deprecated: true - style: form - explode: true - schema: - type: string - example: 33c27874 - page: - name: page - in: query - description: |- - Used to request a specific page of data to be returned. - - The page indexing starts at 0 (the first page is 'page'= 0). Default is `0`. - required: false - style: form - explode: true - schema: - type: integer - example: "0" - securitySchemes: - AuthorizationToken: - type: http - description: OAuth Bearer Token - A valid Bearer token to prove authorization - scheme: bearer - bearerFormat: nonce token or JWT