diff --git a/.github/workflows/generate-schema.yml b/.github/workflows/generate-schema.yml index 644bed38..5892b8fa 100644 --- a/.github/workflows/generate-schema.yml +++ b/.github/workflows/generate-schema.yml @@ -87,9 +87,6 @@ jobs: - name: Generate OpenAPI, GraphQL and OWL working-directory: ./generator run: ./gradlew generateAll - - name: Compare OpenAPI - working-directory: ./generator - run: ./gradlew compareAll - name: Commit generated files if: needs.check.outputs.skip_commit == 'false' uses: stefanzweifel/git-auto-commit-action@v5 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" + ] } } }, diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index e85a1f20..b559f82e 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -353,6 +353,7 @@ "brapi-metadata": { "primaryModel": true, "controlledVocabularyProperties": [ + "observationLevels", "studyType" ] } 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/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 868f5a33..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" @@ -128,8 +133,8 @@ "$ref": "Observation.json#/$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/Observation.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json index 7c5aa97c..5a06d567 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Observation.json @@ -167,6 +167,300 @@ "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

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

\n\n

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

\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 9905e5c6..be4c9c02 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json @@ -366,6 +366,194 @@ "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

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

\n\n

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

\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/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/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 diff --git a/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json b/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json index aa7d660b..b9304327 100644 --- a/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json +++ b/Specification/BrAPI-Schema/Requests/SeedLotTransactionRequest.json @@ -1,28 +1,62 @@ { "$defs": { "SeedLotTransactionRequest": { - "type": "object", - "properties": { - "transactionDbIs": { - "description": "Unique id for a Transaction that has occurred", - "type": "array", - "items": { - "type": "string" - } + "allOf": [ + { + "$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#/$defs/ProgramParameters" + }, + { + "type": "object", + "properties": { + "seedLotDbIds": { + "description": "Unique id for a seed lot on this server", + "type": "array", + "items": { + "type": "string" + } + }, + "crossDbIds": { + "description": "Search for Cross with this unique id", + "type": "array", + "items": { + "type": "string" + } + }, + "crossNames": { + "description": "Search for Cross with this human readable name", + "type": "array", + "items": { + "type": "string" + } + }, + "transactionDbIds": { + "description": "Unique id for a Transaction that has occurred", + "type": "array", + "items": { + "type": "string" + } + }, + "transactionDirection": { + "description": "Filter results to only include transactions directed to the specific Seed Lot (TO), away from the specific Seed Lot (FROM), or both (BOTH). The default value for this parameter is BOTH", + "enum": [ + "TO", + "FROM", + "BOTH" + ], + "type": [ + "null", + "string" + ] + } + } } - }, + ], "brapi-metadata": { "request": true, "subQueryProperties" : [ diff --git a/Specification/BrAPI-Schema/Requests/VariantSetsExtractRequest.json b/Specification/BrAPI-Schema/Requests/VariantSetsExtractRequest.json new file mode 100644 index 00000000..9f190ef4 --- /dev/null +++ b/Specification/BrAPI-Schema/Requests/VariantSetsExtractRequest.json @@ -0,0 +1,90 @@ +{ + "$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/Specification/Generated/brapi_generated.ttl b/Specification/Generated/brapi_generated.ttl deleted file mode 100644 index 5253562d..00000000 --- a/Specification/Generated/brapi_generated.ttl +++ /dev/null @@ -1,6323 +0,0 @@ -PREFIX owl: -PREFIX rdf: -PREFIX rdfs: -PREFIX xsd: - - - 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; - owl:oneOf ( ) -] . - - - 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 "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; - 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: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; - 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: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: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; - 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: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 "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:ObjectProperty; - rdfs:comment "links to various ontology documentation"@en; - rdfs:domain ; - rdfs:label "documentationLinks"@en; - rdfs:range . - - - 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:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:ObjectProperty; - rdfs:comment "germplasm"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - rdf:type owl:ObjectProperty; - 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 "modalities"@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: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 "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: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 , . - - - 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: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; - rdfs:domain ; - rdfs:label "program"@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: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:Class; - owl:oneOf ( ) -] . - - - rdf:type owl:NamedIndividual , . - - - rdf:type owl:ObjectProperty; - rdfs:comment "observationUnits"@en; - rdfs:domain ; - rdfs:label "observationUnits"@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: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: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 "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 "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; - 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: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; - rdfs:domain ; - 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: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 "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 type of randomization use to create the experimental design."@en; - rdfs:domain ; - rdfs:label "randomizationType"@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: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: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; - 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: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; - 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: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 "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: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:DatatypeProperty; - rdfs:comment "Ontology database unique identifier"@en; - rdfs:domain ; - rdfs:label "ontologyDbId"@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: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; - 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: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: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: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; - 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:Class; - owl:oneOf ( ) -] . - - - 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: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: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; - 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: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 date and time when this study was last modified"@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: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: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: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 germplasm using in this content mixture"@en; - rdfs:domain ; - rdfs:label "germplasm"@en; - rdfs:range . - - - 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; - owl:oneOf ( ) -] . - - - 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:Class; - owl:oneOf ( ) -] . - - - 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:NamedIndividual , . - - - 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: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: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: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; - rdfs:domain ; - rdfs:label "calls"@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 . - - - 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:DatatypeProperty; - rdfs:comment "The PUI of the factor which may link to an ontology."@en; - rdfs:domain ; - rdfs:label "factorPUI"@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 "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:Class; - owl:oneOf ( ) -] . - - - 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: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:Class; - owl:oneOf ( ) -] . - - - 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 "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; - 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:ObjectProperty; - rdfs:comment "The factors used in the experimental design."@en; - rdfs:domain ; - rdfs:label "experimentFactors"@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: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: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: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: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 "Analysis associated with a variant set"@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - - - 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 "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: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 "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 "A unique identifier physically attached to the `Sample`"@en; - rdfs:domain ; - rdfs:label "sampleBarcode"@en; - rdfs:range xsd:string . - - - 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:Class; - owl:oneOf ( ) -] . - - - 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:DatatypeProperty; - rdfs:comment "Human readable name of a List"@en; - rdfs:domain ; - rdfs:label "listName"@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:NamedIndividual , . - - - 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 "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:DatatypeProperty; - rdfs:comment "Ontology version (no specific format)"@en; - rdfs:domain ; - rdfs:label "version"@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 "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:DatatypeProperty; - rdfs:comment "Description the storage location"@en; - rdfs:domain ; - rdfs:label "storageLocation"@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 "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; - 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: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: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 "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: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 "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 "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 "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: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; - 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 "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:Class; - owl:oneOf ( ) -] . - - - 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: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: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 "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:Class; - owl:oneOf ( ) -] . - - - 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 "The PUI of the modality which may link to an ontology."@en; - rdfs:domain ; - rdfs:label "modalityPUI"@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: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 rows in a plot."@en; - rdfs:domain ; - rdfs:label "rowsPerPlot"@en; - rdfs:range xsd:double . - - - 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:Class; - owl:oneOf ( ) -] . - - - 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:ObjectProperty; - rdfs:comment "plates"@en; - rdfs:domain ; - rdfs:label "plates"@en; - rdfs:range . - - - rdf:type owl:Class; - rdfs:comment "The date and time when this study was last modified"@en; - rdfs:label "LastUpdate"@en . - - - 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: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: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: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; - rdfs:domain ; - rdfs:label "ontologyReference"@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 ""@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:Class; - owl:oneOf ( ) -] . - - - 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: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 "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: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 "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 "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: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: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: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: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: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: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; - 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:domain ; - rdfs:label "validValues"@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: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: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; - 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 "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; - owl:oneOf ( ) -] . - - - 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 "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; - rdfs:domain ; - 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 "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 "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; - 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: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:Class; - owl:oneOf ( ) -] . - - - 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 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; - 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; - 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 "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; - rdfs:domain ; - rdfs:label "amount"@en; - rdfs:range xsd:double . - - - 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: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:NamedIndividual , . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - 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 "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: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 "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: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:ObjectProperty; - rdfs:comment "plannedCrosses"@en; - rdfs:domain ; - rdfs:label "plannedCrosses"@en; - rdfs:range . - - - 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: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: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: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 "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: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: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; - rdfs:domain ; - rdfs:label "variantCount"@en; - rdfs:range xsd:integer . - - - 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: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:Class; - owl:oneOf ( ) -] . - - - 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: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: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:NamedIndividual , . - - - 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: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:ObjectProperty; - rdfs:comment ""@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: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; - 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: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: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: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 "The literal string \"Polygon\""@en; - rdfs:domain ; - rdfs:label "type"@en; - rdfs:range xsd:string . - - - 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: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; - 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; - rdfs:domain ; - rdfs:label "name"@en; - rdfs:range xsd:string . - - - rdf:type owl:DatatypeProperty; - rdfs:comment "How the trial is layout in the field."@en; - rdfs:domain ; - rdfs:label "layoutPattern"@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; - rdfs:domain ; - rdfs:label "culturalPractices"@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: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 "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: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: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 "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; - rdfs:domain ; - 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: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: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 "A 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 . - - - 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: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 "images"@en; - rdfs:domain ; - rdfs:label "images"@en; - rdfs:range . - - - 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: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: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:ObjectProperty; - rdfs:comment "Formats associated with a variant set"@en; - rdfs:domain ; - rdfs:label "variantSet"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - 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:ObjectProperty; - rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; - rdfs:domain ; - rdfs:label "analysis"@en; - rdfs:range . - - - 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:Class; - owl:oneOf ( ) -] . - - - 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: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 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: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; - 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: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: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: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: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; - 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: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: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: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: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; - rdfs:domain ; - 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:DatatypeProperty; - rdfs:comment "Ontology name"@en; - rdfs:domain ; - rdfs:label "ontologyName"@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: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: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; - owl:oneOf ( ) -] . - - - 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 "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; - 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; - rdfs:domain ; - 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; - 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:ObjectProperty; - rdfs:comment "The study in which the event occurred"@en; - rdfs:domain ; - rdfs:label "study"@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; - 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:Class; - owl:oneOf ( ) -] . - - - 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 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: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: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 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 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: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: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:Class; - owl:oneOf ( ) -] . - - - 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; - rdfs:domain ; - rdfs:label "observationLevels"@en; - rdfs:range . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - 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 "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: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: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: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: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 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; - 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; - 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: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: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; - 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: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: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; - 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 "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: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 date this trial started"@en; - rdfs:domain ; - 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; - rdfs:domain ; - rdfs:label "attributeDescription"@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: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:NamedIndividual , . - - - 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; - rdfs:comment "Timestamp when the entity was first created"@en; - rdfs:domain ; - rdfs:label "dateCreated"@en; - rdfs:range xsd:string . - -[ rdf:type owl:Class; - owl:oneOf ( ) -] . - - - 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: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:NamedIndividual , . - - - 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: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:Class; - owl:oneOf ( ) -] . - - - 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:Class; - owl:oneOf ( ) -] . - - - 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:ObjectProperty; - rdfs:comment "observations"@en; - rdfs:domain ; - rdfs:label "observations"@en; - rdfs:range . - - - 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. **Deprecated in v2.2** Please use `experimentalDesignPUI`. Github issue number #539"@en; - rdfs:domain ; - rdfs:label "PUI"@en; - rdfs:range xsd:string . - - - 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 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; - rdfs:domain ; - rdfs:label "trait"@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 "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/Specification/Generated/brapi_openapi_comparison.md b/Specification/Generated/brapi_openapi_comparison.md deleted file mode 100644 index 213d1260..00000000 --- a/Specification/Generated/brapi_openapi_comparison.md +++ /dev/null @@ -1,522 +0,0 @@ -#### What's New ---- - -##### `GET` /allelematrix - - -##### `GET` /breedingmethods - - -##### `GET` /calls - - -##### `GET` /callsets - - -##### `GET` /crosses - - -##### `PUT` /crosses - - -##### `POST` /crosses - - -##### `GET` /crossingprojects - - -##### `POST` /crossingprojects - - -##### `GET` /events - - -##### `GET` /maps - - -##### `GET` /germplasm - - -##### `POST` /germplasm - - -##### `GET` /attributes - - -##### `POST` /attributes - - -##### `GET` /attributevalues - - -##### `POST` /attributevalues - - -##### `GET` /images - - -##### `POST` /images - - -##### `GET` /lists - - -##### `POST` /lists - - -##### `GET` /locations - - -##### `POST` /locations - - -##### `GET` /markerpositions - - -##### `GET` /methods - - -##### `POST` /methods - - -##### `GET` /observations - - -##### `PUT` /observations - - -##### `POST` /observations - - -##### `GET` /observationunits - - -##### `PUT` /observationunits - - -##### `POST` /observationunits - - -##### `GET` /variables - - -##### `POST` /variables - - -##### `GET` /ontologies - - -##### `POST` /ontologies - - -##### `GET` /pedigree - - -##### `POST` /pedigree - - -##### `GET` /people - - -##### `POST` /people - - -##### `GET` /plannedcrosses - - -##### `PUT` /plannedcrosses - - -##### `POST` /plannedcrosses - - -##### `GET` /plates - - -##### `POST` /plates - - -##### `GET` /programs - - -##### `POST` /programs - - -##### `GET` /references - - -##### `GET` /referencesets - - -##### `GET` /samples - - -##### `PUT` /samples - - -##### `POST` /samples - - -##### `GET` /scales - - -##### `POST` /scales - - -##### `GET` /seasons - - -##### `POST` /seasons - - -##### `GET` /seedlots - - -##### `POST` /seedlots - - -##### `GET` /studies - - -##### `POST` /studies - - -##### `GET` /traits - - -##### `POST` /traits - - -##### `GET` /trials - - -##### `POST` /trials - - -##### `GET` /variants - - -##### `GET` /variantsets - - -##### `GET` /attributes/categories - - -##### `GET` /studytypes - - -##### `GET` /breedingmethods/{breedingMethodDbId} - - -##### `GET` /callsets/{callSetDbId} - - -##### `GET` /callsets/{callSetDbId}/calls - - -##### `GET` /crossingprojects/{crossingProjectDbId} - - -##### `PUT` /crossingprojects/{crossingProjectDbId} - - -##### `GET` /maps/{mapDbId} - - -##### `GET` /maps/{mapDbId}/linkagegroups - - -##### `GET` /germplasm/{germplasmDbId} - - -##### `PUT` /germplasm/{germplasmDbId} - - -##### `GET` /germplasm/{germplasmDbId}/mcpd - - -##### `GET` /attributes/{attributeDbId} - - -##### `PUT` /attributes/{attributeDbId} - - -##### `GET` /attributevalues/{attributeValueDbId} - - -##### `PUT` /attributevalues/{attributeValueDbId} - - -##### `GET` /images/{imageDbId} - - -##### `PUT` /images/{imageDbId} - - -##### `GET` /lists/{listDbId} - - -##### `PUT` /lists/{listDbId} - - -##### `POST` /lists/{listDbId}/data - - -##### `GET` /locations/{locationDbId} - - -##### `PUT` /locations/{locationDbId} - - -##### `GET` /methods/{methodDbId} - - -##### `PUT` /methods/{methodDbId} - - -##### `GET` /observations/{observationDbId} - - -##### `GET` /observationunits/{observationUnitDbId} - - -##### `GET` /variables/{observationVariableDbId} - - -##### `PUT` /variables/{observationVariableDbId} - - -##### `GET` /ontologies/{ontologyDbId} - - -##### `PUT` /ontologies/{ontologyDbId} - - -##### `GET` /people/{personDbId} - - -##### `PUT` /people/{personDbId} - - -##### `GET` /plates/{plateDbId} - - -##### `GET` /programs/{programDbId} - - -##### `PUT` /programs/{programDbId} - - -##### `GET` /references/{referenceDbId} - - -##### `GET` /references/{referenceDbId}/bases - - -##### `GET` /referencesets/{referenceSetDbId} - - -##### `GET` /samples/{sampleDbId} - - -##### `GET` /scales/{scaleDbId} - - -##### `PUT` /scales/{scaleDbId} - - -##### `GET` /seasons/{seasonDbId} - - -##### `PUT` /seasons/{seasonDbId} - - -##### `GET` /seedlots/{seedLotDbId} - - -##### `PUT` /seedlots/{seedLotDbId} - - -##### `GET` /seedlots/{seedLotDbId}/transactions - - -##### `GET` /studies/{studyDbId} - - -##### `PUT` /studies/{studyDbId} - - -##### `GET` /traits/{traitDbId} - - -##### `PUT` /traits/{traitDbId} - - -##### `GET` /trials/{trialDbId} - - -##### `PUT` /trials/{trialDbId} - - -##### `GET` /variants/{variantDbId} - - -##### `GET` /variants/{variantDbId}/calls - - -##### `GET` /variantsets/{variantSetDbId} - - -##### `GET` /variantsets/{variantSetDbId}/calls - - -##### `GET` /variantsets/{variantSetDbId}/callsets - - -##### `GET` /variantsets/{variantSetDbId}/variants - - -##### `POST` /search/allelematrix - - -##### `POST` /search/calls - - -##### `POST` /search/callsets - - -##### `POST` /search/germplasm - - -##### `POST` /search/attributes - - -##### `POST` /search/attributevalues - - -##### `POST` /search/images - - -##### `POST` /search/lists - - -##### `POST` /search/locations - - -##### `POST` /search/markerpositions - - -##### `POST` /search/observations - - -##### `POST` /search/observationunits - - -##### `POST` /search/variables - - -##### `POST` /search/pedigree - - -##### `POST` /search/people - - -##### `POST` /search/plates - - -##### `POST` /search/programs - - -##### `POST` /search/references - - -##### `POST` /search/referencesets - - -##### `POST` /search/samples - - -##### `POST` /search/studies - - -##### `POST` /search/trials - - -##### `POST` /search/variants - - -##### `POST` /search/variantsets - - -##### `GET` /search/allelematrix/{searchResultsDbId} - - -##### `GET` /search/calls/{searchResultsDbId} - - -##### `GET` /search/callsets/{searchResultsDbId} - - -##### `GET` /search/germplasm/{searchResultsDbId} - - -##### `GET` /search/attributes/{searchResultsDbId} - - -##### `GET` /search/attributevalues/{searchResultsDbId} - - -##### `GET` /search/images/{searchResultsDbId} - - -##### `GET` /search/lists/{searchResultsDbId} - - -##### `GET` /search/locations/{searchResultsDbId} - - -##### `GET` /search/markerpositions/{searchResultsDbId} - - -##### `GET` /search/observations/{searchResultsDbId} - - -##### `GET` /search/observationunits/{searchResultsDbId} - - -##### `GET` /search/variables/{searchResultsDbId} - - -##### `GET` /search/pedigree/{searchResultsDbId} - - -##### `GET` /search/people/{searchResultsDbId} - - -##### `GET` /search/plates/{searchResultsDbId} - - -##### `GET` /search/programs/{searchResultsDbId} - - -##### `GET` /search/references/{searchResultsDbId} - - -##### `GET` /search/referencesets/{searchResultsDbId} - - -##### `GET` /search/samples/{searchResultsDbId} - - -##### `GET` /search/studies/{searchResultsDbId} - - -##### `GET` /search/trials/{searchResultsDbId} - - -##### `GET` /search/variants/{searchResultsDbId} - - -##### `GET` /search/variantsets/{searchResultsDbId} - - diff --git a/generator/build.gradle b/generator/build.gradle index 3252eff2..671960ea 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 { @@ -115,32 +115,6 @@ tasks.register("generateAll") { //dependsOn generateOWL } -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 = '../' - def filename1 = "Specification/Generated/brapi_openapi.json" - def filename2 = "Specification/Generated/brapi_generated.json" - def filename = "Specification/Generated/brapi_openapi_comparison.md" - args = ['compare', filename1, filename2, - '-l', 'OPEN_API', - '-f', filename, - '-w', 'MARKDOWN', - '-c', 'Specification/OpenAPI-Components', - '-x', - '-t', - '-r'] -} - -tasks.register("compareAll") { - dependsOn compareOpenAPI - mustRunAfter generateAll -} - tasks.register("runAll") { dependsOn generateAll dependsOn compareAll diff --git a/generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml b/generator/openapi-Supplemental-Spec-V2.2-BrAPI-Core.yaml similarity index 99% rename from generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml rename to generator/openapi-Supplemental-Spec-V2.2-BrAPI-Core.yaml index 70b0e2b5..7fce5dbe 100644 --- a/generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml +++ b/generator/openapi-Supplemental-Spec-V2.2-BrAPI-Core.yaml @@ -1,6 +1,3 @@ -info: - title: BrAPI - version: '' openapi: 3.0.0 paths: /serverinfo: diff --git a/generator/openapi-metadata.yaml b/generator/openapi-metadata.yaml index f4ba2f9d..f1c891d9 100644 --- a/generator/openapi-metadata.yaml +++ b/generator/openapi-metadata.yaml @@ -1,2 +1,2 @@ title: BrAPI -version: 2.1 \ No newline at end of file +version: 2.2 \ No newline at end of file diff --git a/generator/openapi-options.yaml b/generator/openapi-options.yaml index 4debc8da..ff1065c7 100644 --- a/generator/openapi-options.yaml +++ b/generator/openapi-options.yaml @@ -1,799 +1,41 @@ -generate: true -descriptionFormat: TODO Description for %s -supplementalSpecification: '' +# BrAPI OpenAPI generation overrides. +# +# This file only contains values that differ from the defaults shipped in +# brapi-schema-tools' core/src/main/resources/openapi-options.yaml. +# Maps are merged per-key, so any key not listed here keeps its default value. +# +# IMPORTANT: the available options and their defaults are tied to the version +# of brapi-schema-tools used to run generation. That version is pinned in +# generator/build.gradle via the `brapiSchemaToolsVersion` property. Bump +# that property first, then review this file for new defaults that may make +# some entries here redundant (or for newly-required overrides). +# +# See https://github.com/plantbreeding/brapi-schema-tools/wiki/GenerateOptions +# for the full set of available options. + +# Point the BrAPI-Core module at its supplemental specification (extra paths, +# parameters, responses that are not derivable from the JSON schema). supplementalSpecificationFor: - BrAPI-Core: 'C:\Users\ps664\Documents\BrAPI\API\generator\openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml' -separateByModule: true -generateNewRequest: true + BrAPI-Core: generator/openapi-Supplemental-Spec-V2.2-BrAPI-Core.yaml + +# Season needs a *NewRequest schema (default behaviour for Season is to skip it). generateNewRequestFor: - AlleleMatrix: false - BreedingMethod: false - Call: false - CallSet: false - Event: false - GenomeMap: false - MarkerPosition: false - Reference: false - PedigreeNode: false Season: true - #ServerInfo: false - Variant: false - VariantSet: false -newRequestNameFormat: "%sNewRequest" -singleResponseNameFormat: "%sSingleResponse" -listResponseNameFormat: "%sListResponse" -searchRequestNameFormat: "%sSearchRequest" -pluralFor: - AlleleMatrix: AlleleMatrix - #ServerInfo: ServerInfo -pathItemNameFor: - AlleleMatrix: /allelematrix - GenomeMap: /maps - GermplasmAttribute: /attributes - GermplasmAttributeValue: /attributevalues - ObservationUnitHierarchyLevel: /observationlevels - ObservationVariable: /variables - PedigreeNode: /pedigree - #ServerInfo: /serverInfo -pathItemNameForProperty: - GermplasmAttribute: - attributeCategory: - /attributes/categories - Study: - studyType: - /studytypes -tagFor: - BreedingMethod: Germplasm - MarkerPosition: Genome Maps - PlannedCross: Crosses -getWithId: - generate: true - summaryFormat: Get the details of a specific %s - descriptionFormat: Get details for a %s - generateFor: - AlleleMatrix: false - Call: false - Cross: false - Event: false - MarkerPosition: false - ObservationUnitHierarchyLevel: false - PedigreeNode: false - PlannedCross: false - #ServerInfo: false -get: - generate: true - summaryFormat: Get a filtered list of %s - descriptionFormat: Get a list of %s - #generateFor: - #ServerInfo: false - list: true - listFor: - AlleleMatrix: false - pagedDefault: true - paged: - AlleleMatrix: false - pagedTokenDefault: false - pagedToken: - Call: true - Variant: true - inputFor: - BreedingMethod: false - propertiesFromRequest: true - propertyFromRequestFor: - AlleleMatrix: - pagination: false - sampleDbIds : false - AdditionalInfo: - additionalProperties: false - CallSet: - commonCropNames: false - germplasmNames: false - programDbIds: false - programNames: false - studyDbIds: false - studyNames: false - sampleNames: false - trialDbIds: false - trialNames: false - Cross: - programNames: false - CrossingProject: - programNames: false - Event: - studyNames: false - EventDateRange: - event: false - GenomeMap: - programNames: false - studyNames: false - trialNames: false - Germplasm: - familyCodes: false - programNames: false - studyNames: false - instituteCodes: false - trialNames: false - GermplasmAttribute: - dataTypes: false - germplasmNames: false - ontologyDbIds: false - programNames: false - studyDbId: false - studyDbIds: false - studyNames: false - traitClasses: false - traitAttributes: false - traitAttributePUIs: false - traitEntities: false - traitEntityPUIs: false - trialDbIds: false - trialNames: false - GermplasmAttributeValue: - dataTypes: false - germplasmNames: false - methodDbIds: false - ontologyDbIds: false - programNames: false - scaleDbIds: false - traitClasses: false - traitDbIds: false - List: - dateCreatedRangeStart: false - dateCreatedRangeEnd: false - dateModifiedRangeStart: false - dateModifiedRangeEnd: false - listOwnerNames: false - listOwnerPersonDbIds: false - programNames: false - Method: - programNames: false - Image: - programNames: false - imageFileNames: false - imageFileSizeMax: false - imageFileSizeMin: false - imageHeightMax: false - imageHeightMin: false - imageLocation: false - imageTimeStampRangeEnd: false - imageTimeStampRangeStart: false - imageWidthMax: false - imageWidthMin: false - mimeTypes: false - Location: - programNames: false - abbreviations: false - altitudeMin: false - altitudeMax: false - countryCodes: false - countryNames: false - coordinates: false - instituteAddresses: false - instituteNames: false - ObservationUnit: - germplasmNames: false - locationNames: false - observationLevels: false - observationLevelRelationships: false - observationVariableDbIds: false - observationVariableNames: false - observationVariablePUIs: false - programNames: false - studyNames: false - trialNames: false - Observation: - germplasmNames: false - locationNames: false - observationLevels: false - observationLevelRelationships: false - observationVariableNames: false - observationVariablePUIs: false - programNames: false - studyNames: false - trialNames: false - ObservationUnitLevelRelationship: - observationUnit: false - ObservationVariable: - dataTypes: false - programNames: false - studyDbIds: false - studyNames: false - traitAttributes: false - traitAttributePUIs: false - traitEntities: false - traitEntityPUIs: false - trialNames: false - PlannedCross: - programNames: false - PedigreeNode: - programNames: false - studyNames: false - trialNames: false - instituteCodes: false - Person: - programNames: false - emailAddresses: false - mailingAddresses: false - middleNames: false - phoneNumbers: false - Plate: - germplasmNames: false - programNames: false - studyNames: false - trialNames: false - plateBarcodes: false - Program: - leadPersonDbIds: false - leadPersonNames: false - objectives: false - Reference: - germplasmDbIds: false - germplasmNames: false - programNames: false - studyNames: false - trialNames: false - ReferenceSet: - germplasmDbIds: false - germplasmNames: false - programNames: false - studyNames: false - trialNames: false - Sample: - germplasmNames: false - programNames: false - studyNames: false - trialNames: false - Scale: - programNames: false - SeedLot: - programNames: false - Study: - germplasmNames: false - locationNames: false - programNames: false - trialNames: false - observationVariableNames: false - observationVariablePUIs: false - Trait: - programNames: false - Trial: - locationNames: false - observationVariableDbIds: false - observationVariableNames: false - observationVariablePUIs: false - programNames: false - studyNames: false - Variant: - commonCropNames: false - programDbIds: false - programNames: false - studyNames: false - studyDbIds: false - trialDbIds: false - trialNames: false - callSetDbIds: false - end: false - referenceDbIds: false - start: false - VariantSet: - programNames: false - trialDbIds: false - trialNames: false - referenceDbIds: false -search: - generate: true - summaryFormat: Submit a search request for `%s` - descriptionFormat: Submit a search request for `%s`t - searchIdFieldName: searchResultsDbId - submitDescriptionFormat: |- - Submit a search request for `%s`
- 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/%s/{searchResultsDbId}` to retrieve the results of the search.
- Review the Search Services documentation for additional implementation details. - retrieveDescriptionFormat: |- - Get the results of a `%s` search request
- Clients should submit a search request using the corresponding `POST /search/%s` endpoint. - 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 this endpoint to retrieve the results of the search.
- Review the Search Services documentation for additional implementation details. - pagedDefault: true - paged: - AlleleMatrix: false - pagedTokenDefault: false - pagedToken: - Call: true - Variant: true - list: true - listFor: - AlleleMatrix: false - generateFor: - BreedingMethod: false - Cross: false - CrossingProject: false - Event: false - GenomeMap: false - Method: false - ObservationUnitHierarchyLevel: false - Ontology: false - PlannedCross: false - Scale: false - Season: false - SeedLot: false - #ServerInfo: false - Trait: false - propertiesFromRequest: true - propertyFromRequestFor: - AlleleMatrix: - dimensionCallSetPage: false - dimensionCallSetPageSize: false - dimensionVariantPage: false - dimensionVariantPageSize: false - Observation: - observationUnitLevelNames: false - observationUnitLevelOrders: false - observationUnitLevelCodes: false - observationUnitLevelRelationshipNames: false - observationUnitLevelRelationshipOrders: false - observationUnitLevelRelationshipCodes: false - observationUnitLevelRelationshipDbIds: false - ObservationUnit: - observationUnitLevelNames: false - observationUnitLevelOrders: false - observationUnitLevelCodes: false - observationUnitLevelRelationshipNames: false - observationUnitLevelRelationshipOrders: false - observationUnitLevelRelationshipCodes: false - observationUnitLevelRelationshipDbIds: false - Trial: - sortBy: false - sortOrder: false -table: - generate: false - summaryFormat: Get a table of `%s` records as a CSV file. - descriptionFormat: Get a table of `%s` records returned directly as CSV text. - generateFor: - ObservationUnit: true -searchTable: - generate: false - summaryFormat: Generate a table of `%s` in a CSV file, publish the file and return a URI to the file. - descriptionFormat: Generate a table of `%s` in a CSV file, publish the file and return a URI to the file. -post: - generate: true - summaryFormat: Create new %s - descriptionFormat: Add new %s to database - generateFor: - AlleleMatrix: false - BreedingMethod: false - Call: false - CallSet: false - Event: false - GenomeMap: false - MarkerPosition: false - ObservationUnitHierarchyLevel: false - Reference: false - ReferenceSet: false - #ServerInfo: false - Variant: false - VariantSet: false - multiple: false - multipleFor: - GermplasmAttribute: true + +# These three types currently override the default behaviour to *not* generate +# a PUT endpoint. Review whether this is still desired — the defaults have +# been updated to enable PUT for them (see /calls.put, /pedigree.put, /plates.put). put: - generate: true - summaryFormat: Update the details for an existing %s - descriptionFormat: Update the details for an existing %s generateFor: - AlleleMatrix: false - BreedingMethod: false Call: false - CallSet: false - Event: false - GenomeMap: false - MarkerPosition: false - ObservationUnitHierarchyLevel: false - Reference: false - ReferenceSet: false PedigreeNode: false Plate: false - #ServerInfo: false - Variant: false - VariantSet: false - multiple: false - multipleFor: - Call: true - Cross: true - Observation: true - ObservationUnit: true - PlannedCross: true - PedigreeNode: true - Plate: true - Sample: true - useAdditionalProperties: - Cross: true - Observation: true - ObservationUnit: true - PlannedCross: true - PedigreeNode: true - Plate: true - Sample: true -delete: - generate: false - summaryFormat: Delete an existing %s - descriptionFormat: Delete existing %s - generateFor: - AlleleMatrix: false - Call: false - CallSet: false - Event: false - GenomeMap: false - MarkerPosition: false - ObservationUnitHierarchyLevel: false - Reference: false - ServerInfo: false - Variant: false - VariantSet: false + properties: - descriptionFormat: Property %s for type %s - id: - nameFormat: "%sDbId" - link: true - propertyFor: - GermplasmAttribute: attributeDbId - GermplasmAttributeValue: attributeValueDbId - GenomeMap: mapDbId - ObservationUnitHierarchyLevel: levelName - requiredPropertyFor: - GermplasmAttributeValue: - attribute: false - name: - nameFormat: "%sName" - link: true - propertyFor: - GermplasmAttribute: attributeName - GermplasmAttributeValue: attributeValueName - GenomeMap: mapName - EnvironmentParameter: parameterName - ObservationUnitHierarchyLevel: levelName - linkPropertyFor: - Call: - variant: true - CallSet: - sample: false - study: false - GermplasmMCPD: - germplasm: false - Image: - observationUnit: false - List: - listOwnerPerson: false - MarkerPosition: - variant: true - Observation: - season: false - study: false - ObservationUnitLevelRelationship: - observationUnit: false - Plate: - program: false - study: false - trial: false - PedigreeNode: - crossingProject: false - Sample: - observationUnit: false - germplasm: false - program: false - study: false - trial: false - SeedLotTransaction: - fromSeedLot: false - toSeedLot: false - VariantSet: - referenceSet: false - study: false - nullablePropertyFor: - GermplasmChild: - germplasm: true - MarkerPosition: - map: true - variant: true - ListRequest: - listType: true - Program: - leadPerson: true - requiredPropertyFor: - Call: - callSet: false - variantSet: false - GermplasmChild: - germplasm: false - GermplasmParent: - germplasm: false pui: - nameFormat: "%sPUI" - link: true - linkFor: - CallSet: false - CrossingProject: false - GenomeMap: false - Germplasm: false - ObservationUnit: false - PlannedCross: false - Reference: false - ReferenceSet: false - Study: false - Trial: false - VariantSet: false - propertyFor: - EnvironmentParameter: parameterPUI - GermplasmAttribute: attributePUI - GermplasmAttributeValue: attributeValuePUI - GenomeMap: mapPUI linkPropertyFor: - Call: - variant: false - CallSet: - sample: false - study: false - CrossingProject: - program: false - ContentMixture: - cross: false - GermplasmAttributeValue: - attribute: false - Germplasm: - breedingMethod: false - GermplasmMCPD: - germplasm: true - List: - listOwnerPerson: false - Location: - parentLocation: false - MarkerPosition: - variant: false Observation: - observationVariable: false - season: false uploadedByPerson: false - ObservationUnit: - cross: false - location: false - program: false - seedLot: false - observationVariable: false - season: false - OntologyReference: - ontology: false - PedigreeNode: - breedingMethod: false - germplasm: true - Plate: - program: false - Program: - leadPerson: false - Sample: - plate: false - program: false - SeedLot: - location: false - program: false - SeedLotTransaction: - fromSeedLot: false - toSeedLot: false - Study: - location: false - Trial: - program: false - requiredPropertyFor: - PedigreeNode: - germplasm: false linkTypeFor: - AlleleMatrix: - callSets: id - variants: id - variantSets: id - Analysis: - variantSet: none - Attribute: - method: embedded - scale: embedded - trait: embedded - AvailableFormat: - variantSet: none - BreedingMethod: - germplasm: none - pedigreeNodes: none - CallSet: - calls: sub-query - variantSets: id - CallListResponse: - data: embedded - Cross: - observationUnits: none - ContentMixture: - seedLot: none - CrossAttribute: - cross: none - CrossingProject: - crosses: none - plannedCrosses: none - pedigreeNodes: none - DatasetAuthorships: - trial: none - DataMatrix: - alleleMatrix: none - DocumentationLink: - ontologyReference: none - Donor: - germplasm: none - ExperimentalDesign: - study: none - Event: - observationUnits: id - study: id - EventDateRange: - event: none - EnvironmentParameter: - study: none - EventParameter: - event: none - study: none - GeoJSON: - image: none - observation: none - observationUnit: none - germplasmOrigin: none - GeoJSONSearchArea: - image: none - observation: none - observationUnit: none - germplasmOrigin: none - GenomeMap: - linkageGroups: sub-query - GenotypeMetadata: - call: none - Germplasm: - samples: none - attributeValues: none - observations: none - observationUnits: none - mcpd: sub-query - progenyPedigreeNodes: none - parentPedigreeNodes: none - reference: none - referenceSet: none - siblingPedigreeNodes: none - GermplasmAttribute: - attributeValues: none - method: embedded - ontologyReference: embedded - scale: embedded - trait: embedded - GermplasmMCPD: - germplasm: id - GermplasmOrigin: - germplasm: none - GermplasmChild: - pedigreeNode: none - GermplasmParent: - pedigreeNode: none - GrowthFacility: - study: none - Image: - imagecontent: sub-query - LastUpdate: - study: none - LinkageGroup: - genomeMap: none - Location: - childLocations: none - seedLots: none - observationUnits: none - studies: none - MetadataField: - variantSet: none - OntologyTerm: - reference: none - referenceSet: none - Observation: - images: none - season: embedded - ObservationUnit: - samples: none - events: none - images: none - observations: none - ObservationUnitPosition: - observationUnit: none - ObservationTreatment: - observationUnit: none - ObservationVariable: - studies: none - observations: none - method: embedded - ontologyReference: embedded - scale: embedded - trait: embedded - Pagination: - alleleMatrix: none - PedigreeNode: - siblings: embedded Person: - lists: none - programs: none - observations: none - PlannedCross: - crosses: none - PollinationEvent: - cross: none - Program: - crossingProjects: none - leadPerson: id - observationUnits: none - plates: none - samples: none - seedLots: none - trials: none - Plate: - samples: none - Reference: - bases: sub-query - variants: none - Publication: - trial: none - Sample: - callSets: none - variants: none - SeedLot: - transactions: sub-query - observationUnits: none - SourceGermplasm: - reference: none - StorageType: - germplasm: none - Study: - callSets: none - contacts: embedded - events: none - environmentParameters: embedded observations: none - observationUnits: none - observationVariables: id - plates: none - samples: none - variantSets: none - Synonym: - germplasm: none - TaxonId: - germplasm: none - Trial: - contacts: embedded - observationUnits: none - plates: none - samples: none - studies: none - Variable: - method: embedded - scale: embedded - trait: embedded - Variant: - calls: sub-query - variantSets: id - VariantSet: - availableFormats: embedded - calls: sub-query - callSets: sub-query - variants: sub-query - ValidValuesCategory: - validValues: none -controlledVocabulary: - generate: true - summaryFormat: Get the ${property} of ${type} - descriptionFormat: List all available ${type} ${property} - pagedDefault: true -defaultMediaType: application/json -mediaTypeForProperty: - Image: - imageContent: image/* \ No newline at end of file diff --git a/generator/openapi-single-file-options.yaml b/generator/openapi-single-file-options.yaml index 04e17b3a..fc308fbd 100644 --- a/generator/openapi-single-file-options.yaml +++ b/generator/openapi-single-file-options.yaml @@ -1,3 +1,48 @@ +# BrAPI OpenAPI generation overrides (single-file variant). +# +# Identical to generator/openapi-options.yaml apart from: +# * separateByModule: false (emit one combined spec) +# * supplementalSpecification: ... (global supplemental, instead +# of the per-module supplementalSpecificationFor used by openapi-options.yaml) +# +# This file only contains values that differ from the defaults shipped in +# brapi-schema-tools' core/src/main/resources/openapi-options.yaml. +# Maps are merged per-key, so any key not listed here keeps its default value. +# +# IMPORTANT: the available options and their defaults are tied to the version +# of brapi-schema-tools used to run generation. That version is pinned in +# generator/build.gradle via the `brapiSchemaToolsVersion` property. Bump +# that property first, then review this file for new defaults that may make +# some entries here redundant (or for newly-required overrides). +# +# See https://github.com/plantbreeding/brapi-schema-tools/wiki/GenerateOptions +# for the full set of available options. + separateByModule: false -supplementalSpecificationFor: - BrAPI-Core: generator/openapi-Supplemental-Spec-V2.1-BrAPI-Core.yaml \ No newline at end of file + +# Single combined supplemental spec (extra paths, parameters, responses that +# are not derivable from the JSON schema). Applied globally rather than +# per-module because separateByModule is false. +supplementalSpecification: generator/openapi-Supplemental-Spec-V2.2-BrAPI-Core.yaml + +# Season needs a *NewRequest schema (default behaviour for Season is to skip it). +generateNewRequestFor: + Season: true + +# These three types currently override the default behaviour to *not* generate +# a PUT endpoint. Review whether this is still desired — the defaults have +# been updated to enable PUT for them (see /calls.put, /pedigree.put, /plates.put). +put: + generateFor: + Call: false + PedigreeNode: false + Plate: false + +properties: + pui: + linkPropertyFor: + Observation: + uploadedByPerson: false + linkTypeFor: + Person: + observations: none