diff --git a/Makefile b/Makefile index 615bc53..676d7ba 100644 --- a/Makefile +++ b/Makefile @@ -233,15 +233,22 @@ bin/%: ### DEPLOY DATE = $(shell date -u +"%Y-%m-%d") +S3_CACHE_CONTROL = public, max-age=86400 s3-deploy: - aws s3 sync stage s3://bbop-sqlite --acl public-read + aws s3 sync stage s3://bbop-sqlite --acl public-read \ + --cache-control "$(S3_CACHE_CONTROL)" \ + --content-type application/gzip s3-version: - aws s3 sync stage s3://bbop-sqlite/releases/$(DATE) --acl public-read + aws s3 sync stage s3://bbop-sqlite/releases/$(DATE) --acl public-read \ + --cache-control "$(S3_CACHE_CONTROL)" \ + --content-type application/gzip s3-deploy-%: stage/%.db.gz - aws s3 cp $< s3://bbop-sqlite/$*.db.gz --acl public-read + aws s3 cp $< s3://bbop-sqlite/$*.db.gz --acl public-read \ + --cache-control "$(S3_CACHE_CONTROL)" \ + --content-type application/gzip # Test documentation locally diff --git a/db/README.md b/db/README.md deleted file mode 100644 index 42e946c..0000000 --- a/db/README.md +++ /dev/null @@ -1 +0,0 @@ -# sqlite dbs go here diff --git a/ontologies.Makefile b/ontologies.Makefile index 2e009fe..4fba182 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -65,7 +65,7 @@ db/ncit.owl: download/ncit.owl download/fma.owl: STAMP - curl -L -s http://sig.biostr.washington.edu/share/downloads/fma/release/latest/fma.owl > $@.tmp + curl -L -s http://purl.org/sig/ont/fma.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 mv $@.tmp $@ @@ -406,7 +406,7 @@ db/ordo.owl: download/ordo.owl download/gard.owl: STAMP - curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/gard.owl > $@.tmp + curl -L -s https://github.com/monarch-initiative/gard/releases/latest/download/gard.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 mv $@.tmp $@ @@ -867,6 +867,17 @@ db/hcao.owl: download/hcao.owl cp $< $@ +download/ssbd.owl: STAMP + curl -L -s https://raw.githubusercontent.com/openssbd/ssbd-ontology/v20250512-1/ontology/ssbd_integrated.owl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/ssbd.owl + +db/ssbd.owl: download/ssbd.owl + cp $< $@ + + download/hpinternational.owl: STAMP curl -L -s http://purl.obolibrary.org/obo/hp/hp-international.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -1735,4 +1746,4 @@ download/%.owl: STAMP db/%.owl: download/%.owl robot merge -i $< -o $@ -EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio chemrof deb matpo panet phenx pride sosa emi npc modl phenio comploinc hba mba dmba dhba pba bero aio reacto xsmo bcio sio icd10who icd11f ordo gard icd10cm omim mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin metpo d3o biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid ror cpont biolink biopax enanomapper mlo ito chemont molgenie cso obiws biopragmatics-reactome reactome-hs reactome-mm efo hcao hpinternational edam chr sweetAll oboe-core oboe-standards lov schema-dot-org prov dtype vaem qudtunit quantitykind cellosaurus cosmo gist gistBFO fhkb dbpendiaont uberoncm co_324 ppeo interpro pfam hgnc.genegroup hgnc sgd gtdb eccode uniprot uniprot.ptm credit rhea swisslipid drugbank drugcentral complexportal wikipathways pathbank kegg.genome drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context cbo ontie pain como ecosim bervo valuesets micront nmdc_schema mixs kgcl fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time saref saref4city saref4ener saref4bldg hhearvs sdoho pathgo brick minsysont cmso asmo sulo uco d3fend codamos +EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio chemrof deb matpo panet phenx pride sosa emi npc modl phenio comploinc hba mba dmba dhba pba bero aio reacto xsmo bcio sio icd10who icd11f ordo gard icd10cm omim mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin metpo d3o biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid ror cpont biolink biopax enanomapper mlo ito chemont molgenie cso obiws biopragmatics-reactome reactome-hs reactome-mm efo hcao ssbd hpinternational edam chr sweetAll oboe-core oboe-standards lov schema-dot-org prov dtype vaem qudtunit quantitykind cellosaurus cosmo gist gistBFO fhkb dbpendiaont uberoncm co_324 ppeo interpro pfam hgnc.genegroup hgnc sgd gtdb eccode uniprot uniprot.ptm credit rhea swisslipid drugbank drugcentral complexportal wikipathways pathbank kegg.genome drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context cbo ontie pain como ecosim bervo valuesets micront nmdc_schema mixs kgcl fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time saref saref4city saref4ener saref4bldg hhearvs sdoho pathgo brick minsysont cmso asmo sulo uco d3fend codamos diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv index 79af915..b183253 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -162,6 +162,8 @@ cyc,http://sw.cyc.com/concept OBIws,http://purl.obolibrary.org/obo/OBIws_ reactome.obo,http://purl.obolibrary.org/obo/reactome_ reactome.biopax,http://www.reactome.org/biopax/77/48887# +ssbd,http://ssbd.riken.jp/ontology/ +SSBD,http://metadb.riken.jp/ontology/SSBD/ chr,http://purl.obolibrary.org/obo/CHR_ oboe-core,http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl# oboe-standards,http://ecoinformatics.org/oboe/oboe.1.0/oboe-standards.owl# diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index fac0872..6b63dc9 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -99,6 +99,8 @@ cyc,http://sw.cyc.com/concept OBIws,http://purl.obolibrary.org/obo/OBIws_ reactome.obo,http://purl.obolibrary.org/obo/reactome_ reactome.biopax,http://www.reactome.org/biopax/77/48887# +ssbd,http://ssbd.riken.jp/ontology/ +SSBD,http://metadb.riken.jp/ontology/SSBD/ chr,http://purl.obolibrary.org/obo/CHR_ oboe-core,http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl# oboe-standards,http://ecoinformatics.org/oboe/oboe.1.0/oboe-standards.owl# diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index 4b0c72d..f09c2bd 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -42,7 +42,7 @@ ontologies: url: http://purl.obolibrary.org/obo/ncit.owl build_command: "robot relax -i $< merge -o $@" fma: - url: http://sig.biostr.washington.edu/share/downloads/fma/release/latest/fma.owl + url: http://purl.org/sig/ont/fma.owl prefixmap: FMA: http://purl.org/sig/ont/fma/fma maxo: @@ -182,7 +182,7 @@ ontologies: ordo: url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/ordo.owl gard: - url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/gard.owl + url: https://github.com/monarch-initiative/gard/releases/latest/download/gard.owl prefixmap: GARD: http://purl.obolibrary.org/obo/GARD_ icd10cm: @@ -380,6 +380,12 @@ ontologies: has_imports: true hcao: url: https://raw.githubusercontent.com/HumanCellAtlas/ontology/master/hcao.owl + ssbd: + description: SSBD Ontology for interoperable bioimaging metadata + url: https://raw.githubusercontent.com/openssbd/ssbd-ontology/v20250512-1/ontology/ssbd_integrated.owl + prefixmap: + ssbd: http://ssbd.riken.jp/ontology/ + SSBD: http://metadb.riken.jp/ontology/SSBD/ hpinternational: url: http://purl.obolibrary.org/obo/hp/hp-international.owl edam: