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Update ontology registry and S3 deployment metadata #122

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13 changes: 10 additions & 3 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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1 change: 0 additions & 1 deletion db/README.md
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This file was deleted.

17 changes: 14 additions & 3 deletions ontologies.Makefile
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Expand Up @@ -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 $@

Expand Down Expand Up @@ -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 $@

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
2 changes: 2 additions & 0 deletions src/semsql/builder/prefixes/prefixes.csv
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Expand Up @@ -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#
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2 changes: 2 additions & 0 deletions src/semsql/builder/prefixes/prefixes_local.csv
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Expand Up @@ -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#
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10 changes: 8 additions & 2 deletions src/semsql/builder/registry/ontologies.yaml
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Expand Up @@ -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:
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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:
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