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Merge pull request #92 from INCATools/ABA-redux
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Adding 5 Allen brain atlas ontologies.
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cmungall authored Jan 30, 2025
2 parents e2c7fe6 + 85bd277 commit bbb475a
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Showing 4 changed files with 89 additions and 5 deletions.
57 changes: 56 additions & 1 deletion ontologies.Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -174,6 +174,61 @@ db/comploinc.owl: download/comploinc.owl
robot relax -i $< merge -o $@


download/hba.owl: STAMP
curl -L -s https://github.com/brain-bican/human_brain_atlas_ontology/raw/main/hbao-base.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/hba.owl

db/hba.owl: download/hba.owl
cp $< $@


download/mba.owl: STAMP
curl -L -s https://github.com/brain-bican/mouse_brain_atlas_ontology/raw/main/mbao-base.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/mba.owl

db/mba.owl: download/mba.owl
cp $< $@


download/dmba.owl: STAMP
curl -L -s https://github.com/brain-bican/developing_mouse_brain_atlas_ontology/raw/main/dmbao-base.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/dmba.owl

db/dmba.owl: download/dmba.owl
cp $< $@


download/dhba.owl: STAMP
curl -L -s https://github.com/brain-bican/developing_human_brain_atlas_ontology/raw/main/dhbao-base.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/dhba.owl

db/dhba.owl: download/dhba.owl
cp $< $@


download/pba.owl: STAMP
curl -L -s https://github.com/brain-bican/primate_brain_atlas_ontology/raw/main/pbao-base.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
mv $@.tmp $@

.PRECIOUS: download/pba.owl

db/pba.owl: download/pba.owl
cp $< $@


download/bero.owl: STAMP
curl -L -s https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl > $@.tmp
sha256sum -b $@.tmp > $@.sha256
Expand Down Expand Up @@ -1262,4 +1317,4 @@ download/%.owl: STAMP
db/%.owl: download/%.owl
robot merge -i $< -o $@

EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio pride modl phenio phenio_test comploinc bero aio reacto xsmo bcio icd10who ordo gard mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid 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 fhkb dbpendiaont uberoncm icd10cm omim co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways pathbank kegg.genome drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context ontie ecosim nmdc_schema mixs kgcl fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time
EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio pride modl phenio phenio_test comploinc hba mba dmba dhba pba bero aio reacto xsmo bcio icd10who ordo gard mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid 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 fhkb dbpendiaont uberoncm icd10cm omim co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways pathbank kegg.genome drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context ontie ecosim nmdc_schema mixs kgcl fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time
6 changes: 6 additions & 0 deletions src/semsql/builder/prefixes/prefixes.csv
Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,11 @@ modl,https://archive.org/services/purl/purl/modular_ontology_design_library#
biolink,https://w3id.org/biolink/vocab/
biolink,https://w3id.org/biolink/vocab/
loinc,https://loinc.org/
HBA,https://purl.brain-bican.org/ontology/hbao/HBA_
MBA,https://purl.brain-bican.org/ontology/mbao/MBA_
DMBA,https://purl.brain-bican.org/ontology/dmbao/DMBA_
DHBA,https://purl.brain-bican.org/ontology/dhbao/DHBA_
PBA,https://purl.brain-bican.org/ontology/pbao/PBA_
XSMO,http://purl.obolibrary.org/obo/XSMO_
BCIO,http://humanbehaviourchange.org/ontology/BCIO_
BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_
Expand Down Expand Up @@ -163,6 +168,7 @@ pathbank,http://purl.obolibrary.org/obo/pathbank_
pathbank,http://purl.obolibrary.org/obo/kegg.genome_
MESH,http://id.nlm.nih.gov/mesh/
RXNORM,http://purl.bioontology.org/ontology/RXNORM/
VCCF,http://purl.obolibrary.org/obo/VCCF_
OBT,http://purl.obolibrary.org/obo/OBT_
NANDO,http://nanbyodata.jp/ontology/NANDO_
ECSO,http://purl.dataone.org/odo/ECSO_
Expand Down
6 changes: 6 additions & 0 deletions src/semsql/builder/prefixes/prefixes_local.csv
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,11 @@ modl,https://archive.org/services/purl/purl/modular_ontology_design_library#
biolink,https://w3id.org/biolink/vocab/
biolink,https://w3id.org/biolink/vocab/
loinc,https://loinc.org/
HBA,https://purl.brain-bican.org/ontology/hbao/HBA_
MBA,https://purl.brain-bican.org/ontology/mbao/MBA_
DMBA,https://purl.brain-bican.org/ontology/dmbao/DMBA_
DHBA,https://purl.brain-bican.org/ontology/dhbao/DHBA_
PBA,https://purl.brain-bican.org/ontology/pbao/PBA_
XSMO,http://purl.obolibrary.org/obo/XSMO_
BCIO,http://humanbehaviourchange.org/ontology/BCIO_
BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_
Expand Down Expand Up @@ -100,6 +105,7 @@ pathbank,http://purl.obolibrary.org/obo/pathbank_
pathbank,http://purl.obolibrary.org/obo/kegg.genome_
MESH,http://id.nlm.nih.gov/mesh/
RXNORM,http://purl.bioontology.org/ontology/RXNORM/
VCCF,http://purl.obolibrary.org/obo/VCCF_
OBT,http://purl.obolibrary.org/obo/OBT_
NANDO,http://nanbyodata.jp/ontology/NANDO_
ECSO,http://purl.dataone.org/odo/ECSO_
Expand Down
25 changes: 21 additions & 4 deletions src/semsql/builder/registry/ontologies.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,27 @@ ontologies:
build_command: "robot relax -i $< merge -o $@"
prefixmap:
loinc: https://loinc.org/
# See https://github.com/obophenotype/uberon/issues/3267
hba:
url: https://github.com/brain-bican/human_brain_atlas_ontology/raw/main/hbao-base.owl
prefixmap:
HBA: https://purl.brain-bican.org/ontology/hbao/HBA_
mba:
url: https://github.com/brain-bican/mouse_brain_atlas_ontology/raw/main/mbao-base.owl
prefixmap:
MBA: https://purl.brain-bican.org/ontology/mbao/MBA_
dmba:
url: https://github.com/brain-bican/developing_mouse_brain_atlas_ontology/raw/main/dmbao-base.owl
prefixmap:
DMBA: https://purl.brain-bican.org/ontology/dmbao/DMBA_
dhba:
url: https://github.com/brain-bican/developing_human_brain_atlas_ontology/raw/main/dhbao-base.owl
prefixmap:
DHBA: https://purl.brain-bican.org/ontology/dhbao/DHBA_
pba:
url: https://github.com/brain-bican/primate_brain_atlas_ontology/raw/main/pbao-base.owl
prefixmap:
PBA: https://purl.brain-bican.org/ontology/pbao/PBA_
bero:
url: https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl
aio:
Expand All @@ -120,10 +141,6 @@ ontologies:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10who.owl
prefixmap:
icd10who: https://icd.who.int/browse10/2019/en#/
omim:
url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/omim.owl
prefixmap:
icd10who: https://icd.who.int/browse10/2019/en#/
#icd11f:
# url: https://github.com/monarch-initiative/icd11/releases/latest/download/icd11foundation.owl
# prefixmap:
Expand Down

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