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Adding 5 Allen brain atlas ontologies. #85

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Adding 5 Allen brain atlas ontologies. 
See obophenotype/uberon#3267
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@cmungall
cmungall committed Apr 29, 2024
commit 519da04779688bde12814a2b3dd39be295601b42
57 changes: 56 additions & 1 deletion ontologies.Makefile
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Expand Up @@ -130,6 +130,61 @@ 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 @@ -932,4 +987,4 @@ download/%.owl: STAMP
db/%.owl: download/%.owl
robot merge -i $< -o $@

EXTRA_ONTOLOGIES = upheno chiro ncit fma maxo foodon chebiplus msio modl phenio phenio_test comploinc bero aio reacto bcio icd10who ordo gard mondo-ingest oeo sdgio biovoices omop cco occo iof upa go go-lego go-amigo neo bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo hcao hpinternational edam sweetAll lov schema-dot-org prov cellosaurus cosmo fhkb dbpendiaont uberoncm icd10cm co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways drugmechdb rxnorm vccf ontobiotope nando ontie ecosim nmdc_schema mixs fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time
EXTRA_ONTOLOGIES = upheno chiro ncit fma maxo foodon chebiplus msio modl phenio phenio_test comploinc hba mba dmba dhba pba bero aio reacto bcio icd10who ordo gard mondo-ingest oeo sdgio biovoices omop cco occo iof upa go go-lego go-amigo neo bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo hcao hpinternational edam sweetAll lov schema-dot-org prov cellosaurus cosmo fhkb dbpendiaont uberoncm icd10cm co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways drugmechdb rxnorm vccf ontobiotope nando ontie ecosim nmdc_schema mixs fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time
5 changes: 5 additions & 0 deletions src/semsql/builder/prefixes/prefixes.csv
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Expand Up @@ -69,6 +69,11 @@ 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_
BCIO,http://humanbehaviourchange.org/ontology/BCIO_
BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_
icd10who,https://icd.who.int/browse10/2019/en#/
Expand Down
5 changes: 5 additions & 0 deletions src/semsql/builder/prefixes/prefixes_local.csv
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Expand Up @@ -6,6 +6,11 @@ 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_
BCIO,http://humanbehaviourchange.org/ontology/BCIO_
BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_
icd10who,https://icd.who.int/browse10/2019/en#/
Expand Down
21 changes: 21 additions & 0 deletions src/semsql/builder/registry/ontologies.yaml
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Expand Up @@ -63,6 +63,27 @@ 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 Down
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