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Adding 5 Allen brain atlas ontologies.
Redo of #85
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‎ontologies.Makefile‎

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@@ -174,6 +174,61 @@ db/comploinc.owl: download/comploinc.owl
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robot relax -i $< merge -o $@
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download/hba.owl: STAMP
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curl -L -s https://github.com/brain-bican/human_brain_atlas_ontology/raw/main/hbao-base.owl > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
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mv $@.tmp $@
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.PRECIOUS: download/hba.owl
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db/hba.owl: download/hba.owl
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cp $< $@
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download/mba.owl: STAMP
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curl -L -s https://github.com/brain-bican/mouse_brain_atlas_ontology/raw/main/mbao-base.owl > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
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mv $@.tmp $@
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.PRECIOUS: download/mba.owl
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db/mba.owl: download/mba.owl
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cp $< $@
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download/dmba.owl: STAMP
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curl -L -s https://github.com/brain-bican/developing_mouse_brain_atlas_ontology/raw/main/dmbao-base.owl > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
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mv $@.tmp $@
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.PRECIOUS: download/dmba.owl
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db/dmba.owl: download/dmba.owl
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cp $< $@
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download/dhba.owl: STAMP
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curl -L -s https://github.com/brain-bican/developing_human_brain_atlas_ontology/raw/main/dhbao-base.owl > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
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mv $@.tmp $@
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.PRECIOUS: download/dhba.owl
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db/dhba.owl: download/dhba.owl
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cp $< $@
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download/pba.owl: STAMP
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curl -L -s https://github.com/brain-bican/primate_brain_atlas_ontology/raw/main/pbao-base.owl > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
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mv $@.tmp $@
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.PRECIOUS: download/pba.owl
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db/pba.owl: download/pba.owl
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cp $< $@
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download/bero.owl: STAMP
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curl -L -s https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl > $@.tmp
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sha256sum -b $@.tmp > $@.sha256
@@ -1262,4 +1317,4 @@ download/%.owl: STAMP
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db/%.owl: download/%.owl
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robot merge -i $< -o $@
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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
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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

‎src/semsql/builder/prefixes/prefixes.csv‎

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Original file line numberDiff line numberDiff line change
@@ -85,6 +85,11 @@ modl,https://archive.org/services/purl/purl/modular_ontology_design_library#
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biolink,https://w3id.org/biolink/vocab/
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biolink,https://w3id.org/biolink/vocab/
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loinc,https://loinc.org/
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HBA,https://purl.brain-bican.org/ontology/hbao/HBA_
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MBA,https://purl.brain-bican.org/ontology/mbao/MBA_
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DMBA,https://purl.brain-bican.org/ontology/dmbao/DMBA_
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DHBA,https://purl.brain-bican.org/ontology/dhbao/DHBA_
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PBA,https://purl.brain-bican.org/ontology/pbao/PBA_
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XSMO,http://purl.obolibrary.org/obo/XSMO_
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BCIO,http://humanbehaviourchange.org/ontology/BCIO_
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BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_
@@ -163,6 +168,7 @@ pathbank,http://purl.obolibrary.org/obo/pathbank_
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pathbank,http://purl.obolibrary.org/obo/kegg.genome_
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MESH,http://id.nlm.nih.gov/mesh/
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RXNORM,http://purl.bioontology.org/ontology/RXNORM/
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VCCF,http://purl.obolibrary.org/obo/VCCF_
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OBT,http://purl.obolibrary.org/obo/OBT_
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NANDO,http://nanbyodata.jp/ontology/NANDO_
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ECSO,http://purl.dataone.org/odo/ECSO_

‎src/semsql/builder/prefixes/prefixes_local.csv‎

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Original file line numberDiff line numberDiff line change
@@ -22,6 +22,11 @@ modl,https://archive.org/services/purl/purl/modular_ontology_design_library#
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biolink,https://w3id.org/biolink/vocab/
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biolink,https://w3id.org/biolink/vocab/
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loinc,https://loinc.org/
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HBA,https://purl.brain-bican.org/ontology/hbao/HBA_
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MBA,https://purl.brain-bican.org/ontology/mbao/MBA_
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DMBA,https://purl.brain-bican.org/ontology/dmbao/DMBA_
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DHBA,https://purl.brain-bican.org/ontology/dhbao/DHBA_
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PBA,https://purl.brain-bican.org/ontology/pbao/PBA_
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XSMO,http://purl.obolibrary.org/obo/XSMO_
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BCIO,http://humanbehaviourchange.org/ontology/BCIO_
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BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_
@@ -100,6 +105,7 @@ pathbank,http://purl.obolibrary.org/obo/pathbank_
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pathbank,http://purl.obolibrary.org/obo/kegg.genome_
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MESH,http://id.nlm.nih.gov/mesh/
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RXNORM,http://purl.bioontology.org/ontology/RXNORM/
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VCCF,http://purl.obolibrary.org/obo/VCCF_
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OBT,http://purl.obolibrary.org/obo/OBT_
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NANDO,http://nanbyodata.jp/ontology/NANDO_
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ECSO,http://purl.dataone.org/odo/ECSO_

‎src/semsql/builder/registry/ontologies.yaml‎

Lines changed: 21 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -101,6 +101,27 @@ ontologies:
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build_command: "robot relax -i $< merge -o $@"
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prefixmap:
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loinc: https://loinc.org/
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# See https://github.com/obophenotype/uberon/issues/3267
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hba:
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url: https://github.com/brain-bican/human_brain_atlas_ontology/raw/main/hbao-base.owl
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prefixmap:
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HBA: https://purl.brain-bican.org/ontology/hbao/HBA_
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mba:
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url: https://github.com/brain-bican/mouse_brain_atlas_ontology/raw/main/mbao-base.owl
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prefixmap:
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MBA: https://purl.brain-bican.org/ontology/mbao/MBA_
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dmba:
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url: https://github.com/brain-bican/developing_mouse_brain_atlas_ontology/raw/main/dmbao-base.owl
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prefixmap:
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DMBA: https://purl.brain-bican.org/ontology/dmbao/DMBA_
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dhba:
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url: https://github.com/brain-bican/developing_human_brain_atlas_ontology/raw/main/dhbao-base.owl
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prefixmap:
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DHBA: https://purl.brain-bican.org/ontology/dhbao/DHBA_
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pba:
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url: https://github.com/brain-bican/primate_brain_atlas_ontology/raw/main/pbao-base.owl
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prefixmap:
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PBA: https://purl.brain-bican.org/ontology/pbao/PBA_
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bero:
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url: https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl
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aio:
@@ -120,10 +141,6 @@ ontologies:
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url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10who.owl
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prefixmap:
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icd10who: https://icd.who.int/browse10/2019/en#/
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omim:
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url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/omim.owl
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prefixmap:
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icd10who: https://icd.who.int/browse10/2019/en#/
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#icd11f:
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# url: https://github.com/monarch-initiative/icd11/releases/latest/download/icd11foundation.owl
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# prefixmap:

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