From 85bd2770bcb283404151d8f9ec52d3c274fe5a2d Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Thu, 30 Jan 2025 11:35:13 -0800 Subject: [PATCH] Adding 5 Allen brain atlas ontologies. Redo of #85 --- ontologies.Makefile | 57 ++++++++++++++++++- src/semsql/builder/prefixes/prefixes.csv | 6 ++ .../builder/prefixes/prefixes_local.csv | 6 ++ src/semsql/builder/registry/ontologies.yaml | 25 ++++++-- 4 files changed, 89 insertions(+), 5 deletions(-) diff --git a/ontologies.Makefile b/ontologies.Makefile index f96c11d..87ec914 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -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 @@ -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 diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv index 9fa4fa5..16ac6f3 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -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_ @@ -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_ diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index b0fb225..7c0060d 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -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_ @@ -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_ diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index fe10919..a46086a 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -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: @@ -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: