From 519da04779688bde12814a2b3dd39be295601b42 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 29 Apr 2024 13:13:12 -0700 Subject: [PATCH] Adding 5 Allen brain atlas ontologies. See https://github.com/obophenotype/uberon/issues/3267 --- ontologies.Makefile | 57 ++++++++++++++++++- src/semsql/builder/prefixes/prefixes.csv | 5 ++ .../builder/prefixes/prefixes_local.csv | 5 ++ src/semsql/builder/registry/ontologies.yaml | 21 +++++++ 4 files changed, 87 insertions(+), 1 deletion(-) diff --git a/ontologies.Makefile b/ontologies.Makefile index eb569ad..032a0f1 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -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 @@ -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 diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv index 093b53c..6485f49 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -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#/ diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index cf5ec45..4d7d251 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -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#/ diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index 272ddc6..4784454 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -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: