Adding 5 Allen brain atlas ontologies.

See obophenotype/uberon#3267

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

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#/

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#/

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: