Merge branch 'main' into new-entries-and-uri-resolution

Author: cmungall

ontologies.Makefile

@@ -284,6 +284,17 @@ db/bcio.owl: download/bcio.owl
 	cp $< $@
 
 
+download/sio.owl: STAMP
+	curl -L -s http://semanticscience.org/ontology/sio.owl > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/sio.owl
+
+db/sio.owl: download/sio.owl
+	cp $< $@
+
+
 download/icd10who.owl: STAMP
 	curl -L -s https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10who.owl > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -1361,4 +1372,4 @@ 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 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 ror 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 pfam hgnc.genegroup hgnc sgd gtdb eccode uniprot uniprot.ptm credit 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 sio 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 ror 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 pfam hgnc.genegroup hgnc sgd gtdb eccode uniprot uniprot.ptm credit 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

@@ -93,6 +93,7 @@ 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_
+SIO,http://semanticscience.org/resource/SIO_
 icd10who,https://icd.who.int/browse10/2019/en#/
 GARD,http://purl.obolibrary.org/obo/GARD_
 OMIM,https://omim.org/entry/

src/semsql/builder/prefixes/prefixes_local.csv

@@ -30,6 +30,7 @@ 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_
+SIO,http://semanticscience.org/resource/SIO_
 icd10who,https://icd.who.int/browse10/2019/en#/
 GARD,http://purl.obolibrary.org/obo/GARD_
 OMIM,https://omim.org/entry/

src/semsql/builder/registry/ontologies.yaml

@@ -137,6 +137,11 @@ ontologies:
     prefixmap:
       BCIO: http://humanbehaviourchange.org/ontology/BCIO_
       BCIOR: http://humanbehaviourchange.org/ontology/BCIOR_
+  sio:
+    url: http://semanticscience.org/ontology/sio.owl
+    # TBD: see https://github.com/biopragmatics/bioregistry/issues/1394
+    prefixmap:
+      SIO: http://semanticscience.org/resource/SIO_
   icd10who:
     url: https://github.com/monarch-initiative/mondo-ingest/releases/latest/download/icd10who.owl
     prefixmap: