Adding overrides for SWO prefixes.

See OBOFoundry/OBOFoundry.github.io#2307 (comment)

ontologies.Makefile

@@ -9,6 +9,17 @@ db/upheno.owl: download/upheno.owl
 	robot merge -i $<  -o $@
 
 
+download/swo.owl: STAMP
+	curl -L -s http://purl.obolibrary.org/obo/swo.owl > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/swo.owl
+
+db/swo.owl: download/swo.owl
+	robot merge -i $<  -o $@
+
+
 download/chiro.owl: STAMP
 	curl -L -s http://purl.obolibrary.org/obo/chiro.owl > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -1086,4 +1097,4 @@ 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 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 cso obiws reactome-hs reactome-mm efo hcao hpinternational edam chr sweetAll lov schema-dot-org prov dtype vaem qudtunit quantitykind 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 ecso enigma_context ontie ecosim nmdc_schema mixs fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time
+EXTRA_ONTOLOGIES = upheno swo chiro ncit fma maxo foodon chebiplus msio modl phenio phenio_test comploinc bero aio reacto bcio icd10who ordo gard mondo-ingest oeo 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 cso obiws reactome-hs reactome-mm efo hcao hpinternational edam chr sweetAll lov schema-dot-org prov dtype vaem qudtunit quantitykind 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 ecso enigma_context ontie ecosim nmdc_schema mixs fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time

src/semsql/builder/prefixes/prefixes.csv

@@ -62,6 +62,17 @@ semapv,https://w3id.org/semapv/vocab/
 sssom,https://w3id.org/sssom/
 CLINGEN,https://www.clinicalgenome.org/affiliation/
 prefix,base
+SWO,http://www.ebi.ac.uk/swo/SWO_
+SWO.organization,http://www.ebi.ac.uk/swo/organization/SWO_
+SWO.maturity,http://www.ebi.ac.uk/swo/maturity/SWO_
+SWO.objective,http://www.ebi.ac.uk/swo/objective/SWO_
+SWO.license,http://www.ebi.ac.uk/swo/license/SWO_
+SWO.version,http://www.ebi.ac.uk/swo/version/SWO_
+SWO.data,http://www.ebi.ac.uk/swo/data/SWO_
+SWO.interface,http://www.ebi.ac.uk/swo/interface/SWO_
+SWO.algorithm,http://www.ebi.ac.uk/swo/algorithm/SWO_
+OntoDM,http://www.ontodm.com/OntoDM-core/OntoDM_
+OntoDM.kdd,http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD
 FMA,http://purl.org/sig/ont/fma/fma
 MSIO,http://purl.obolibrary.org/obo/MSIO_
 nmrCV,http://nmrML.org/nmrCV#NMR:
@@ -100,11 +111,12 @@ cyc,http://sw.cyc.com/concept
 OBIws,http://purl.obolibrary.org/obo/OBIws_
 chr,http://purl.obolibrary.org/obo/CHR_
 prov,http://www.w3.org/ns/prov#
-voag,http://voag.linkedmodel.org/voag#
 dtype,http://www.linkedmodel.org/schema/dtype#
+voag,http://voag.linkedmodel.org/voag#
 vaem,http://www.linkedmodel.org/schema/vaem#
 qudtschema,http://qudt.org/schema/qudt/
 qudtunit,http://qudt.org/vocab/unit/
+si-quantity,https://si-digital-framework.org/SI/quantities/
 quantitykind,http://qudt.org/vocab/quantitykind/
 cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
 fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb#

src/semsql/builder/prefixes/prefixes_local.csv

@@ -1,4 +1,15 @@
 prefix,base
+SWO,http://www.ebi.ac.uk/swo/SWO_
+SWO.organization,http://www.ebi.ac.uk/swo/organization/SWO_
+SWO.maturity,http://www.ebi.ac.uk/swo/maturity/SWO_
+SWO.objective,http://www.ebi.ac.uk/swo/objective/SWO_
+SWO.license,http://www.ebi.ac.uk/swo/license/SWO_
+SWO.version,http://www.ebi.ac.uk/swo/version/SWO_
+SWO.data,http://www.ebi.ac.uk/swo/data/SWO_
+SWO.interface,http://www.ebi.ac.uk/swo/interface/SWO_
+SWO.algorithm,http://www.ebi.ac.uk/swo/algorithm/SWO_
+OntoDM,http://www.ontodm.com/OntoDM-core/OntoDM_
+OntoDM.kdd,http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD
 FMA,http://purl.org/sig/ont/fma/fma
 MSIO,http://purl.obolibrary.org/obo/MSIO_
 nmrCV,http://nmrML.org/nmrCV#NMR:
@@ -42,6 +53,7 @@ voag,http://voag.linkedmodel.org/voag#
 vaem,http://www.linkedmodel.org/schema/vaem#
 qudtschema,http://qudt.org/schema/qudt/
 qudtunit,http://qudt.org/vocab/unit/
+si-quantity,https://si-digital-framework.org/SI/quantities/
 quantitykind,http://qudt.org/vocab/quantitykind/
 cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
 fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb#

src/semsql/builder/registry/ontologies.yaml

@@ -5,6 +5,22 @@ ontologies:
   upheno:
     url: http://purl.obolibrary.org/obo/upheno.owl
     build_command: "robot merge -i $<  -o $@"
+  swo:
+    url: http://purl.obolibrary.org/obo/swo.owl
+    build_command: "robot merge -i $<  -o $@"
+    # runoak -i sqlite:obo:swo
+    prefixmap:
+      SWO: http://www.ebi.ac.uk/swo/SWO_
+      SWO.organization:  http://www.ebi.ac.uk/swo/organization/SWO_
+      SWO.maturity:  http://www.ebi.ac.uk/swo/maturity/SWO_
+      SWO.objective:  http://www.ebi.ac.uk/swo/objective/SWO_
+      SWO.license:  http://www.ebi.ac.uk/swo/license/SWO_
+      SWO.version:  http://www.ebi.ac.uk/swo/version/SWO_
+      SWO.data:  http://www.ebi.ac.uk/swo/data/SWO_
+      SWO.interface:  http://www.ebi.ac.uk/swo/interface/SWO_
+      SWO.algorithm:  http://www.ebi.ac.uk/swo/algorithm/SWO_
+      OntoDM: http://www.ontodm.com/OntoDM-core/OntoDM_
+      OntoDM.kdd: "http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD"
   chiro:
     url: http://purl.obolibrary.org/obo/chiro.owl
     build_command: "robot relax -i $< merge -o $@"