Merge pull request #90 from INCATools/additional-sources2

additional sources2

ontologies.Makefile

@@ -461,7 +461,7 @@ db/enanomapper.owl: download/enanomapper.owl
 
 
 download/mlo.owl: STAMP
-	curl -L -s https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/external/ml-ontology-202010021305.owl > $@.tmp
+	curl -L -s https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/v2023-09-11/external/ml-ontology-202010021305.owl > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
 	mv $@.tmp $@
 
@@ -482,6 +482,28 @@ db/ito.owl: download/ito.owl
 	cp $< $@
 
 
+download/cso.owl: STAMP
+	curl -L -s https://cso.kmi.open.ac.uk/download/version-3.3/CSO.3.3.owl.zip > $@.zip.tmp && unzip -p $@.zip.tmp CSO.3.3.owl > $@.tmp && rm $@.zip.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/cso.owl
+
+db/cso.owl: download/cso.owl
+	cp $< $@
+
+
+download/obiws.owl: STAMP
+	curl -L -s https://data.bioontology.org/ontologies/OBIWS/submissions/2/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/obiws.owl
+
+db/obiws.owl: download/obiws.owl
+	cp $< $@
+
+
 download/reactome-hs.owl: STAMP
 	curl -L -s https://reactome.org/download/current/biopax.zip > $@.zip.tmp && unzip -p $@.zip.tmp Homo_sapiens.owl > $@.tmp && rm $@.zip.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -548,6 +570,17 @@ db/edam.owl: download/edam.owl
 	cp $< $@
 
 
+download/chr.owl: STAMP
+	curl -L -s https://raw.githubusercontent.com/monarch-initiative/monochrom/master/chr.owl > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/chr.owl
+
+db/chr.owl: download/chr.owl
+	cp $< $@
+
+
 download/sweetAll.owl: STAMP
 	curl -L -s http://sweetontology.net/sweetAll > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -592,6 +625,50 @@ db/prov.owl: download/prov.owl
 	cp $< $@
 
 
+download/dtype.owl: STAMP
+	curl -L -s http://www.linkedmodel.org/schema/dtype > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/dtype.owl
+
+db/dtype.owl: download/dtype.owl
+	cp $< $@
+
+
+download/vaem.owl: STAMP
+	curl -L -s http://www.linkedmodel.org/schema/vaem > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/vaem.owl
+
+db/vaem.owl: download/vaem.owl
+	cp $< $@
+
+
+download/qudtunit.owl: STAMP
+	curl -L -s http://qudt.org/vocab/unit > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/qudtunit.owl
+
+db/qudtunit.owl: download/qudtunit.owl
+	robot merge -i $<  -o $@
+
+
+download/quantitykind.owl: STAMP
+	curl -L -s http://qudt.org/vocab/quantitykind > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/quantitykind.owl
+
+db/quantitykind.owl: download/quantitykind.owl
+	robot merge -i $<  -o $@
+
+
 download/cellosaurus.owl: STAMP
 	curl -L -s https://raw.githubusercontent.com/calipho-sib/cellosaurus/master/cellosaurus.obo > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -1009,4 +1086,4 @@ 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 reactome-hs reactome-mm 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 ecso enigma_context 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 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/cli.py

@@ -72,7 +72,7 @@ def make(path, docker, **kwargs):
         steps = builder.get_postprocessing_steps(ontology, path)
         for step in steps:
             print(f"RUNNING: {step}")
-            subprocess.run(step, shell=True)
+            subprocess.run(step, shell=True)  # noqa S602
 
 
 @main.command()

src/semsql/builder/prefixes/prefixes.csv

@@ -92,7 +92,20 @@ orcid,https://orcid.org/
 evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
 old.fix,http://purl.org/obo/owl/FIX#
 mlo,http://www.a2rd.net.br/mlo#
+ito,https://identifiers.org/ito:
+cso,https://cso.kmi.open.ac.uk/topics/
+freebase,http://rdf.freebase.com/ns/
+yago,http://yago-knowledge.org/resource/
+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#
+vaem,http://www.linkedmodel.org/schema/vaem#
+qudtschema,http://qudt.org/schema/qudt/
+qudtunit,http://qudt.org/vocab/unit/
+quantitykind,http://qudt.org/vocab/quantitykind/
 cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
 fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb#
 dbpediaont,http://dbpedia.org/ontology/

src/semsql/builder/prefixes/prefixes_local.csv

@@ -29,7 +29,20 @@ orcid,https://orcid.org/
 evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
 old.fix,http://purl.org/obo/owl/FIX#
 mlo,http://www.a2rd.net.br/mlo#
+ito,https://identifiers.org/ito:
+cso,https://cso.kmi.open.ac.uk/topics/
+freebase,http://rdf.freebase.com/ns/
+yago,http://yago-knowledge.org/resource/
+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#
+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/
+quantitykind,http://qudt.org/vocab/quantitykind/
 cellosaurus,http://purl.obolibrary.org/obo/Cellosaurus#CVCL_
 fhkb,http://owl.cs.manchester.ac.uk/tutorials/fhkb#
 dbpediaont,http://dbpedia.org/ontology/

src/semsql/builder/registry/ontologies.yaml

@@ -178,13 +178,27 @@ ontologies:
       evs.ncit: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
       old.fix: http://purl.org/obo/owl/FIX#
   mlo:
-    url: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/external/ml-ontology-202010021305.owl
+    url: https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/v2023-09-11/external/ml-ontology-202010021305.owl
     has_imports: true
     prefixmap:
       mlo: http://www.a2rd.net.br/mlo#
   ito:
     url: https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip
-    zip_extract_file: ITO.owl      
+    zip_extract_file: ITO.owl
+    prefixmap:
+      ito: "https://identifiers.org/ito:"
+  cso:
+    url: https://cso.kmi.open.ac.uk/download/version-3.3/CSO.3.3.owl.zip
+    zip_extract_file: CSO.3.3.owl
+    prefixmap:
+      cso: https://cso.kmi.open.ac.uk/topics/
+      freebase: http://rdf.freebase.com/ns/
+      yago: http://yago-knowledge.org/resource/
+      cyc: http://sw.cyc.com/concept
+  obiws:
+    url: https://data.bioontology.org/ontologies/OBIWS/submissions/2/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
+    prefixmap:
+      OBIws: http://purl.obolibrary.org/obo/OBIws_
   reactome-hs:
     url: https://reactome.org/download/current/biopax.zip
     zip_extract_file: Homo_sapiens.owl
@@ -204,6 +218,10 @@ ontologies:
     url:  http://purl.obolibrary.org/obo/hp/hp-international.owl
   edam:
     url: http://edamontology.org/EDAM.owl
+  chr:
+    url: https://raw.githubusercontent.com/monarch-initiative/monochrom/master/chr.owl
+    prefixmap:
+      chr: http://purl.obolibrary.org/obo/CHR_
   sweetAll:
     url: http://sweetontology.net/sweetAll
     has_imports: true
@@ -220,10 +238,32 @@ ontologies:
     url: http://www.w3.org/ns/prov.owl
     prefixmap:
       prov: "http://www.w3.org/ns/prov#"
-  #qudtunit:
-  #  url: http://qudt.org/2.1/vocab/unit
+  #voag:
+  #  url: http://voag.linkedmodel.org/voag
+  #  build_command: "robot merge -i $<  -o $@"
   #  prefixmap:
-  #    qudtunit: http://qudt.org/2.1/vocab/unit/
+  #    voag: http://voag.linkedmodel.org/voag#
+  dtype:
+    url: http://www.linkedmodel.org/schema/dtype
+    prefixmap:
+      dtype: http://www.linkedmodel.org/schema/dtype#
+      voag: http://voag.linkedmodel.org/voag#      
+  vaem:
+    url: http://www.linkedmodel.org/schema/vaem
+    prefixmap:
+      vaem: http://www.linkedmodel.org/schema/vaem#
+  qudtunit:
+    url: http://qudt.org/vocab/unit
+    build_command: "robot merge -i $<  -o $@"
+    prefixmap:
+      qudtschema: http://qudt.org/schema/qudt/
+      qudtunit: http://qudt.org/vocab/unit/
+      si-quantity: https://si-digital-framework.org/SI/quantities/
+  quantitykind:
+    url: http://qudt.org/vocab/quantitykind
+    build_command: "robot merge -i $<  -o $@"
+    prefixmap:
+      quantitykind: http://qudt.org/vocab/quantitykind/
   cellosaurus:
     url: https://raw.githubusercontent.com/calipho-sib/cellosaurus/master/cellosaurus.obo
     format: obo