Merge pull request #194 from obophenotype/ODK-Release-January-16-2024

Odk release january 16 2024
obophenotype · Jan 16, 2024 · 53847de · 53847de
2 parents d7502a7 + c8e1257
commit 53847de
Show file tree

Hide file tree

Showing 30 changed files with 353,891 additions and 2,129,304 deletions.
diff --git a/patterns/definitions.owl b/patterns/definitions.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/wbphenotype/patterns/definitions.owl>
-<http://purl.obolibrary.org/obo/wbphenotype/releases/2023-09-26/patterns/definitions.owl>
-Annotation(owl:versionInfo "2023-09-26")
+<http://purl.obolibrary.org/obo/wbphenotype/releases/2024-01-16/patterns/definitions.owl>
+Annotation(owl:versionInfo "2024-01-16")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CARO_0010004>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_15355>))

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for wbphenotype
 # Generated using ontology-development-kit
-# ODK Version: v1.4.2
+# ODK Version: v1.4.3
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use wbphenotype.Makefile instead
 
@@ -43,7 +43,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS = 
 SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by 
 SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE = v1.4.2
+ODK_VERSION_MAKEFILE = v1.4.3
 
 TODAY ?= $(shell date +%Y-%m-%d)
 OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
@@ -442,18 +442,16 @@ mirror-chebi: | $(TMPDIR)
 .PHONY: mirror-pato
 .PRECIOUS: $(MIRRORDIR)/pato.owl
 mirror-pato: | $(TMPDIR)
- if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pato.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 &&\
- $(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl &&\
- mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+ if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pato/pato-base.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 &&\
+ $(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: cl
 .PHONY: mirror-cl
 .PRECIOUS: $(MIRRORDIR)/cl.owl
 mirror-cl: | $(TMPDIR)
- if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cl.owl --create-dirs -o $(MIRRORDIR)/cl.owl --retry 4 --max-time 200 &&\
- $(ROBOT) convert -i $(MIRRORDIR)/cl.owl -o $@.tmp.owl &&\
- mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+ if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cl/cl-base.owl --create-dirs -o $(MIRRORDIR)/cl.owl --retry 4 --max-time 200 &&\
+ $(ROBOT) convert -i $(MIRRORDIR)/cl.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: iao

diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/wbphenotype/imports/bfo_import.owl>
-<http://purl.obolibrary.org/obo/wbphenotype/releases/2023-09-26/imports/bfo_import.owl>
+<http://purl.obolibrary.org/obo/wbphenotype/releases/2024-01-16/imports/bfo_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl>)
-Annotation(owl:versionInfo "2023-09-26")
+Annotation(owl:versionInfo "2024-01-16")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))

diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/wbphenotype/imports/chebi_import.owl>
-<http://purl.obolibrary.org/obo/wbphenotype/releases/2023-09-26/imports/chebi_import.owl>
-Annotation(owl:versionInfo "2023-09-26")
+<http://purl.obolibrary.org/obo/wbphenotype/releases/2024-01-16/imports/chebi_import.owl>
+Annotation(owl:versionInfo "2024-01-16")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10545>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_131604>))
@@ -127,6 +127,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_18723>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_19129>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_193111>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_194338>))
+Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_197506>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_19834>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_20702>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_20706>))
@@ -5355,14 +5356,13 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/charge> <http://purl.o
 AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/formula> <http://purl.obolibrary.org/obo/CHEBI_18140> "HX")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/mass> <http://purl.obolibrary.org/obo/CHEBI_18140> "1.008")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/monoisotopicmass> <http://purl.obolibrary.org/obo/CHEBI_18140> "1.00783")
-AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/smiles> <http://purl.obolibrary.org/obo/CHEBI_18140> "[F,Cl,Br,I]")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/smiles> <http://purl.obolibrary.org/obo/CHEBI_18140> "*[H]")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> <http://purl.obolibrary.org/obo/CHEBI_18140> "CHEBI:13368")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> <http://purl.obolibrary.org/obo/CHEBI_18140> "CHEBI:37140")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> <http://purl.obolibrary.org/obo/CHEBI_18140> "CHEBI:5599")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "IUPAC") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CHEBI_18140> "hydrogen halide")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "IUPAC") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/chebi#IUPAC_NAME>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CHEBI_18140> "hydrogen halides")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_18140> "chebi_ontology")
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "UniProt") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_18140> "HX")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_18140> "hydrogen halides")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/CHEBI_18140> "CHEBI:18140")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CHEBI_18140> <http://purl.obolibrary.org/obo/chebi#3_STAR>)
@@ -5825,6 +5825,16 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CHEBI_194338> "T-type calcium channel blocker")
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_194338> <http://purl.obolibrary.org/obo/CHEBI_38215>)
 
+# Class: <http://purl.obolibrary.org/obo/CHEBI_197506> (medium-chain fatty alcohol)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CHEBI_197506> "Any fatty alcohol with a chain length between C6 and C12.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_197506> "chebi_ontology")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_197506> "medium-chain fatty alcohols")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/CHEBI_197506> "CHEBI:197506")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CHEBI_197506> <http://purl.obolibrary.org/obo/chebi#3_STAR>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CHEBI_197506> "medium-chain fatty alcohol")
+SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_197506> <http://purl.obolibrary.org/obo/CHEBI_24026>)
+
 # Class: <http://purl.obolibrary.org/obo/CHEBI_19834> (3',5'-cyclic purine nucleotide)
 
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_19834> "chebi_ontology")
@@ -6739,6 +6749,7 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_24026> "chebi_ontology")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_24026> "Fettalkohol")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_24026> "Fettalkohole")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "UniProt") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_24026> "a fatty alcohol")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_24026> "alcool gras")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_24026> "fatty alcohols")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "LIPID_MAPS") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_24026> "fatty alcohols")
@@ -16644,7 +16655,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CHEBI_37868> <http://purl.obolibrary.org/obo/chebi#3_STAR>)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CHEBI_37868> "octanol")
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_37868> <http://purl.obolibrary.org/obo/CHEBI_134179>)
-SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_37868> <http://purl.obolibrary.org/obo/CHEBI_24026>)
+SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_37868> <http://purl.obolibrary.org/obo/CHEBI_197506>)
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_37868> <http://purl.obolibrary.org/obo/CHEBI_50584>)
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_37868> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/chebi#has_parent_hydride> <http://purl.obolibrary.org/obo/CHEBI_17590>))
 
@@ -24605,8 +24616,7 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/CHEBI_83813> "CHEBI:83813")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CHEBI_83813> <http://purl.obolibrary.org/obo/chebi#3_STAR>)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CHEBI_83813> "proteinogenic amino acid")
-SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_83813> <http://purl.obolibrary.org/obo/CHEBI_33575>)
-SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_83813> <http://purl.obolibrary.org/obo/CHEBI_35352>)
+SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_83813> <http://purl.obolibrary.org/obo/CHEBI_33709>)
 
 # Class: <http://purl.obolibrary.org/obo/CHEBI_83820> (non-proteinogenic amino acid)
 
@@ -24962,6 +24972,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_88230> <http://purl.obolibrary.
 # Class: <http://purl.obolibrary.org/obo/CHEBI_90710> (receptor modulator)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CHEBI_90710> "A drug that acts as an antagonist, agonist, reverse agonist, or in some other fashion when interacting with cellular receptors.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> <http://purl.obolibrary.org/obo/CHEBI_90710> "CHEBI:189678")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_90710> "Wikipedia:Receptor_modulator")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_90710> "chebi_ontology")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_90710> "receptor modulators")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/CHEBI_90710> "CHEBI:90710")