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Odk release january 16 2024 #194

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Jan 16, 2024
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Odk release january 16 2024 #194

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271546f
Update Makefile
chris-grove Jan 9, 2024
6a2c0a4
Update wbphenotype-odk.yaml
chris-grove Jan 16, 2024
cd564bb
Update Makefile
chris-grove Jan 16, 2024
c8e1257
ODK Release January 16 2024
chris-grove Jan 16, 2024
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4 changes: 2 additions & 2 deletions patterns/definitions.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -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>))
Expand Down
14 changes: 6 additions & 8 deletions src/ontology/Makefile
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@@ -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

Expand Down Expand Up @@ -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')
Expand Down Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions src/ontology/imports/bfo_import.owl
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Expand Up @@ -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>))
Expand Down
26 changes: 19 additions & 7 deletions src/ontology/imports/chebi_import.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -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>))
Expand Down Expand Up @@ -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>))
Expand Down Expand Up @@ -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>)
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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>))

Expand Down Expand Up @@ -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)

Expand Down Expand Up @@ -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")
Expand Down
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