Merge pull request #198 from obophenotype/ODK-release-2024-09-26

Odk release 2024 09 26
obophenotype · Sep 26, 2024 · bf53752 · bf53752
2 parents ac92085 + 3c9f2cc
commit bf53752
Show file tree

Hide file tree

Showing 35 changed files with 4,807 additions and 7,781 deletions.
diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.1
+    container: obolibrary/odkfull:v1.5.2
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

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/2024-06-05/patterns/definitions.owl>
-Annotation(owl:versionInfo "2024-06-05")
+<http://purl.obolibrary.org/obo/wbphenotype/releases/2024-09-26/patterns/definitions.owl>
+Annotation(owl:versionInfo "2024-09-26")
 
 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: v1.5.1
+# ODK Version: v1.5.2
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use wbphenotype.Makefile instead
 
@@ -46,7 +46,7 @@ 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 =      v1.5.1
+ODK_VERSION_MAKEFILE =      v1.5.2
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')

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/2024-06-05/imports/bfo_import.owl>
+<http://purl.obolibrary.org/obo/wbphenotype/releases/2024-09-26/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 "2024-06-05")
+Annotation(owl:versionInfo "2024-09-26")
 
 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/2024-06-05/imports/chebi_import.owl>
-Annotation(owl:versionInfo "2024-06-05")
+<http://purl.obolibrary.org/obo/wbphenotype/releases/2024-09-26/imports/chebi_import.owl>
+Annotation(owl:versionInfo "2024-09-26")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10545>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_131604>))
@@ -172,6 +172,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_23019>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_23114>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_23116>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_23117>))
+Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_231587>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_23357>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_23359>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_23367>))
@@ -1889,6 +1890,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <ht
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "Europe PMC") <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_149548> "PMID:5985282")
 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_149548> "(2S)-6',7',10,11-tetramethoxyemetan-2',5-diium")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_149548> "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_149548> "emetine")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_149548> "emetine dication")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/CHEBI_149548> "CHEBI:149548")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CHEBI_149548> <http://purl.obolibrary.org/obo/chebi#3_STAR>)
@@ -5645,8 +5647,9 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#sou
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "KEGG COMPOUND") <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_18367> "CAS:14265-44-2")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "Gmelin") <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_18367> "Gmelin:1997")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_18367> "KEGG:C00009")
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_18367> "PDBeChem:PO4")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_18367> "PDBeChem:PO4")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "Reaxys") <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_18367> "Reaxys:3903772")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_18367> "Wikipedia:Phosphate")
 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_18367> "phosphate")
 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_18367> "tetraoxidophosphate(3-)")
 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_18367> "tetraoxophosphate(3-)")
@@ -6471,6 +6474,25 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CHEBI_23117> "chl
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_23117> <http://purl.obolibrary.org/obo/CHEBI_24471>)
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_23117> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/CHEBI_23116>))
 
+# Class: <http://purl.obolibrary.org/obo/CHEBI_231587> (cephaeline(2+))
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CHEBI_231587> "Major species at pH 7.3.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/charge> <http://purl.obolibrary.org/obo/CHEBI_231587> "+2")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/formula> <http://purl.obolibrary.org/obo/CHEBI_231587> "C28H40N2O4")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/inchi> <http://purl.obolibrary.org/obo/CHEBI_231587> "InChI=1S/C28H38N2O4/c1-5-17-16-30-9-7-19-13-27(33-3)28(34-4)15-22(19)24(30)11-20(17)10-23-21-14-26(32-2)25(31)12-18(21)6-8-29-23/h12-15,17,20,23-24,29,31H,5-11,16H2,1-4H3/p+2/t17-,20-,23+,24-/m0/s1")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/inchikey> <http://purl.obolibrary.org/obo/CHEBI_231587> "DTGZHCFJNDAHEN-OZEXIGSWSA-P")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/mass> <http://purl.obolibrary.org/obo/CHEBI_231587> "468.637")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/monoisotopicmass> <http://purl.obolibrary.org/obo/CHEBI_231587> "468.29771")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/smiles> <http://purl.obolibrary.org/obo/CHEBI_231587> "C=1C(=C(C=C2C1CC[NH+]3C[C@@H]([C@@](C[C@@]23[H])([H])C[C@@]4([H])[NH2+]CCC=5C4=CC(=C(C5)O)OC)CC)OC)OC")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "SUBMITTER") <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_231587> "MetaCyc:CPD-14816")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_231587> "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_231587> "cephaeline")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/CHEBI_231587> "CHEBI:231587")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CHEBI_231587> <http://purl.obolibrary.org/obo/chebi#2_STAR>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CHEBI_231587> "cephaeline(2+)")
+SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_231587> <http://purl.obolibrary.org/obo/CHEBI_35274>)
+SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_231587> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/chebi#is_conjugate_acid_of> <http://purl.obolibrary.org/obo/CHEBI_3533>))
+
 # Class: <http://purl.obolibrary.org/obo/CHEBI_23357> (cofactor)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CHEBI_23357> "An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).")
@@ -7895,7 +7917,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_25608> "KEGG:C01329")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_25608> "chebi_ontology")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "KEGG_COMPOUND") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_25608> "NMP")
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "KEGG_COMPOUND") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_25608> "Nucleoside monophosphate")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_25608> "nucleoside phosphates")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/CHEBI_25608> "CHEBI:25608")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CHEBI_25608> <http://purl.obolibrary.org/obo/chebi#3_STAR>)
@@ -8797,6 +8818,7 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CHEBI_26710> "sod
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_26710> <http://purl.obolibrary.org/obo/CHEBI_36093>)
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_26710> <http://purl.obolibrary.org/obo/CHEBI_38702>)
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_26710> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000087> <http://purl.obolibrary.org/obo/CHEBI_149552>))
+SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_26710> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000087> <http://purl.obolibrary.org/obo/CHEBI_228364>))
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_26710> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000087> <http://purl.obolibrary.org/obo/CHEBI_79314>))
 
 # Class: <http://purl.obolibrary.org/obo/CHEBI_26712> (sodium molecular entity)
@@ -14426,6 +14448,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CHEBI_3533> "cephaeline")
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_3533> <http://purl.obolibrary.org/obo/CHEBI_61692>)
 SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_3533> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/chebi#has_parent_hydride> <http://purl.obolibrary.org/obo/CHEBI_36380>))
+SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_3533> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/chebi#is_conjugate_base_of> <http://purl.obolibrary.org/obo/CHEBI_231587>))
 
 # Class: <http://purl.obolibrary.org/obo/CHEBI_35337> (central nervous system stimulant)
 
@@ -18407,7 +18430,6 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasAlternative
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "Beilstein") <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_47013> "Beilstein:1904878")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "KEGG COMPOUND") <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_47013> "CAS:50-69-1")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "ChemIDplus") <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_47013> "CAS:613-83-2")
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_47013> "GlyGen:G31080DL")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_47013> "GlyTouCan:G31080DL")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "Gmelin") <http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_47013> "Gmelin:364108")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_47013> "KEGG:C00121")
@@ -21440,7 +21462,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/smiles> <http://purl.o
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_59558> "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_59558> "MCFA anion")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_59558> "MCFA anions")
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "UniProt") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_59558> "a medium chain fatty acid")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "UniProt") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_59558> "a medium-chain fatty acid")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_59558> "medium-chain FA anion")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_59558> "medium-chain FA anions")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_59558> "medium-chain fatty acid anions")