Merge pull request #344 from obophenotype/protein_terms_4_GWAS#2245

Added protein terms_4
obophenotype · Sep 12, 2024 · 343841b · 343841b
2 parents 8faeba2 + 13666c6
commit 343841b
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Showing 3 changed files with 44 additions and 5 deletions.
diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/oba/imports/merged_import.owl>
-<http://purl.obolibrary.org/obo/oba/releases/2024-09-06/imports/merged_import.owl>
-Annotation(owl:versionInfo "2024-09-06")
+<http://purl.obolibrary.org/obo/oba/releases/2024-09-11/imports/merged_import.owl>
+Annotation(owl:versionInfo "2024-09-11")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
@@ -29482,6 +29482,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012890>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012891>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012892>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012895>))
+Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012896>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012898>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012899>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012901>))
@@ -35336,6 +35337,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PR_O35955>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_O35969>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_O35988>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_O43150>))
+Declaration(Class(<http://purl.obolibrary.org/obo/PR_O43157>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_O43173>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_O43175>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_O43181>))
@@ -41607,6 +41609,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8CJ91>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8CJF9>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8CJG0>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8CJG1>))
+Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8CJH3>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8HW98>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8IU57>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8IU80>))
@@ -55377,7 +55380,7 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0004023> "caus
 SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0004023> <http://purl.obolibrary.org/obo/RO_0002410>)
 SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0004023> <http://purl.obolibrary.org/obo/RO_0040035>)
 
-# Object Property: <http://purl.obolibrary.org/obo/RO_0004024> (disease causes disruption of)
+# Object Property: <http://purl.obolibrary.org/obo/RO_0004024> (disease disrupts)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0004024> "A relationship between a disease and a process where the disease process disrupts the execution of the process.")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0004024> "disease causes disruption of")
@@ -269394,6 +269397,12 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_000012895> "
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PR_000012895> "plexin-A4")
 SubClassOf(<http://purl.obolibrary.org/obo/PR_000012895> <http://purl.obolibrary.org/obo/PR_000000001>)
 
+# Class: <http://purl.obolibrary.org/obo/PR_000012896> (plexin-B1)
+
+AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_000012896> "Category=gene.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PR_000012896> "plexin-B1")
+SubClassOf(<http://purl.obolibrary.org/obo/PR_000012896> <http://purl.obolibrary.org/obo/PR_000000001>)
+
 # Class: <http://purl.obolibrary.org/obo/PR_000012898> (plexin-B3)
 
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_000012898> "Category=gene.")
@@ -314010,6 +314019,15 @@ SubClassOf(<http://purl.obolibrary.org/obo/PR_O43150> <http://purl.obolibrary.or
 SubClassOf(<http://purl.obolibrary.org/obo/PR_O43150> <http://purl.obolibrary.org/obo/PR_000029067>)
 SubClassOf(<http://purl.obolibrary.org/obo/PR_O43150> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_9606>))
 
+# Class: <http://purl.obolibrary.org/obo/PR_O43157> (plexin-B1 (human))
+
+AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_O43157> "Category=organism-gene.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PR_O43157> "plexin-B1 (human)")
+EquivalentClasses(<http://purl.obolibrary.org/obo/PR_O43157> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_000012896> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_9606>)))
+SubClassOf(<http://purl.obolibrary.org/obo/PR_O43157> <http://purl.obolibrary.org/obo/PR_000012896>)
+SubClassOf(<http://purl.obolibrary.org/obo/PR_O43157> <http://purl.obolibrary.org/obo/PR_000029067>)
+SubClassOf(<http://purl.obolibrary.org/obo/PR_O43157> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_9606>))
+
 # Class: <http://purl.obolibrary.org/obo/PR_O43173> (sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase (human))
 
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_O43173> "Category=organism-gene.")
@@ -370406,6 +370424,15 @@ SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJG1> <http://purl.obolibrary.or
 SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJG1> <http://purl.obolibrary.org/obo/PR_000029032>)
 SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJG1> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_10090>))
 
+# Class: <http://purl.obolibrary.org/obo/PR_Q8CJH3> (plexin-B1 (mouse))
+
+AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_Q8CJH3> "Category=organism-gene.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PR_Q8CJH3> "plexin-B1 (mouse)")
+EquivalentClasses(<http://purl.obolibrary.org/obo/PR_Q8CJH3> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_000012896> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_10090>)))
+SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJH3> <http://purl.obolibrary.org/obo/PR_000012896>)
+SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJH3> <http://purl.obolibrary.org/obo/PR_000029032>)
+SubClassOf(<http://purl.obolibrary.org/obo/PR_Q8CJH3> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_10090>))
+
 # Class: <http://purl.obolibrary.org/obo/PR_Q8HW98> (IgLON family member 5 (mouse))
 
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PR_Q8HW98> "Category=organism-gene.")

diff --git a/src/patterns/data/default/entity_attribute_location.tsv b/src/patterns/data/default/entity_attribute_location.tsv
@@ -7055,3 +7055,4 @@ OBA:2051958	level of lymphocyte antigen 75 isoform 4 and LY75-CD302 fusion isofo
 OBA:2051959	level of neuroendocrine secretory protein 55 isoform Nesp55 (human) in blood	PR:O95467-1	neuroendocrine secretory protein 55 isoform Nesp55 (human)	PATO:0000070	amount	UBERON:0000178	blood				PMID:37794183	https://orcid.org/0000-0001-6757-4744	
 OBA:2051960	level of immunoglobulin lambda constant 2 (human) in blood	PR:P0DOY2	immunoglobulin lambda constant 2 (human)	PATO:0000070	amount	UBERON:0000178	blood				PMID:37794183	https://orcid.org/0000-0001-6757-4744	
 OBA:2051961	level of progesterone-induced-blocking factor 1 (human) in blood	PR:Q8WXW3	progesterone-induced-blocking factor 1 (human)	PATO:0000070	amount	UBERON:0000178	blood				PMID:37794183	https://orcid.org/0000-0001-6757-4744	
+OBA:2051962	level of plexin-B1 in blood	PR:000012896	plexin-B1	PATO:0000070	amount	UBERON:0000178	blood				PMID:34857772	https://orcid.org/0000-0001-6757-4744	
diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/oba/patterns/definitions.owl>
-<http://purl.obolibrary.org/obo/oba/releases/2024-09-09/patterns/definitions.owl>
-Annotation(owl:versionInfo "2024-09-09")
+<http://purl.obolibrary.org/obo/oba/releases/2024-09-12/patterns/definitions.owl>
+Annotation(owl:versionInfo "2024-09-12")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10033>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10112>))
@@ -14192,6 +14192,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2051958>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2051959>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2051960>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2051961>))
+Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2051962>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2060000>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2060001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2060002>))
@@ -20227,6 +20228,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012890>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012891>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012892>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012895>))
+Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012896>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012898>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012899>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000012901>))
@@ -121479,6 +121481,15 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2051961> "level of progesterone-induced-blocking factor 1 (human) in blood")
 EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2051961> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000070> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_Q8WXW3> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000178>)))))
 
+# Class: <http://purl.obolibrary.org/obo/OBA_2051962> (level of plexin-B1 in blood)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2051962> "The amount of a plexin-B1 when measured in blood.")
+AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/OBA_2051962> "https://orcid.org/0000-0001-6757-4744")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/OBA_2051962> "PMID:34857772")
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute_location") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/OBA_2051962> "blood plexin-B1 amount")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/OBA_2051962> "level of plexin-B1 in blood")
+EquivalentClasses(<http://purl.obolibrary.org/obo/OBA_2051962> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000070> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_000012896> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0000178>)))))
+
 # Class: <http://purl.obolibrary.org/obo/OBA_2060000> (aggressive behavior towards inanimate objects rate)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "AUTO:patterns/patterns/entity_attribute") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/OBA_2060000> "The rate of a aggressive behavior towards inanimate objects.")