From 4021e2004b286fbc0b9ef203f750a5582e315e06 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Fri, 17 Nov 2023 10:37:36 +0000 Subject: [PATCH] Fix duplicate class Resolve #300 --- src/ontology/imports/merged_import.owl | 41 ++----------------- .../data/default/entity_attribute.tsv | 2 +- src/patterns/definitions.owl | 25 +++++------ 3 files changed, 18 insertions(+), 50 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 1bd3aba2..e7fde3bf 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-11-16") + +Annotation(owl:versionInfo "2023-11-17") Declaration(Class()) Declaration(Class()) @@ -24772,9 +24772,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -24857,7 +24854,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -50389,7 +50385,7 @@ SubObjectPropertyOf( "disease has primary infectious agent") SubObjectPropertyOf( ) -# Object Property: (characteristic of) +# Object Property: (inheres in) AnnotationAssertion( "inheres in"@en) AnnotationAssertion( "this fragility is a characteristic of this vase"@en) @@ -52858,7 +52854,7 @@ AnnotationAssertion(rdfs:label "caus SubObjectPropertyOf( ) SubObjectPropertyOf( ) -# Object Property: (disease causes disruption of) +# Object Property: (disease disrupts) AnnotationAssertion( "A relationship between a disease and a process where the disease process disrupts the execution of the process.") AnnotationAssertion( "disease causes disruption of (disease to process)") @@ -249992,27 +249988,6 @@ SubClassOf( "stratification") SubClassOf( ) -# Class: (affinity) - -AnnotationAssertion(rdfs:label "affinity") -SubClassOf( ) - -# Class: (increased affinity) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "increased affinity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - -# Class: (decreased affinity) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "decreased affinity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (movement behavioral quality) AnnotationAssertion(rdfs:label "movement behavioral quality") @@ -250501,14 +250476,6 @@ EquivalentClasses( ObjectIntersecti SubClassOf( ) SubClassOf( ) -# Class: (normal affinity) - -AnnotationAssertion( "An affinity which is relatively normal or average.") -AnnotationAssertion(rdfs:label "normal affinity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (normal age) AnnotationAssertion( "An age which is relatively normal or average.") diff --git a/src/patterns/data/default/entity_attribute.tsv b/src/patterns/data/default/entity_attribute.tsv index 5915b986..665dfca1 100644 --- a/src/patterns/data/default/entity_attribute.tsv +++ b/src/patterns/data/default/entity_attribute.tsv @@ -4360,7 +4360,7 @@ OBA:2045414 UBERON:0001088 urine PATO:0000957 opacity https://orcid.org/0000- OBA:2045415 UBERON:0001088 urine PATO:0002027 osmolality https://orcid.org/0000-0001-8314-2140 OBA:2045416 synovial fluid attribute UBERON:0001090 synovial fluid PATO:0000001 quality https://orcid.org/0000-0001-8314-2140 OBA:2045417 UBERON:0001090 synovial fluid PATO:0000992 viscosity https://orcid.org/0000-0001-8314-2140 -OBA:2045418 cerebrospinal fluid attribute UBERON:0001359 cerebrospinal fluid PATO:0000001 quality https://orcid.org/0000-0001-8314-2140 +OBA:2045418 appearance of cerebrospinal fluid UBERON:0001359 cerebrospinal fluid PATO:0001300 optical quality https://orcid.org/0000-0001-8314-2140 OBA:2045419 UBERON:0001359 cerebrospinal fluid PATO:0000014 color https://orcid.org/0000-0001-8314-2140 OBA:2045420 UBERON:0001417 skin of neck PATO:0000915 thickness https://orcid.org/0000-0001-8314-2140 OBA:2045421 semen attribute UBERON:0001968 semen PATO:0000001 quality https://orcid.org/0000-0001-8314-2140 diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index a3c54398..629f907a 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-11-16") + +Annotation(owl:versionInfo "2023-11-17") Declaration(Class()) Declaration(Class()) @@ -14987,6 +14987,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -101755,13 +101756,13 @@ AnnotationAssertion(Annotation( "synovial fluid viscosity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (cerebrospinal fluid attribute) +# Class: (appearance of cerebrospinal fluid) -AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The quality of a cerebrospinal fluid.") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The optical quality of a cerebrospinal fluid.") AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") -AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "quality of cerebrospinal fluid") -AnnotationAssertion(rdfs:label "cerebrospinal fluid attribute") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "optical quality of cerebrospinal fluid") +AnnotationAssertion(rdfs:label "appearance of cerebrospinal fluid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (cerebrospinal fluid color) @@ -102018,17 +102019,17 @@ EquivalentClasses( ObjectIntersectio # Class: (attribute of response to allergen in serum) -AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The http://purl.obolibrary.org/obo/OBA_2045453 of a blood serum.") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The attribute of response to allergen of a blood serum.") AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") -AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "http://purl.obolibrary.org/obo/OBA_2045453 of blood serum") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "attribute of response to allergen of blood serum") AnnotationAssertion(rdfs:label "attribute of response to allergen in serum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (attribute of response to thyroid hormone in plasma) -AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The http://purl.obolibrary.org/obo/OBA_2045454 of a blood plasma.") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The attribute of response to thyroid hormone of a blood plasma.") AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") -AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "http://purl.obolibrary.org/obo/OBA_2045454 of blood plasma") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "attribute of response to thyroid hormone of blood plasma") AnnotationAssertion(rdfs:label "attribute of response to thyroid hormone in plasma") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -121298,7 +121299,6 @@ SubClassOf(ObjectIntersectionOf( Ob SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) -SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) @@ -124576,6 +124576,7 @@ SubClassOf(ObjectIntersectionOf( Ob SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))