diff --git a/src/ontology/efo-3-edit.owl b/src/ontology/efo-3-edit.owl index 249e4bb5..97268659 100644 --- a/src/ontology/efo-3-edit.owl +++ b/src/ontology/efo-3-edit.owl @@ -26414,6 +26414,7 @@ Declaration(Class(:EFO_0009946)) Declaration(Class(:EFO_0009947)) Declaration(Class(:EFO_0009948)) Declaration(Class(:EFO_0009949)) +Declaration(Class(:EFO_0009950)) Declaration(Class(:EFO_0009951)) Declaration(Class(:EFO_0009952)) Declaration(Class(:EFO_0009953)) @@ -26582,6 +26583,17 @@ Declaration(Class(:EFO_0010117)) Declaration(Class(:EFO_0010118)) Declaration(Class(:EFO_0010119)) Declaration(Class(:EFO_0010120)) +Declaration(Class(:EFO_0010123)) +Declaration(Class(:EFO_0010124)) +Declaration(Class(:EFO_0010125)) +Declaration(Class(:EFO_0010126)) +Declaration(Class(:EFO_0010127)) +Declaration(Class(:EFO_0010128)) +Declaration(Class(:EFO_0010129)) +Declaration(Class(:EFO_0010130)) +Declaration(Class(:EFO_0010131)) +Declaration(Class(:EFO_0010132)) +Declaration(Class(:EFO_0010133)) Declaration(Class(:EFO_1000003)) Declaration(Class(:EFO_1000012)) Declaration(Class(:EFO_1000013)) @@ -28364,7 +28376,6 @@ Declaration(Class(:EFO_1002048)) Declaration(Class(:EFO_1002049)) Declaration(Class(:EFO_1002050)) Declaration(Class(:EFO_1002051)) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -35308,7 +35319,7 @@ AnnotationAssertion(rdfs:label "loca AnnotationAssertion(rdfs:label "has_plasma_membrane_part"^^xsd:string) -# Object Property: (only_in_taxon) +# Object Property: (only in taxon) AnnotationAssertion(Annotation( "PMID:20973947"^^xsd:string) "S only_in_taxon T iff: S SubClassOf in_taxon only T"^^xsd:string) AnnotationAssertion( "RO:0002160"^^xsd:string) @@ -91474,7 +91485,7 @@ AnnotationAssertion( "Hypervolemia"^^xsd:string) SubClassOf( ) -# Class: (Hypovolemia) +# Class: (hypovolemia) AnnotationAssertion( "A decrease in the amount of intravascular fluid, particularly in the volume of circulating blood. [database_cross_reference: HPO:probinson]"^^xsd:string) AnnotationAssertion(Annotation( "HPO:probinson"^^xsd:string) "An decrease in the amount of intravascular fluid, particularly in the volume of the circulating blood."^^xsd:string) @@ -249910,7 +249921,7 @@ AnnotationAssertion(rdfs:label " SubClassOf( ) SubClassOf( ) -# Class: (ectopterygoid) +# Class: (ectopterygoid bone) AnnotationAssertion(Annotation( ) "A palatal bone which -- like many palatal bones -- may originally have developed as a dermal bone replacing part of the palatoquadrate, the primitive upper jaw. Like the palatine (also called dermopalatine), the ectopterygoid replaces the middle part of the autopalatine. It may be serially homologous with the palatine(s), but is somewhat specialized, being the last (most posterior in palatal view) of the series and bordering the fossa for the jaw muscles. In a typical tetrapod it abuts the palatine anteriorly, the maxilla laterally, the pterygoid or the fossa mandubuaris medially, and the fossa posteriorly"^^xsd:string) AnnotationAssertion( "The ectopterygoid is dermal bone located at the anterior part of the palatoquadrate. It is first visible as a very thin ossification along the anteroventral border of the palatoquadrate cartilage (6.4 mm). In adults it is a long sliver of bone that is narrow anteriorly where it meets the entopterygoid in a synostosis. It is slightly wider at its posterior synostosis with the quadrate."^^xsd:string) @@ -405492,7 +405503,7 @@ AnnotationAssertion(Annotation( "http: AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0009321 "UMLS_CUI:C0730285"^^xsd:string) AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0009321 "DME"^^xsd:string) AnnotationAssertion(rdfs:label :EFO_0009321 "diabetic macular edema"^^xsd:string) -SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0009321 :EFO_0003770) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0009321 :EFO_0010133) # Class: :EFO_0009322 (proliferative diabetic retinopathy) @@ -411501,7 +411512,7 @@ AnnotationAssertion( :EFO_0009948 "inflammation of fetal membrane"^^xsd:string) AnnotationAssertion( :EFO_0009948 "intra-amniotic infection"^^xsd:string) AnnotationAssertion(rdfs:label :EFO_0009948 "chorioamnionitis"^^xsd:string) -SubClassOf(:EFO_0009948 ) +SubClassOf(:EFO_0009948 :EFO_0009950) # Class: :EFO_0009949 (KANNO antigen measurement) @@ -411512,6 +411523,13 @@ AnnotationAssertion(Annotation( "http: AnnotationAssertion(rdfs:label :EFO_0009949 "KANNO antigen measurement"^^xsd:string) SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0009949 :EFO_0007937) +# Class: :EFO_0009950 (disease of extraembryonic membrane) + +AnnotationAssertion( :EFO_0009950 "A disease or disorder that involves the extraembryonic membrane."^^xsd:string) +AnnotationAssertion(:gwas_trait :EFO_0009950 "true"^^xsd:boolean) +AnnotationAssertion( :EFO_0009950 "MONDO:0045013"^^xsd:string) +AnnotationAssertion(rdfs:label :EFO_0009950 "disease of extraembryonic membrane"^^xsd:string) + # Class: :EFO_0009951 (response to surgery) AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0009951 "Any process that results in a change in state or activity of a cell or an organism as a result of surgical intervention."^^xsd:string) @@ -413072,6 +413090,114 @@ SubClassOf(Annotation( "http://www.ebi SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010120 ObjectSomeValuesFrom( )) SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010120 ObjectSomeValuesFrom( :EFO_0001360)) +# Class: :EFO_0010123 (response to antiviral drug) + +AnnotationAssertion( :EFO_0010123 "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antiviral drug stimulus. Antiviral drugs are a class of medication used specifically for treating viral infections."^^xsd:string) +AnnotationAssertion( :EFO_0010123 "Elliot Sollis"^^xsd:string) +AnnotationAssertion(:gwas_trait :EFO_0010123 "true"^^xsd:boolean) +AnnotationAssertion(rdfs:label :EFO_0010123 "response to antiviral drug"^^xsd:string) +SubClassOf(:EFO_0010123 ) + +# Class: :EFO_0010124 (response to atorvastatin) + +AnnotationAssertion( :EFO_0010124 "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an atorvastatin stimulus. Atorvastatin is a statin used as a cholesterol-lowering and anti-cardiovascular disease drug."^^xsd:string) +AnnotationAssertion( :EFO_0010124 "Laura Harris"^^xsd:string) +AnnotationAssertion(:gwas_trait :EFO_0010124 "true"^^xsd:boolean) +AnnotationAssertion(rdfs:label :EFO_0010124 "response to atorvastatin"^^xsd:string) +SubClassOf(:EFO_0010124 ) +SubClassOf(:EFO_0010124 ObjectSomeValuesFrom( )) + +# Class: :EFO_0010125 (viral load) + +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010125 "A measurement of the quantity of virus in a given volume of body fluid."^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010125 "Elliot Sollis"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :gwas_trait :EFO_0010125 "true"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010125 "PMID:31260374"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010125 "https://en.wikipedia.org/wiki/Viral_load"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010125 "viral burden"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010125 "viral titer"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010125 "viral titre"^^xsd:string) +AnnotationAssertion(rdfs:label :EFO_0010125 "viral load"^^xsd:string) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010125 :EFO_0001444) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010125 ObjectSomeValuesFrom( :EFO_0000544)) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010125 ObjectSomeValuesFrom( :EFO_0000763)) + +# Class: :EFO_0010126 (time to first cigarette measurement) + +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010126 "Quantification of how soon after waking up an individual smokes their first cigarette of the day."^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010126 "Laura Harris"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :gwas_trait :EFO_0010126 "true"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010126 "PMID:31294817"^^xsd:string) +AnnotationAssertion(rdfs:label :EFO_0010126 "time to first cigarette measurement"^^xsd:string) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010126 :EFO_0005671) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010126 ObjectSomeValuesFrom( :EFO_0003768)) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010126 ObjectSomeValuesFrom( :EFO_0004318)) + +# Class: :EFO_0010127 (serum immunoglobulin measurement) + +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010127 "Quantification of the amount of immunglobulin in a serum sample."^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010127 "Laura Harris"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :gwas_trait :EFO_0010127 "true"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010127 "PMID:28628107"^^xsd:string) +AnnotationAssertion(rdfs:label :EFO_0010127 "serum immunoglobulin measurement"^^xsd:string) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010127 :EFO_0004556) + +# Class: :EFO_0010128 (immunoglobulin isotype switching measurement) + +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010128 "Quantification of the switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin."^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010128 "Laura Harris"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :gwas_trait :EFO_0010128 "true"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010128 "PMID:28628107"^^xsd:string) +AnnotationAssertion(rdfs:label :EFO_0010128 "immunoglobulin isotype switching measurement"^^xsd:string) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010128 :EFO_0004556) + +# Class: :EFO_0010129 (breakfast skipping measurement) + +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010129 "Quantification of the frequency which an individual omits to eat breakfast. Breakfast skipping is often considered as a sub-clinical eating disorder."^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010129 "Laura Harris"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :gwas_trait :EFO_0010129 "true"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010129 "PMID:31190057"^^xsd:string) +AnnotationAssertion(rdfs:label :EFO_0010129 "breakfast skipping measurement"^^xsd:string) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010129 :EFO_0006848) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010129 ObjectSomeValuesFrom( :EFO_0005203)) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010129 ObjectSomeValuesFrom( :EFO_0007829)) + +# Class: :EFO_0010130 (health study participation) + +AnnotationAssertion( :EFO_0010130 "Characteristic of an individual defined by their participation in a health study, e.g. by volunteering for or completing specific surveys, questionnaires or tasks."^^xsd:string) +AnnotationAssertion( :EFO_0010130 "Laura Harris"^^xsd:string) +AnnotationAssertion(:gwas_trait :EFO_0010130 "true"^^xsd:boolean) +AnnotationAssertion( :EFO_0010130 "health questionnaire participation"^^xsd:string) +AnnotationAssertion( :EFO_0010130 "health survey participation"^^xsd:string) +AnnotationAssertion(rdfs:label :EFO_0010130 "health study participation"^^xsd:string) +SubClassOf(:EFO_0010130 :EFO_0000651) + +# Class: :EFO_0010131 (decreased walking ability) + +AnnotationAssertion( :EFO_0010131 "A decrease in an individual's ability to walk."^^xsd:string) +AnnotationAssertion( :EFO_0010131 "Joannella Morales"^^xsd:string) +AnnotationAssertion(:gwas_trait :EFO_0010131 "true"^^xsd:boolean) +AnnotationAssertion(rdfs:label :EFO_0010131 "decreased walking ability"^^xsd:string) +SubClassOf(:EFO_0010131 ) + +# Class: :EFO_0010132 (decreased fine motor function) + +AnnotationAssertion( :EFO_0010132 "A decrease in an individual's ability to perform fine motor function tasks."^^xsd:string) +AnnotationAssertion( :EFO_0010132 "Joannella Morales"^^xsd:string) +AnnotationAssertion(:gwas_trait :EFO_0010132 "true"^^xsd:boolean) +AnnotationAssertion(rdfs:label :EFO_0010132 "decreased fine motor function"^^xsd:string) +SubClassOf(:EFO_0010132 ) + +# Class: :EFO_0010133 (diabetic maculopathy) + +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010133 "Diabetic maculopathy (DM) is a type of diabetic retinopathy and it is a major eye complication and visual impairment amongst people with diabetes. It is a condition that affects the macula, a highly sensitive region located centrally on the retina which is responsible for sharp, clear, and accurate colour vision."^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010133 "Joannella Morales"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010133 "PMID:31264924"^^xsd:string) +AnnotationAssertion(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010133 "DM"^^xsd:string) +AnnotationAssertion(rdfs:label :EFO_0010133 "diabetic maculopathy"^^xsd:string) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010133 :EFO_0003770) +SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_0010133 ObjectSomeValuesFrom(:EFO_0000784 ObjectUnionOf( ObjectSomeValuesFrom( )))) + # Class: :EFO_1000003 (Zinc deficiency) AnnotationAssertion( :EFO_1000003 "A deficiency of the essential metal Zinc; an essential cofactor for many enzymes. Zinc deficiency is caused by a lack of zinc in the diet, loss of zinc after absorption, for example through loss through burns, inability to absorb Zinc, or increased loss through exercise. "^^xsd:string) @@ -433358,13 +433484,6 @@ AnnotationAssertion(Annotation( "http: AnnotationAssertion(rdfs:label :EFO_1002051 "facial nerve disease"^^xsd:string) SubClassOf(Annotation( "http://www.ebi.ac.uk/ontology/webulous#OPPL_pattern"^^xsd:string) :EFO_1002051 :EFO_0009387) -# Class: (disease of extraembryonic membrane) - -AnnotationAssertion( "A disease or disorder that involves the extraembryonic membrane."^^xsd:string) -AnnotationAssertion(:gwas_trait "true"^^xsd:boolean) -AnnotationAssertion( "MONDO:0045013"^^xsd:string) -AnnotationAssertion(rdfs:label "disease of extraembryonic membrane"^^xsd:string) - # Class: (disposition) AnnotationAssertion( "For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease."^^xsd:string) diff --git a/src/ontology/imports/mondo_efo_mappings.tsv b/src/ontology/imports/mondo_efo_mappings.tsv index 5d9749f5..6d415ac1 100644 --- a/src/ontology/imports/mondo_efo_mappings.tsv +++ b/src/ontology/imports/mondo_efo_mappings.tsv @@ -8543,4 +8543,4 @@ http://purl.obolibrary.org/obo/MONDO_0021085 http://www.ebi.ac.uk/efo/EFO_000389 http://purl.obolibrary.org/obo/MONDO_0021245 http://www.ebi.ac.uk/efo/EFO_0003868 oral cavity neoplasm mouth neoplasm http://purl.obolibrary.org/obo/MONDO_0015075 http://www.ebi.ac.uk/efo/EFO_0002892 thyroid gland carcinoma thyroid carcinoma http://purl.obolibrary.org/obo/MONDO_0003847 http://www.ebi.ac.uk/efo/EFO_0000508 inherited genetic disorder genetic disorder -http://purl.obolibrary.org/obo/MONDO_0045013 http://www.ebi.ac.uk/efo/http://www.ebi.ac.uk/efo/EFO_0009950 disease of extraembryonic membrane disease of extraembryonic membrane \ No newline at end of file +http://purl.obolibrary.org/obo/MONDO_0045013 http://www.ebi.ac.uk/efo/EFO_0009950 disease of extraembryonic membrane disease of extraembryonic membrane \ No newline at end of file