From bc17af452b137065b7e51ca1cea15d26b8834d61 Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Wed, 13 Nov 2024 22:02:28 +0100 Subject: [PATCH] new terms --- src/ontology/hp-edit.owl | 85 ++++++++++++++++++++++++++++++---------- 1 file changed, 65 insertions(+), 20 deletions(-) diff --git a/src/ontology/hp-edit.owl b/src/ontology/hp-edit.owl index 7ed25fe7b..bd370315e 100644 --- a/src/ontology/hp-edit.owl +++ b/src/ontology/hp-edit.owl @@ -19507,6 +19507,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -20603,6 +20606,7 @@ AnnotationAssertion( "UMLS:C0042580") AnnotationAssertion( "Ureteral reflux") AnnotationAssertion( "Ureteric reflux") +AnnotationAssertion(Annotation( ) "VUR") AnnotationAssertion( "Vesico-ureteral reflux") AnnotationAssertion( "Vesicoureteric reflux") AnnotationAssertion( "HP:0000076") @@ -23211,10 +23215,11 @@ AnnotationAssertion(rdfs:label "Broa EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) -# Class: (Abnormality of the forehead) +# Class: (Abnormal forehead morphology) AnnotationAssertion(Annotation( ) "An anomaly of the forehead.") AnnotationAssertion( "UMLS:C4025867") +AnnotationAssertion( "Abnormality of the forehead") AnnotationAssertion(Annotation( ) "Abnormality of the forehead") AnnotationAssertion(Annotation( ) "Abnormality of the frontal region of the face") AnnotationAssertion(Annotation( ) Annotation( ) "Anomaly of the forehead") @@ -23222,7 +23227,7 @@ AnnotationAssertion(Annotation( ) Annotation( ) "Malformation of the forehead") AnnotationAssertion( "HP:0000290") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "Abnormality of the forehead") +AnnotationAssertion(rdfs:label "Abnormal forehead morphology") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) @@ -27327,10 +27332,12 @@ SubClassOf( (Decreased lacrimation) -AnnotationAssertion(Annotation( ) "Abnormally decreased lacrimation, that is, reduced ability to produce tears.") +AnnotationAssertion(Annotation( ) Annotation( "PMID:35925585") "Abnormally decreased lacrimation, that is, reduced tear production.") AnnotationAssertion( "UMLS:C0235857") AnnotationAssertion(Annotation( ) Annotation( ) "Decreased tear secretion") +AnnotationAssertion( "Hypolacrimia") AnnotationAssertion( "HP:0000633") +AnnotationAssertion(rdfs:comment "As part of the lacrimal apparatus, the lacrimal gland participates in the maintenance of a healthy eye surface by producing the aqueous part of the tear film. Alacrimia and hypolacrimia, which are relatively rare during childhood or young adulthood, have their origin in a number of mechanisms which include agenesia, aplasia, hypoplasia, or incorrect maturation of the gland.") AnnotationAssertion(rdfs:label "Decreased lacrimation") SubClassOf( ) @@ -29124,7 +29131,7 @@ AnnotationAssertion( "Structural abnormality of the chest wall") AnnotationAssertion( "HP:0000765") AnnotationAssertion(rdfs:label "Abnormal thorax morphology") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) # Class: (Abnormal sternum morphology) @@ -29519,13 +29526,14 @@ AnnotationAssertion(rdfs:label "Urin EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) -# Class: (Abnormal external genitalia) +# Class: (Abnormal external genitalia morphology) +AnnotationAssertion( "A structural anomaly of the external genitalia.") AnnotationAssertion( "UMLS:C4025825") AnnotationAssertion(Annotation( ) "Abnormal external genitalia") AnnotationAssertion( "HP:0000811") -AnnotationAssertion(rdfs:label "Abnormal external genitalia") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) +AnnotationAssertion(rdfs:label "Abnormal external genitalia morphology") +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) # Class: (Abnormal internal genitalia) @@ -36243,6 +36251,7 @@ AnnotationAssertion( "SNOMEDCT_US:432788009") AnnotationAssertion( "UMLS:C0231246") AnnotationAssertion( "UMLS:C2315100") +AnnotationAssertion(Annotation( ) "FTT") AnnotationAssertion(Annotation( ) Annotation( ) "Faltering weight") AnnotationAssertion( "Postnatal failure to thrive") AnnotationAssertion(Annotation( ) Annotation( ) "Weight faltering") @@ -55030,16 +55039,17 @@ AnnotationAssertion(rdfs:label "Urin EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) SubClassOf( ) -# Class: (Increased serum pyruvate) +# Class: (Increased circulating pyruvate concentration) -AnnotationAssertion(Annotation( "HPO_CONTRIBUTOR:gcarletti") "An increased concentration of pyruvate in the blood.") +AnnotationAssertion(Annotation( "HPO_CONTRIBUTOR:gcarletti") "The concentration of pyruvate in the blood circulation is above the upper limit of normal.") AnnotationAssertion( "UMLS:C1849488") +AnnotationAssertion( "Increased serum pyruvate") AnnotationAssertion( "Increased serum pyruvic acid") AnnotationAssertion( "HP:0003542") AnnotationAssertion(rdfs:comment "An abnormal increase in the concentration of pyruvate in the blood. Pyruvate is involved in energy metabolism, forming part of glycolysis and the citric acid cycle.") -AnnotationAssertion(rdfs:label "Increased serum pyruvate") +AnnotationAssertion(rdfs:label "Increased circulating pyruvate concentration") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) # Class: (Exercise intolerance) @@ -61034,16 +61044,14 @@ AnnotationAssertion(rdfs:label "Abno EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) SubClassOf( ) -# Class: (Abnormality of glycolysis) +# Class: (obsolete Abnormality of glycolysis) -AnnotationAssertion(Annotation( ) "An abnormality of glycolysis.") +AnnotationAssertion( "HP:0011013") AnnotationAssertion(dcterms:creator ) AnnotationAssertion( "2008-03-17T05:00:00Z") -AnnotationAssertion( "UMLS:C4025334") AnnotationAssertion( "HP:0004366") -AnnotationAssertion(rdfs:label "Abnormality of glycolysis") -EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +AnnotationAssertion(rdfs:label "obsolete Abnormality of glycolysis") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Class: (obsolete Abnormality of glycoprotein metabolism) @@ -63623,6 +63631,7 @@ AnnotationAssertion( "UMLS:C0030590") AnnotationAssertion( "UMLS:C4280507") AnnotationAssertion( "Episodic supraventricular tachycardia") +AnnotationAssertion(Annotation( ) "PSVT") AnnotationAssertion( "HP:0004763") AnnotationAssertion(rdfs:comment "PSVT is a term used to denote intermittent supraventricular tachycardia other than atrial fibrillation, atrial flutter and multifocal atrial tachycardia (AT). The major causes are atrioventricular reentrant tachycardia (AVNRT), atrioventricular reentrant tachycardia (AVRT), and sinoatrial node reentrant tachycardia (SNRT).") AnnotationAssertion(rdfs:label "Paroxysmal supraventricular tachycardia") @@ -64388,7 +64397,6 @@ AnnotationAssertion( "HP:0004878") AnnotationAssertion(rdfs:label "Intercostal muscle weakness") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -75365,6 +75373,7 @@ AnnotationAssertion(Annotation( "UMLS:C4025018") AnnotationAssertion( "HP:0006581") AnnotationAssertion(rdfs:label "Depletion of mitochondrial DNA in liver") +SubClassOf( ) SubClassOf( ) # Class: (Reye syndrome-like episodes) @@ -85064,7 +85073,7 @@ SubClassOf( (Premature ovarian insufficiency) -AnnotationAssertion(Annotation( ) "Amenorrhea due to loss of ovarian function before the age of 40. Primary ovarian inssuficiency (POI) is a state of female hypergonadotropic hypogonadism. It can manifest as primary amenorrhea with onset before menarche or secondary amenorrhea.") +AnnotationAssertion(Annotation( ) "Amenorrhea due to loss of ovarian function before the age of 40. Primary ovarian insuficiency (POI) is a state of female hypergonadotropic hypogonadism. It can manifest as primary amenorrhea with onset before menarche or secondary amenorrhea.") AnnotationAssertion( "HP:0001587") AnnotationAssertion( "HP:0100805") AnnotationAssertion( "SNOMEDCT_US:373717006") @@ -90611,6 +90620,7 @@ AnnotationAssertion( "HP:0009141") AnnotationAssertion(rdfs:label "Depletion of mitochondrial DNA in muscle tissue") SubClassOf( ) +SubClassOf( ) # Class: (Duplication of bones involving the upper extremities) @@ -115187,6 +115197,7 @@ SubClassOf( ) "A deviation from the normal concentration of a carbohydrate in the blood circulation.") AnnotationAssertion(dcterms:creator ) AnnotationAssertion( "2011-02-21T09:47:27Z") +AnnotationAssertion( "HP:0004366") AnnotationAssertion( "UMLS:C4023599") AnnotationAssertion( "HP:0011013") AnnotationAssertion(rdfs:comment "An abnormality of the metabolism (include abnormality of the concentration) of a carbohydrate, including monosaccharides, oligosaccharides and polysaccharides, and substances derived from them.") @@ -122558,6 +122569,12 @@ AnnotationAssertion(dcterms:creator AnnotationAssertion( "2012-04-08T10:57:14Z") AnnotationAssertion( "SNOMEDCT_US:718216009") AnnotationAssertion( "UMLS:C4023290") +AnnotationAssertion(Annotation( ) "Incomplete AVSD") +AnnotationAssertion( "Incomplete atrioventricular septal defect") +AnnotationAssertion(Annotation( ) "PAVSD") +AnnotationAssertion(Annotation( ) "Partial AVC defect") +AnnotationAssertion(Annotation( ) "Partial AVSD") +AnnotationAssertion( "Partial atrioventricular septal defect") AnnotationAssertion( "HP:0011577") AnnotationAssertion(rdfs:label "Partial atrioventricular canal defect") SubClassOf( ) @@ -182290,7 +182307,7 @@ SubClassOf( (Peripheral cyanosis) -AnnotationAssertion(Annotation( ) Annotation( "PMID:32644593") "Bluish discoloration of the distal extremities (hands, fingertips, toes), and can sometimes involve circumoral and periorbital areas. Mucous membranes are generally not involved.") +AnnotationAssertion(Annotation( ) Annotation( "PMID:32644593") "Bluish discoloration of the distal extremities in the absence of cold temperature or stress. Peripheral cyanosis can involve hands, fingertips, or toes, and sometimes circumoral and periorbital areas. Mucous membranes are generally not involved.") AnnotationAssertion(dc:date "2021-09-24T13:36:17Z"^^xsd:dateTime) AnnotationAssertion(dcterms:creator ) AnnotationAssertion(rdfs:label "Peripheral cyanosis") @@ -231403,6 +231420,34 @@ AnnotationAssertion(dcterms:contributor "Elevated urinary adipic acid") SubClassOf( ) +# Class: (EEG with temporal slowing) + +AnnotationAssertion(Annotation( "PMID:31085562") "Slow-wave activity observed in the temporal area of the scalp electro-encephalogram (EEG).") +AnnotationAssertion( ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion( "EEG with slow activity in temporal lobes") +AnnotationAssertion( "EEG with slow-wave activity involving the temporal lobes") +AnnotationAssertion(rdfs:label "EEG with temporal slowing") +SubClassOf( ) + +# Class: (History of high-pressure injection injury of the hand) + +AnnotationAssertion(Annotation( "PMID:31194367") "Medical history of the hand having come into contact with the nozzle of a high-pressure injecting system such as a paint gun or air compressor.") +AnnotationAssertion( ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion(rdfs:label "History of high-pressure injection injury of the hand") +SubClassOf( ) + +# Class: (Hypertrophic ulnar styloid process) + +AnnotationAssertion(Annotation( "PMID:31192047") "Excessively long styloid process of the ulna.") +AnnotationAssertion( ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion( "Ulnar styloid large") +AnnotationAssertion(rdfs:comment "Ulnar styloid impaction syndrome involves impaction between the tip of the ulnar styloid process and the triquetrum bone. This syndrome is most commonly seen in patients with excessively long or hypertrophic ulnar styloid processes and is not necessarily associated with positive ulnar variance. The ulnar styloid process index (USPI), calculated as the difference between the ulnar styloid length and the ulnar variance divided by the transverse diameter of the ulnar head, is commonly used to assess the size of the ulnar styloid. An excessively long ulnar styloid has a length greater than 6 mm or a USPI more than 0.21. Repetitive friction of the proximal pole of the triquetrum and the ulnar styloid tip leads to chondromalacia, synovitis, and ulnar-sided wrist pain.") +AnnotationAssertion(rdfs:label "Hypertrophic ulnar styloid process") +SubClassOf( ) + SubObjectPropertyOf(ObjectPropertyChain( ) ) ) \ No newline at end of file