From 02fe18db64a3250dd313e444d99f3a1cc9a87ee4 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Wed, 13 Dec 2023 13:15:11 -0800 Subject: [PATCH 1/2] Review of "craniofacial cleft" MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Closes #10256 Was done in this PR: - rename or update labels: - Rename “Facial cleft” (HP:0000315) to “Tessier Cleft” - Rename “Non-midline cleft upper lip” to “Non-midline cleft of the upper lip” - Rename “Median cleft lip” (HP:0000161) to “Median cleft upper lip” - create new terms: - Craniofacial cleft (HP:5201015), parent of “Tessier cleft” and “orofacial cleft” - Submucous cleft palate (HP:5201016), parent of submucous cleft soft / hard palate terms - update classification such that: - orofacial cleft refers specifically to cleft palate, cleft of upper lip (non-medial), and cleft of maxillary alveolar ridge - ‘Cleft lower alveolar ridge’ is not a ‘Cleft maxillary alveolar ridge’ - update definitions to clarify terms. Definitions were updated for - Complete cleft of hard palate | HP:5201003 - Incomplete cleft of hard palate | HP:5201004 - Complete cleft of soft palate | HP:5201005 - Incomplete cleft of soft palate | HP:5201006 - Orofacial Cleft | HP:0000202 - Non-midline cleft of the upper lip | HP:0100335 - Cleft upper lip | HP:0000204 - Incomplete cleft of the upper lip | HP:0011340 - update comment to add usage of the following terms: - Complete cleft of the upper lip HP:5201009 - Microform cleft of the upper lip HP:5201010 - Incomplete cleft of the upper lip HP:0011340 --- src/ontology/hp-edit.owl | 64 +++++++++++++++++++++++++++------------- 1 file changed, 43 insertions(+), 21 deletions(-) diff --git a/src/ontology/hp-edit.owl b/src/ontology/hp-edit.owl index ba74c2536..e2066037b 100644 --- a/src/ontology/hp-edit.owl +++ b/src/ontology/hp-edit.owl @@ -18076,6 +18076,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(AnnotationProperty()) @@ -20192,7 +20194,7 @@ AnnotationAssertion(rdfs:label "Narr EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) -# Class: (Median cleft lip) +# Class: (Median cleft upper lip) AnnotationAssertion(Annotation( ) "A type of cleft lip presenting as a midline (median) gap in the upper lip.") AnnotationAssertion( "UMLS:C1850256") @@ -20200,7 +20202,7 @@ AnnotationAssertion(Annotation( "Midline cleft lip") AnnotationAssertion( "HP:0000161") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "Median cleft lip") +AnnotationAssertion(rdfs:label "Median cleft upper lip") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) @@ -20397,7 +20399,8 @@ AnnotationAssertion( "HP:0000176") AnnotationAssertion(rdfs:label "Submucous cleft hard palate") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (Abnormal upper lip morphology) @@ -20695,7 +20698,7 @@ SubClassOf( (Orofacial cleft) -AnnotationAssertion(Annotation( ) Annotation( "PMID:21331089") "The presence of a cleft in the oral cavity, the two main types of which are cleft lip and cleft palate. In cleft lip, there is the congenital failure of the maxillary and median nasal processes to fuse, forming a groove or fissure in the lip. In cleft palate, there is a congenital failure of the palate to fuse properly, forming a grooved depression or fissure in the roof of the mouth. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately.") +AnnotationAssertion(Annotation( ) Annotation( "PMID:21331089") Annotation( "https://orcid.org/0000-0002-4142-7153") Annotation( "https://www.cdc.gov/ncbddd/birthdefects/surveillancemanual/chapters/chapter-4/chapter4-6.html") "The presence of a cleft (gap, opening, or groove) in the oral cavity, including cleft of the upper lip and/or cleft of the palate. Cleft of the upper lip is visible as a groove or fissure in the lip, most frequently due to a congenital failure of the maxillary and median nasal processes to fuse. Cleft palate is characterized by a grooved depression or fissure in the roof of the mouth, most often resulting from a congenital failure of the palate to fuse properly. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately.") AnnotationAssertion( "SNOMEDCT_US:253983005") AnnotationAssertion( "SNOMEDCT_US:66948001") AnnotationAssertion( "UMLS:C0158646") @@ -20708,10 +20711,11 @@ AnnotationAssertion( "HP:0000202") AnnotationAssertion(rdfs:label "Orofacial cleft") SubClassOf( ) +SubClassOf( ) # Class: (Cleft upper lip) -AnnotationAssertion(Annotation( ) "A gap in the upper lip. This is a congenital defect resulting from nonfusion of tissues of the lip during embryonal development.") +AnnotationAssertion(Annotation( ) "A gap or groove in the upper lip. This is a congenital defect resulting from nonfusion of tissues of the lip during embryonal development.") AnnotationAssertion( "Fyler:4875") AnnotationAssertion( "MSH:D002971") AnnotationAssertion( "SNOMEDCT_US:80281008") @@ -40195,7 +40199,7 @@ AnnotationAssertion(rdfs:label "Larg EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) -# Class: (Facial cleft) +# Class: (Tessier cleft) AnnotationAssertion(Annotation( ) "A congenital malformation with a cleft (gap or opening) in the face.") AnnotationAssertion( "SNOMEDCT_US:92821006") @@ -40207,9 +40211,10 @@ AnnotationAssertion(Annotation( "HP:0002006") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "The categories of facial cleft (subterms) correspond to Tessier, P (1976) Classification of rare craniofacial clefts, Journal of Maxillofacial Surgery; 4:69-92. There exists a competing classification system by Van der Meulen that divides different types of clefts based on where the development arrest occurs in the embryogenesis. The HPO uses the Tessier classification because it is based on phenotype rather than pathophysiological considerations.") -AnnotationAssertion(rdfs:label "Facial cleft") +AnnotationAssertion(rdfs:label "Tessier cleft") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) +SubClassOf( ) # Class: (Frontal bossing) @@ -89895,7 +89900,6 @@ AnnotationAssertion(Annotation( "HP:0009094") AnnotationAssertion(rdfs:label "Cleft lower alveolar ridge") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) # Class: (Chronic oral candidiasis) @@ -89936,6 +89940,7 @@ AnnotationAssertion(rdfs:comment "Su AnnotationAssertion(rdfs:label "Submucous cleft lip") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) SubClassOf( ) +SubClassOf( ) # Class: (Anterior open-bite malocclusion) @@ -119567,7 +119572,7 @@ SubClassOf( (Incomplete cleft of the upper lip) -AnnotationAssertion(Annotation( ) "A subtle unilateral cleft of the upper lip, which may appear as a small indentation.") +AnnotationAssertion(Annotation( ) Annotation( "https://orcid.org/0000-0002-4142-7153") "Cleft of the upper lip that does not go all the way from the bottom of the upper lip until the nasal cavity.") AnnotationAssertion(dcterms:creator ) AnnotationAssertion( "2012-02-26T01:55:36Z") AnnotationAssertion( "UMLS:C4021158") @@ -119577,7 +119582,7 @@ AnnotationAssertion(Annotation( ) Annotation( ) "Notched cleft of the upper lip") AnnotationAssertion(Annotation( ) Annotation( ) "Partial cleft of the upper lip") AnnotationAssertion( "HP:0011340") -AnnotationAssertion(rdfs:comment "If the cleft lip is on only one side, use 'Incomplete unilateral cleft lip' (HP:5201000).") +AnnotationAssertion(rdfs:comment "If the cleft lip is on only one side, use 'Incomplete unilateral cleft lip' (HP:5201000). This term was created to be used in association with a left (HP:0012835) or right (HP:0012834) modifier to annotate completeness of a cleft lip.") AnnotationAssertion(rdfs:label "Incomplete cleft of the upper lip") SubClassOf( ) @@ -125409,6 +125414,7 @@ AnnotationAssertion(rdfs:comment "Of AnnotationAssertion(rdfs:label "Submucous cleft soft palate") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) SubClassOf( ) +SubClassOf( ) # Class: (Membranous choanal atresia) @@ -199022,9 +199028,9 @@ AnnotationAssertion( "Unilateral cleft palate") SubClassOf( ) -# Class: (Non-midline cleft lip) +# Class: (Non-midline cleft of the upper lip) -AnnotationAssertion(Annotation( ) "Clefting of the upper lip affecting the lateral portions of the upper lip rather than the midline/median region.") +AnnotationAssertion(Annotation( ) "Clefting (gap or groove) of the upper lip affecting the lateral portions of the upper lip rather than the midline/median region.") AnnotationAssertion(dcterms:creator ) AnnotationAssertion( "2010-10-13T04:12:24Z") AnnotationAssertion( "HP:0010283") @@ -199033,7 +199039,8 @@ AnnotationAssertion( "Non-midline cleft of the upper lip") AnnotationAssertion( "Paramedian cleft of the upper lip") AnnotationAssertion( "HP:0100335") -AnnotationAssertion(rdfs:label "Non-midline cleft lip") +AnnotationAssertion(rdfs:label "Non-midline cleft of the upper lip") +SubClassOf( ) SubClassOf( ) # Class: (Bilateral cleft lip) @@ -208478,7 +208485,6 @@ AnnotationAssertion(Annotation( "Cleft of the lip") AnnotationAssertion(rdfs:label "Cleft lip") EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) -SubClassOf( ) # Class: (Submucous cleft of soft and hard palate) @@ -208486,7 +208492,9 @@ AnnotationAssertion(Annotation( "2017-06-20T23:09:33Z"^^xsd:dateTime) AnnotationAssertion(dcterms:creator ) AnnotationAssertion(rdfs:label "Submucous cleft of soft and hard palate") -SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) # Class: (obsolete Cleft of uvula) @@ -219524,28 +219532,28 @@ SubClassOf( (Complete cleft hard palate) -AnnotationAssertion(Annotation( "PMID:21331089") Annotation( "PMID:26171570") "Cleft hard palate in which the cleft goes through the entire length of the hard palate.") +AnnotationAssertion(Annotation( "PMID:21331089") Annotation( "PMID:26171570") "Cleft hard palate in which the cleft goes through the entire length of the hard palate, ie. from the incisor foramen to the anterior border of the soft palate.") AnnotationAssertion(dcterms:creator ) AnnotationAssertion(rdfs:label "Complete cleft hard palate") SubClassOf( ) # Class: (Incomplete cleft hard palate) -AnnotationAssertion(Annotation( "PMID:21331089") Annotation( "PMID:26171570") "Cleft hard palate in which the cleft doe not goes through the entire length of the hard palate.") +AnnotationAssertion(Annotation( "PMID:21331089") Annotation( "PMID:26171570") "Cleft hard palate in which the cleft does not go through the entire length of the hard palate, ie. the cleft does not go from the incisor foramen to the anterior border of the soft palate.") AnnotationAssertion(dcterms:creator ) AnnotationAssertion(rdfs:label "Incomplete cleft hard palate") SubClassOf( ) # Class: (Complete cleft soft palate) -AnnotationAssertion(Annotation( "PMID:21331089") Annotation( "PMID:26171570") "Cleft soft palate in which the cleft goes through the entire length of the soft palate.") +AnnotationAssertion(Annotation( "PMID:21331089") Annotation( "PMID:26171570") "Cleft soft palate in which the cleft goes through the entire length of the soft palate, i.e. from the posterior border of the hard palate until the uvula.") AnnotationAssertion(dcterms:creator ) AnnotationAssertion(rdfs:label "Complete cleft soft palate") SubClassOf( ) # Class: (Incomplete cleft soft palate) -AnnotationAssertion(Annotation( "PMID:21331089") Annotation( "PMID:26171570") "Cleft soft palate in which the cleft doe not goes through the entire length of the soft palate.") +AnnotationAssertion(Annotation( "PMID:21331089") Annotation( "PMID:26171570") "Cleft soft palate in which the cleft does not go through the entire length of the soft palate, i.e. the cleft does not go from the posterior border of the hard palate until the uvula.") AnnotationAssertion(dcterms:creator ) AnnotationAssertion(rdfs:label "Incomplete cleft soft palate") SubClassOf( ) @@ -219568,7 +219576,7 @@ SubClassOf( "PMID:21331089") Annotation( "PMID:26171570") Annotation( "PMID:33729631") "Cleft of the upper lip that starts from the bottom of the upper lip and reaches the nasal cavity.") AnnotationAssertion(dcterms:creator ) -AnnotationAssertion(rdfs:comment "If the cleft lip is on only one side, use 'Complete unilateral cleft lip' (HP:5201001)") +AnnotationAssertion(rdfs:comment "If the cleft lip is on only one side, use 'Complete unilateral cleft lip' (HP:5201001). This term was created to be used in association with a left (HP:0012835) or right (HP:0012834) modifier to annotate completeness of a cleft lip.") AnnotationAssertion(rdfs:label "Complete cleft of the upper lip") SubClassOf( ) @@ -219576,7 +219584,7 @@ SubClassOf( "PMID:21331089") Annotation( "PMID:26171570") Annotation( "PMID:33729631") "Notch, groove, or scar of the upper lip without noticeable rupture of the lip.") AnnotationAssertion(dcterms:creator ) -AnnotationAssertion(rdfs:comment "If the cleft lip is on only one side, use 'Microform unilateral cleft lip' (HP:5201002).") +AnnotationAssertion(rdfs:comment "If the cleft lip is on only one side, use 'Microform unilateral cleft lip' (HP:5201002). This term was created to be used in association with a left (HP:0012835) or right (HP:0012834) modifier to annotate completeness of a cleft lip.") AnnotationAssertion(rdfs:label "Microform cleft of the upper lip") SubClassOf( ) @@ -219609,6 +219617,20 @@ AnnotationAssertion(rdfs:comment "Co AnnotationAssertion(rdfs:label "Asymmetric bilateral cleft lip") SubClassOf( ) +# Class: (Craniofacial cleft) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-4142-7153") "Congenital abnormality with cleft (gap or opening) in the craniofacial bones. Craniofacial cleft includes facial cleft, orofacial clef, and cleft of the jaw.") +AnnotationAssertion(dcterms:creator ) +AnnotationAssertion(rdfs:label "Craniofacial cleft"@en) +SubClassOf( ) + +# Class: (Submucous cleft palate) + +AnnotationAssertion(Annotation( "PMID:21112097") Annotation( "https://orcid.org/0000-0002-4142-7153") "A cleft of the muscular portion of the palate that is covered by mucous membrane.") +AnnotationAssertion(dcterms:creator ) +AnnotationAssertion(rdfs:label "Submucous cleft palate"@en) +SubClassOf( ) + SubObjectPropertyOf(ObjectPropertyChain( ) ) ) \ No newline at end of file From 79c52cf1c8c6fc30701cc4c549dea5d70b8155f2 Mon Sep 17 00:00:00 2001 From: Sabrina Toro Date: Wed, 13 Dec 2023 13:29:58 -0800 Subject: [PATCH 2/2] updated orcid format --- src/ontology/hp-edit.owl | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/src/ontology/hp-edit.owl b/src/ontology/hp-edit.owl index 0c7c40b35..178653c1d 100644 --- a/src/ontology/hp-edit.owl +++ b/src/ontology/hp-edit.owl @@ -20720,7 +20720,7 @@ SubClassOf( (Orofacial cleft) -AnnotationAssertion(Annotation( ) Annotation( "PMID:21331089") Annotation( "https://orcid.org/0000-0002-4142-7153") Annotation( "https://www.cdc.gov/ncbddd/birthdefects/surveillancemanual/chapters/chapter-4/chapter4-6.html") "The presence of a cleft (gap, opening, or groove) in the oral cavity, including cleft of the upper lip and/or cleft of the palate. Cleft of the upper lip is visible as a groove or fissure in the lip, most frequently due to a congenital failure of the maxillary and median nasal processes to fuse. Cleft palate is characterized by a grooved depression or fissure in the roof of the mouth, most often resulting from a congenital failure of the palate to fuse properly. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately.") +AnnotationAssertion(Annotation( ) Annotation( ) Annotation( "PMID:21331089") Annotation( "https://www.cdc.gov/ncbddd/birthdefects/surveillancemanual/chapters/chapter-4/chapter4-6.html") "The presence of a cleft (gap, opening, or groove) in the oral cavity, including cleft of the upper lip and/or cleft of the palate. Cleft of the upper lip is visible as a groove or fissure in the lip, most frequently due to a congenital failure of the maxillary and median nasal processes to fuse. Cleft palate is characterized by a grooved depression or fissure in the roof of the mouth, most often resulting from a congenital failure of the palate to fuse properly. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately.") AnnotationAssertion( "SNOMEDCT_US:253983005") AnnotationAssertion( "SNOMEDCT_US:66948001") AnnotationAssertion( "UMLS:C0158646") @@ -119599,7 +119599,7 @@ SubClassOf( (Incomplete cleft of the upper lip) -AnnotationAssertion(Annotation( ) Annotation( "https://orcid.org/0000-0002-4142-7153") "Cleft of the upper lip that does not go all the way from the bottom of the upper lip until the nasal cavity.") +AnnotationAssertion(Annotation( ) Annotation( ) "Cleft of the upper lip that does not go all the way from the bottom of the upper lip until the nasal cavity.") AnnotationAssertion(dcterms:creator ) AnnotationAssertion( "2012-02-26T01:55:36Z") AnnotationAssertion( "UMLS:C4021158") @@ -219711,19 +219711,18 @@ SubClassOf( (Craniofacial cleft) -AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-4142-7153") "Congenital abnormality with cleft (gap or opening) in the craniofacial bones. Craniofacial cleft includes facial cleft, orofacial clef, and cleft of the jaw.") +AnnotationAssertion(Annotation( ) "Congenital abnormality with cleft (gap or opening) in the craniofacial bones. Craniofacial cleft includes facial cleft, orofacial clef, and cleft of the jaw.") AnnotationAssertion(dcterms:creator ) AnnotationAssertion(rdfs:label "Craniofacial cleft"@en) SubClassOf( ) # Class: (Submucous cleft palate) -AnnotationAssertion(Annotation( "PMID:21112097") Annotation( "https://orcid.org/0000-0002-4142-7153") "A cleft of the muscular portion of the palate that is covered by mucous membrane.") +AnnotationAssertion(Annotation( ) Annotation( "PMID:21112097") "A cleft of the muscular portion of the palate that is covered by mucous membrane.") AnnotationAssertion(dcterms:creator ) AnnotationAssertion(rdfs:label "Submucous cleft palate"@en) SubClassOf( ) - # Class: (Left-right disorientation) AnnotationAssertion(Annotation( "PMID:19903731") "A tendency to mix up left and right in one's own body space, typically elicited by asking a person to perform a two-stage command involving specified lateralized anatomy.")