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monarch-initiative · Oct 15, 2018 · 09f959c · 09f959c
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diff --git a/imports/equivalencies.obo b/imports/equivalencies.obo
diff --git a/imports/equivalencies.owl b/imports/equivalencies.owl
diff --git a/imports/foodon_import.obo b/imports/foodon_import.obo
diff --git a/imports/foodon_import.owl b/imports/foodon_import.owl
diff --git a/imports/hgnc_import.obo b/imports/hgnc_import.obo
@@ -8706,6 +8706,11 @@ id: http://identifiers.org/hgnc/2514
 name: CTNNB1
 is_a: SO:0001217
 
+[Term]
+id: http://identifiers.org/hgnc/2515
+name: CTNND1
+is_a: SO:0001217
+
 [Term]
 id: http://identifiers.org/hgnc/25151
 name: ADAT3

diff --git a/imports/hgnc_import.owl b/imports/hgnc_import.owl
@@ -15690,6 +15690,15 @@
 
 
 
+    <!-- http://identifiers.org/hgnc/2515 -->
+
+    <owl:Class rdf:about="http://identifiers.org/hgnc/2515">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0001217"/>
+        <rdfs:label>CTNND1</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://identifiers.org/hgnc/25151 -->
 
     <owl:Class rdf:about="http://identifiers.org/hgnc/25151">

diff --git a/imports/hp_import.obo b/imports/hp_import.obo
@@ -4003,6 +4003,15 @@ synonym: "X-linked recessive" EXACT [HPO:skoehler]
 xref: UMLS:C1845977
 is_a: HP:0001417 ! X-linked inheritance
 
+[Term]
+id: HP:0001423
+name: X-linked dominant inheritance
+namespace: human_phenotype
+def: "A mode of inheritance that is observed for dominant traits related to a gene encoded on the X chromosome. In the context of medical genetics, X-linked dominant disorders tend to manifest very severely in affected males. The severity of manifestation in females may depend on the degree of skewed X inactivation." [HPO:curators]
+synonym: "X-linked dominant" EXACT [HPO:skoehler]
+xref: UMLS:C1847879
+is_a: HP:0001417 ! X-linked inheritance
+
 [Term]
 id: HP:0001433
 name: Hepatosplenomegaly
@@ -7581,6 +7590,23 @@ xref: SNOMEDCT_US:8915006
 xref: UMLS:C0266013
 is_a: HP:0010311 ! Aplasia/Hypoplasia of the breasts
 
+[Term]
+id: HP:0003198
+name: Myopathy
+namespace: human_phenotype
+alt_id: HP:0003569
+alt_id: HP:0003705
+alt_id: HP:0003742
+alt_id: HP:0003802
+def: "A disorder of muscle unrelated to impairment of innervation or neuromuscular junction." [HPO:probinson]
+comment: The diagnosis of myopathy is often confirmed on the basis of myopathic changes in muscle biopsy.
+synonym: "Muscle tissue disease" EXACT layperson [ORCID:0000-0001-5208-3432]
+synonym: "Myopathic changes" EXACT []
+xref: MSH:D009135
+xref: SNOMEDCT_US:129565002
+xref: UMLS:C0026848
+is_a: HP:0011805 ! Abnormality of muscle morphology
+
 [Term]
 id: HP:0003202
 name: Skeletal muscle atrophy
@@ -12481,6 +12507,19 @@ is_a: HP:0012824 ! Severity
 created_by: peter
 creation_date: 2014-06-06T06:41:33Z
 
+[Term]
+id: HP:0012828
+name: Severe
+namespace: human_phenotype
+def: "Having a high degree of severity. For quantitative traits, a deviation of between four and five standard deviations from the appropriate population mean." [HPO:probinson]
+comment: PATO:0000396, severe.
+synonym: "Severe" EXACT layperson []
+xref: SNOMEDCT_US:24484000
+xref: UMLS:C0205082
+is_a: HP:0012824 ! Severity
+created_by: peter
+creation_date: 2014-06-06T07:03:17Z
+
 [Term]
 id: HP:0012862
 name: Abnormal germ cell morphology

diff --git a/imports/hp_import.owl b/imports/hp_import.owl
@@ -10557,6 +10557,32 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/HP_0001423 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0001423">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/HP_0001417"/>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A mode of inheritance that is observed for dominant traits related to a gene encoded on the X chromosome. In the context of medical genetics, X-linked dominant disorders tend to manifest very severely in affected males. The severity of manifestation in females may depend on the degree of skewed X inactivation.</obo:IAO_0000115>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UMLS:C1847879</oboInOwl:hasDbXref>
+        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X-linked dominant</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">human_phenotype</oboInOwl:hasOBONamespace>
+        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HP:0001423</oboInOwl:id>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X-linked dominant inheritance</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/HP_0001423"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A mode of inheritance that is observed for dominant traits related to a gene encoded on the X chromosome. In the context of medical genetics, X-linked dominant disorders tend to manifest very severely in affected males. The severity of manifestation in females may depend on the degree of skewed X inactivation.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HPO:curators</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/HP_0001423"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X-linked dominant</owl:annotatedTarget>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HPO:skoehler</oboInOwl:hasDbXref>
+    </owl:Axiom>
+
+
+
     <!-- http://purl.obolibrary.org/obo/HP_0001433 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0001433">
@@ -13324,26 +13350,26 @@
     </owl:Class>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/HP_0001962"/>
-        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
-        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Palpitations</owl:annotatedTarget>
-        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/hp#layperson"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A sensation that the heart is pounding or racing, which is a non-specific sign but may be a manifestation of arrhythmia.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HPO:probinson</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/HP_0001962"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
-        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Skipped heart beat</owl:annotatedTarget>
+        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Missed heart beat</owl:annotatedTarget>
         <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/hp#layperson"/>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/HP_0001962"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A sensation that the heart is pounding or racing, which is a non-specific sign but may be a manifestation of arrhythmia.</owl:annotatedTarget>
-        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HPO:probinson</oboInOwl:hasDbXref>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Palpitations</owl:annotatedTarget>
+        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/hp#layperson"/>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/HP_0001962"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
-        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Missed heart beat</owl:annotatedTarget>
+        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Skipped heart beat</owl:annotatedTarget>
         <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/hp#layperson"/>
     </owl:Axiom>
 
@@ -19060,6 +19086,41 @@ Dysfunction leads to weakness, impairment of fine motor movements, spasticity, h
 
 
 
+    <!-- http://purl.obolibrary.org/obo/HP_0003198 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0003198">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/HP_0011805"/>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A disorder of muscle unrelated to impairment of innervation or neuromuscular junction.</obo:IAO_0000115>
+        <oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HP:0003569</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HP:0003705</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HP:0003742</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HP:0003802</oboInOwl:hasAlternativeId>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MSH:D009135</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SNOMEDCT_US:129565002</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UMLS:C0026848</oboInOwl:hasDbXref>
+        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Muscle tissue disease</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Myopathic changes</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">human_phenotype</oboInOwl:hasOBONamespace>
+        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HP:0003198</oboInOwl:id>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The diagnosis of myopathy is often confirmed on the basis of myopathic changes in muscle biopsy.</rdfs:comment>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Myopathy</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/HP_0003198"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A disorder of muscle unrelated to impairment of innervation or neuromuscular junction.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HPO:probinson</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/HP_0003198"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Muscle tissue disease</owl:annotatedTarget>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ORCID:0000-0001-5208-3432</oboInOwl:hasDbXref>
+        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/hp#layperson"/>
+    </owl:Axiom>
+
+
+
     <!-- http://purl.obolibrary.org/obo/HP_0003202 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0003202">
@@ -29755,6 +29816,36 @@ and two otolith organs that are sensitive to linear acceleration.</rdfs:comment>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/HP_0012828 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0012828">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/HP_0012824"/>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Having a high degree of severity. For quantitative traits, a deviation of between four and five standard deviations from the appropriate population mean.</obo:IAO_0000115>
+        <oboInOwl:created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">peter</oboInOwl:created_by>
+        <oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2014-06-06T07:03:17Z</oboInOwl:creation_date>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SNOMEDCT_US:24484000</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UMLS:C0205082</oboInOwl:hasDbXref>
+        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Severe</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">human_phenotype</oboInOwl:hasOBONamespace>
+        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HP:0012828</oboInOwl:id>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PATO:0000396, severe.</rdfs:comment>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Severe</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/HP_0012828"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Having a high degree of severity. For quantitative traits, a deviation of between four and five standard deviations from the appropriate population mean.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HPO:probinson</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/HP_0012828"/>
+        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
+        <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Severe</owl:annotatedTarget>
+        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/hp#layperson"/>
+    </owl:Axiom>
+
+
+
     <!-- http://purl.obolibrary.org/obo/HP_0012862 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0012862">