1st Nov 2022 DO-KB release

DiseaseOntology · Nov 1, 2022 · cc9ca3c · cc9ca3c
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diff --git a/src/ontology/HumanDO.obo b/src/ontology/HumanDO.obo
@@ -1,6 +1,6 @@
 format-version: 1.2
-data-version: doid/releases/2022-10-31/doid-non-classified.obo
-date: 31:10:2022 13:04
+data-version: doid/releases/2022-11-01/doid-non-classified.obo
+date: 01:11:2022 09:50
 saved-by: lschriml
 subsetdef: DO_AGR_slim "DO_AGR_slim"
 subsetdef: DO_cancer_slim "DO_cancer_slim"
@@ -93322,11 +93322,12 @@ is_obsolete: true
 
 [Term]
 id: DOID:2088
-name: outlet dysfunction constipation
+name: obsolete outlet dysfunction constipation
+comment: reviewed 10/2022 & determined to be a symptom
 xref: ICD10CM:K59.02
 xref: ICD9CM:564.02
 xref: UMLS_CUI:C0949134
-is_a: DOID:9779 ! bowel dysfunction
+is_obsolete: true
 
 [Term]
 id: DOID:2089

diff --git a/src/ontology/HumanDO.owl b/src/ontology/HumanDO.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/doid/doid-non-classified.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/doid/releases/2022-10-31/doid-non-classified.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/doid/releases/2022-11-01/doid-non-classified.owl"/>
         <obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/DOID_4"/>
         <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.</dc:description>
         <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Human Disease Ontology</dc:title>
@@ -199287,13 +199287,14 @@ OMIM mapping confirmed by DO. [SN].</rdfs:comment>
     <!-- http://purl.obolibrary.org/obo/DOID_2088 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_2088">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DOID_9779"/>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD10CM:K59.02</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD9CM:564.02</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UMLS_CUI:C0949134</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease_ontology</oboInOwl:hasOBONamespace>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:2088</oboInOwl:id>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">outlet dysfunction constipation</rdfs:label>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">reviewed 10/2022 &amp; determined to be a symptom</rdfs:comment>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete outlet dysfunction constipation</rdfs:label>
+        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
 
 

diff --git a/src/ontology/doid-base.owl b/src/ontology/doid-base.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/doid/doid-base.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/doid/releases/2022-10-31/doid-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/doid/releases/2022-11-01/doid-base.owl"/>
         <obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/DOID_4"/>
         <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.</dc:description>
         <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Human Disease Ontology</dc:title>
@@ -177346,12 +177346,6 @@ OMIM mapping confirmed by DO. [SN].</rdfs:comment>
     <!-- http://purl.obolibrary.org/obo/DOID_10456 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_10456">
-        <owl:equivalentClass>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002452"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SYMP_0020055"/>
-            </owl:Restriction>
-        </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DOID_974"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -177395,6 +177389,12 @@ OMIM mapping confirmed by DO. [SN].</rdfs:comment>
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SYMP_0019174"/>
             </owl:Restriction>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002452"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SYMP_0020055"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An upper respiratory tract disease which is characterized by inflammation of the tonsils resulting from bacterial (Group A streptococcus) and viral (Epstein-Barr virus, adenovirus) infections. Symptoms include a severe sore throat, painful or difficult swallowing, coughing, headache, myalgia, fever and chills.</obo:IAO_0000115>
         <oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:10454</oboInOwl:hasAlternativeId>
         <oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:13751</oboInOwl:hasAlternativeId>
@@ -241335,19 +241335,14 @@ OMIM mapping confirmed by DO. [SN].</rdfs:comment>
     <!-- http://purl.obolibrary.org/obo/DOID_2088 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_2088">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DOID_9779"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002452"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SYMP_0019180"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD10CM:K59.02</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD9CM:564.02</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UMLS_CUI:C0949134</oboInOwl:hasDbXref>
         <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease_ontology</oboInOwl:hasOBONamespace>
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:2088</oboInOwl:id>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">outlet dysfunction constipation</rdfs:label>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">reviewed 10/2022 &amp; determined to be a symptom</rdfs:comment>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete outlet dysfunction constipation</rdfs:label>
+        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
 
 
@@ -346993,12 +346988,6 @@ OMIM mapping confirmed by DO. [SN].</rdfs:comment>
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
-        <owl:equivalentClass>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002452"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SYMP_0020048"/>
-            </owl:Restriction>
-        </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DOID_0050339"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -347024,6 +347013,12 @@ OMIM mapping confirmed by DO. [SN].</rdfs:comment>
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SYMP_0000654"/>
             </owl:Restriction>
         </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002452"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SYMP_0020048"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A commensal bacterial infectious disease that is characterized by widespread erythema, peeling, and necrosis of the skin, that is caused by a toxin produced by a bacterium of the genus Staphylococcus (S. aureus). The infection has_symptom redness of skin, has_symptom fluid-filled blister formation, has_symptom fever and has_symptom irritability.</obo:IAO_0000115>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD10CM:L00</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD9CM:695.81</oboInOwl:hasDbXref>

diff --git a/src/ontology/doid-merged.obo b/src/ontology/doid-merged.obo
@@ -1,6 +1,6 @@
 format-version: 1.2
-data-version: doid/releases/2022-10-31/doid-merged.obo
-date: 31:10:2022 13:28
+data-version: doid/releases/2022-11-01/doid-merged.obo
+date: 01:11:2022 09:51
 saved-by: lschriml
 subsetdef: DO_AGR_slim "DO_AGR_slim"
 subsetdef: DO_cancer_slim "DO_cancer_slim"
@@ -5149,7 +5149,6 @@ synonym: "respiratory anthrax" EXACT []
 synonym: "wool-sorters' disease" EXACT []
 synonym: "woolsorters' disease" EXACT []
 xref: MESH:C571912
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:7427 ! anthrax disease
 
 [Term]
@@ -5421,7 +5420,6 @@ id: DOID:0050196
 name: Venezuelan hemorrhagic fever
 def: "A viral infectious disease that is a hemorrhagic fever, has_material_basis_in Guanarito virus, which is transmitted_by cotton rat, Sigmodon alstoni or transmitted_by cane mouse, Zygodontomys brevicauda. The infection has_symptom fever, has_symptom headache, has_symptom myalgia, has_symptom sore throat, has_symptom weakness, has_symptom anorexia, has_symptom nausea, has_symptom vomiting, has_symptom convulsions, has_symptom epistaxis, has_symptom bleeding gums, has_symptom hematemesis, has_symptom melena, and has_symptom menorrhagia." [url:https\://pubmed.ncbi.nlm.nih.gov/34917387/, url:https\://pubmed.ncbi.nlm.nih.gov/7840443/]
 subset: zoonotic_infectious_disease
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:934 ! viral infectious disease
 
 [Term]
@@ -72966,7 +72964,6 @@ xref: MESH:D006232
 xref: NCI:C128439
 xref: SNOMEDCT_US_2022_03_01:175497008
 xref: UMLS_CUI:C0018572
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:934 ! viral infectious disease
 
 [Term]
@@ -72997,7 +72994,6 @@ xref: ICD9CM:074.0
 xref: MESH:D006557
 xref: SNOMEDCT_US_2022_03_01:154358007
 xref: UMLS_CUI:C0019338
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:403 ! mouth disease
 is_a: DOID:934 ! viral infectious disease
 
@@ -82595,8 +82591,8 @@ xref: ICD9CM:110.4
 xref: MESH:D014008
 xref: SNOMEDCT_US_2022_03_01:186993002
 xref: UMLS_CUI:C0040259
+is_a: DOID:37 ! skin disease
 is_a: DOID:8913 ! dermatophytosis
-is_a: DOID:9063 ! Ritter's disease
 
 [Term]
 id: DOID:12404
@@ -87021,7 +87017,6 @@ synonym: "Pneumonia due to Mycoplasma pneumoniae (disorder)" EXACT []
 xref: ICD10CM:J15.7
 xref: ICD9CM:483.0
 xref: MESH:D011019
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:874 ! bacterial pneumonia
 
 [Term]
@@ -87521,8 +87516,8 @@ xref: ICD9CM:110.2
 xref: MESH:C000656824
 xref: SNOMEDCT_US_2022_03_01:48971001
 xref: UMLS_CUI:C0153246
+is_a: DOID:37 ! skin disease
 is_a: DOID:8913 ! dermatophytosis
-is_a: DOID:9063 ! Ritter's disease
 
 [Term]
 id: DOID:13371
@@ -91744,7 +91739,7 @@ xref: MESH:D012772
 xref: NCI:C35498
 xref: SNOMEDCT_US_2022_03_01:18504008
 xref: UMLS_CUI:C0600327
-is_a: DOID:9063 ! Ritter's disease
+is_a: DOID:0050339 ! commensal bacterial infectious disease
 
 [Term]
 id: DOID:14116
@@ -99888,11 +99883,12 @@ is_obsolete: true
 
 [Term]
 id: DOID:2088
-name: outlet dysfunction constipation
+name: obsolete outlet dysfunction constipation
+comment: reviewed 10/2022 & determined to be a symptom
 xref: ICD10CM:K59.02
 xref: ICD9CM:564.02
 xref: UMLS_CUI:C0949134
-is_a: DOID:9779 ! bowel dysfunction
+is_obsolete: true
 
 [Term]
 id: DOID:2089
@@ -101941,7 +101937,6 @@ xref: ICD9CM:066.4
 xref: MESH:D014901
 xref: SNOMEDCT_US_2022_03_01:12381007
 xref: UMLS_CUI:C0043124
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:934 ! viral infectious disease
 
 [Term]
@@ -105327,7 +105322,6 @@ xref: NCI:C27151
 xref: SNOMEDCT_US_2022_03_01:110979008
 xref: UMLS_CUI:C0162823
 is_a: DOID:2773 ! contact dermatitis
-is_a: DOID:9063 ! Ritter's disease
 
 [Term]
 id: DOID:2773
@@ -118085,7 +118079,6 @@ xref: MESH:D019142
 xref: NCI:C36171
 xref: SNOMEDCT_US_2022_03_01:123323003
 xref: UMLS_CUI:C0282687
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:934 ! viral infectious disease
 
 [Term]
@@ -118107,7 +118100,6 @@ xref: MESH:D008379
 xref: NCI:C84883
 xref: SNOMEDCT_US_2022_03_01:123322008
 xref: UMLS_CUI:C0024788
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:934 ! viral infectious disease
 
 [Term]
@@ -123038,7 +123030,6 @@ xref: MESH:D011051
 xref: NCI:C35550
 xref: SNOMEDCT_US_2022_03_01:54839009
 xref: UMLS_CUI:C0032371
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:574 ! peripheral nervous system disease
 is_a: DOID:934 ! viral infectious disease
 
@@ -125307,7 +125298,6 @@ xref: MESH:D015658
 xref: NCI:C3108
 xref: SNOMEDCT_US_2022_03_01:86406008
 xref: UMLS_CUI:C0019693
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:934 ! viral infectious disease
 
 [Term]
@@ -144278,7 +144268,6 @@ xref: ICD9CM:266.0
 xref: MESH:D012257
 xref: SNOMEDCT_US_2022_03_01:20307000
 xref: UMLS_CUI:C0035528
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:5113 ! nutritional deficiency disease
 
 [Term]
@@ -144420,7 +144409,7 @@ xref: MESH:D007251
 xref: NCI:C53482
 xref: SNOMEDCT_US_2022_03_01:155559006
 xref: UMLS_CUI:C0021400
-is_a: DOID:10456 ! tonsillitis
+is_a: DOID:1579 ! respiratory system disease
 is_a: DOID:934 ! viral infectious disease
 
 [Term]
@@ -146239,7 +146228,6 @@ xref: MESH:D002644
 xref: NCI:C97132
 xref: SNOMEDCT_US_2022_03_01:186508005
 xref: UMLS_CUI:C0008049
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:934 ! viral infectious disease
 property_value: exactMatch MESH:D002644 xsd:string
 
@@ -146877,7 +146865,6 @@ xref: NCI:C111888
 xref: SNOMEDCT_US_2022_03_01:156328004
 xref: UMLS_CUI:C0036508
 is_a: DOID:2723 ! dermatitis
-is_a: DOID:9063 ! Ritter's disease
 
 [Term]
 id: DOID:8742
@@ -149915,7 +149902,6 @@ xref: MESH:D011146
 xref: SNOMEDCT_US_2022_03_01:402567004
 xref: UMLS_CUI:C0032633
 is_a: DOID:1383 ! sweat gland disease
-is_a: DOID:9063 ! Ritter's disease
 
 [Term]
 id: DOID:9234
@@ -152021,7 +152007,6 @@ xref: MESH:D007835
 xref: NCI:C128418
 xref: SNOMEDCT_US_2022_03_01:19065005
 xref: UMLS_CUI:C0023092
-is_a: DOID:10456 ! tonsillitis
 is_a: DOID:934 ! viral infectious disease
 
 [Term]