diff --git a/.gitignore b/.gitignore index 2a892bb..e7af6fc 100644 --- a/.gitignore +++ b/.gitignore @@ -46,3 +46,6 @@ site pull-request.md omrse/catalog-v001.xml omrse/language/catalog-v001.xml + +.idea/ +*.py diff --git a/deprecated-class-historical-taxonomy.owl b/deprecated-class-historical-taxonomy.owl new file mode 100644 index 0000000..91bd4a8 --- /dev/null +++ b/deprecated-class-historical-taxonomy.owl @@ -0,0 +1,359 @@ + + + + + + + + + + + + + + + has participant + + + + + + + + has active participant + + + + + + + + + + + + + + material entity + + + + + + + + social act + + + + + + + + human social role + + + + + + + + + obsolete OMB ethnic identity datum + true + + + + + + + + + obsolete socio-legal human social role + true + + + + + + + + + obsolete racial identity datum + true + + + + + + + + + obsolete ethnic identity datum + true + + + + + + + + + obsolete hispanic or latino identity datum + true + + + + + + + + + obsolete not hispanic or latino identity datum + true + + + + + + + + + obsolete identity datum + true + + + + + + + + + obsolete gender identity datum + true + + + + + + + + + obsolete female gender identity datum + true + + + + + + + + + obsolete male gender identity datum + true + + + + + + + + + obsolete self-identity data item + true + + + + + + + + + obsolete medical advice + true + + + + + + + + obsolete questions asking process + true + + + + + + + + + obsolete material information bearer of question text plus answer set + true + + + + + + + + + obsolete identity question asking process + true + + + + + + + + + obsolete ethnic identity question asking process + true + + + + + + + + + obsolete race identity question asking process + true + + + + + + + + answer to identity question + + + + + + + + + obsolete American Indian or Alaska Native identity datum + true + + + + + + + + + obsolete Asian identity datum + true + + + + + + + + + obsolete black or African American identity datum + true + + + + + + + + + obsolete Native Hawaiian or other Pacific Islander identity datum + true + + + + + + + + + obsolete white identity datum + true + + + + + + + + + obsolete OMB racial identity datum + true + + + + + + + + obsolete communication + true + + + + + + + + + obsolete expression of preferred language + true + + + + + + + + + obsolete non-binary gender identity datum + true + + + + + + + + is-aggregate-of + + + + + + + diff --git a/src/ontology/omrse-edit.owl b/src/ontology/omrse-edit.owl index cdb8f52..bb0fe1d 100644 --- a/src/ontology/omrse-edit.owl +++ b/src/ontology/omrse-edit.owl @@ -1342,7 +1342,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000083 "Amanda Hicks"@en) AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000083 "OMB ethnic identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000083 "obsolete OMB ethnic identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000083 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000083 obo:OMRSE_00000100) +SubClassOf(obo:OMRSE_00000083 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000084 (enrollment end date) @@ -1445,7 +1445,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:OMRSE_00000098 "A racial identity is an AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000098 "racial identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000098 "obsolete racial identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000098 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000098 obo:OMRSE_00000132) +SubClassOf(obo:OMRSE_00000098 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000099 (racial identification process) @@ -1459,7 +1459,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000100 "Amanda Hicks") AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000100 "ethnic identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000100 "obsolete ethnic identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000100 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000100 obo:OMRSE_00000132) +SubClassOf(obo:OMRSE_00000100 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000101 (ethnic identification process) @@ -1665,7 +1665,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000127 "Amanda Hicks"@en) AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000127 "OMB Hispanic or Latino identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000127 "obsolete hispanic or latino identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000127 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000127 obo:OMRSE_00000083) +SubClassOf(obo:OMRSE_00000127 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000128 (obsolete not hispanic or latino identity datum) @@ -1674,7 +1674,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000128 "Amanda Hicks"@en) AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000128 "OMB not Hispanic or Latino identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000128 "obsolete not hispanic or latino identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000128 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000128 obo:OMRSE_00000083) +SubClassOf(obo:OMRSE_00000128 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000129 (US physician assistant role) @@ -1702,7 +1702,7 @@ AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000132 "social identity informat AnnotationAssertion(dc:creator obo:OMRSE_00000132 "Amanda Hicks") AnnotationAssertion(rdfs:label obo:OMRSE_00000132 "obsolete identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000132 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000132 obo:OMRSE_00000179) +SubClassOf(obo:OMRSE_00000132 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000133 (obsolete gender identity datum) @@ -1711,7 +1711,7 @@ AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000133 "gender identity informat AnnotationAssertion(dc:creator obo:OMRSE_00000133 "Amanda Hicks") AnnotationAssertion(rdfs:label obo:OMRSE_00000133 "obsolete gender identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000133 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000133 obo:OMRSE_00000132) +SubClassOf(obo:OMRSE_00000133 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000134 (identification process) @@ -1731,7 +1731,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000138 "Amanda Hicks"@en) AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000138 "female gender identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000138 "obsolete female gender identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000138 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000138 obo:OMRSE_00000133) +SubClassOf(obo:OMRSE_00000138 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000139 (surgeon role) @@ -1753,7 +1753,7 @@ AnnotationAssertion(obo:IAO_0000119 obo:OMRSE_00000141 ""@en) AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000141 "male gender identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000141 "obsolete male gender identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000141 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000141 obo:OMRSE_00000133) +SubClassOf(obo:OMRSE_00000141 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000142 (human traveling information) @@ -1786,7 +1786,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:OMRSE_00000145 "an identity datum that h AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000145 "Amanda Hicks") AnnotationAssertion(rdfs:label obo:OMRSE_00000145 "obsolete self-identity data item"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000145 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000145 obo:OMRSE_00000132) +SubClassOf(obo:OMRSE_00000145 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000146 (employment process) @@ -1898,7 +1898,7 @@ SubClassOf(obo:OMRSE_00000161 ObjectSomeValuesFrom(obo:RO_0002087 obo:OGMS_00000 AnnotationAssertion(rdfs:label obo:OMRSE_00000162 "obsolete medical advice"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000162 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000162 obo:IAO_0021003) +SubClassOf(obo:OMRSE_00000162 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000163 (response to a question asking process) @@ -1963,7 +1963,7 @@ SubClassOf(obo:OMRSE_00000172 obo:BFO_0000034) AnnotationAssertion(rdfs:label obo:OMRSE_00000173 "obsolete material information bearer of question text plus answer set"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000173 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000173 obo:BFO_0000040) +SubClassOf(obo:OMRSE_00000173 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000174 (refusal to answer datum) @@ -1979,21 +1979,21 @@ SubClassOf(obo:OMRSE_00000175 obo:OMRSE_00000163) AnnotationAssertion(rdfs:label obo:OMRSE_00000176 "obsolete identity question asking process"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000176 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000176 obo:OMRSE_00000168) +SubClassOf(obo:OMRSE_00000176 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000177 (obsolete ethnic identity question asking process) AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000177 "http://purl.obolibrary.org/obo/OMRSE_00000199") AnnotationAssertion(rdfs:label obo:OMRSE_00000177 "obsolete ethnic identity question asking process"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000177 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000177 obo:OMRSE_00000176) +SubClassOf(obo:OMRSE_00000177 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000178 (obsolete race identity question asking process) AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000178 "http://purl.obolibrary.org/obo/OMRSE_00000200") AnnotationAssertion(rdfs:label obo:OMRSE_00000178 "obsolete race identity question asking process"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000178 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000178 obo:OMRSE_00000176) +SubClassOf(obo:OMRSE_00000178 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000179 (answer to identity question) @@ -2007,7 +2007,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000180 "Amanda Hicks") AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000180 "OMB American Indian or Alaska Native identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000180 "obsolete American Indian or Alaska Native identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000180 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000180 obo:OMRSE_00000185) +SubClassOf(obo:OMRSE_00000180 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000181 (obsolete Asian identity datum) @@ -2016,7 +2016,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000181 "Amanda Hicks") AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000181 "OMB Asian identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000181 "obsolete Asian identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000181 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000181 obo:OMRSE_00000185) +SubClassOf(obo:OMRSE_00000181 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000182 (obsolete black or African American identity datum) @@ -2025,7 +2025,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000182 "Amanda Hicks") AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000182 "OMB black or African American identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000182 "obsolete black or African American identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000182 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000182 obo:OMRSE_00000185) +SubClassOf(obo:OMRSE_00000182 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000183 (obsolete Native Hawaiian or other Pacific Islander identity datum) @@ -2034,7 +2034,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000183 "Amanda Hicks") AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000183 "OMB Native Hawaiian or other Pacific Islander identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000183 "obsolete Native Hawaiian or other Pacific Islander identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000183 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000183 obo:OMRSE_00000185) +SubClassOf(obo:OMRSE_00000183 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000184 (obsolete white identity datum) @@ -2043,7 +2043,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000184 "Amanda Hicks") AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000184 "OMB white identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000184 "obsolete white identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000184 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000184 obo:OMRSE_00000185) +SubClassOf(obo:OMRSE_00000184 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000185 (obsolete OMB racial identity datum) @@ -2052,7 +2052,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:OMRSE_00000185 "Amanda Hicks") AnnotationAssertion(obo:IAO_0100001 obo:OMRSE_00000185 "OMB racial identity information content entity"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000185 "obsolete OMB racial identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000185 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000185 obo:OMRSE_00000098) +SubClassOf(obo:OMRSE_00000185 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000186 (heavy smoker role) @@ -2147,7 +2147,7 @@ AnnotationAssertion(dc:contributor obo:OMRSE_00000196 "Matthew Diller"@en) AnnotationAssertion(dc:contributor obo:OMRSE_00000196 "William R. Hogan"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000196 "obsolete expression of preferred language"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000196 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000196 obo:OMRSE_00000192) +SubClassOf(obo:OMRSE_00000196 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00000197 (obsolete preferred language information content entity) @@ -3019,7 +3019,7 @@ AnnotationAssertion(rdfs:comment obo:OMRSE_00000507 "Alternatively: A gender ide Examples of usage: ‘Non-binary’, ‘Trigender’, ‘Agender’, ‘Genderfluid’, ‘2’ (intended to refer to a non-binary gender role)"@en) AnnotationAssertion(rdfs:label obo:OMRSE_00000507 "obsolete non-binary gender identity datum"@en) AnnotationAssertion(owl:deprecated obo:OMRSE_00000507 "true"^^xsd:boolean) -SubClassOf(obo:OMRSE_00000507 obo:OMRSE_00000133) +SubClassOf(obo:OMRSE_00000507 oboInOwl:ObsoleteClass) # Class: obo:OMRSE_00002029 (education process)