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Merge pull request #27 from KnowledgeCaptureAndDiscovery/update_core
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Fix Typos
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@hvarg
hvarg authored Jun 12, 2024
2 parents 7282da9 + 0f69e42 commit e5e8c97
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Showing 3 changed files with 79 additions and 43 deletions.
82 changes: 59 additions & 23 deletions development/CohortOntology.owl
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<terms:contributor>MiHyun Jang</terms:contributor>
<terms:contributor>Michael Bornstein</terms:contributor>
<terms:contributor>Ryan Espiritu</terms:contributor>
<terms:contributor>Aarya Vakharia</terms:contributor>
<terms:creator>Daniel Garijo</terms:creator>
<terms:creator>Haripriya Dharmala</terms:creator>
<terms:creator>Hernan Vargas</terms:creator>
<terms:creator>Joanna Bright</terms:creator>
<terms:creator>Josh Boyd</terms:creator>
<terms:creator>Neda Jahanshad</terms:creator>
<terms:creator>Wesley Surento</terms:creator>
<terms:creator>Yolanda Gil</terms:creator>
<terms:creator>Hernan Vargas</terms:creator>
<terms:description xml:lang="en">An ontology to describe cohorts of patients participating in ENIGMA projects.</terms:description>
<terms:license rdf:resource="http://creativecommons.org/licenses/by/2.0/"/>
<terms:title xml:lang="en">The Cohort Ontology</terms:title>
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<!-- https://w3id.org/enigma#has_location -->

<owl:ObjectProperty rdf:about="https://w3id.org/enigma#has_location">
<rdfs:domain rdf:resource="https://w3id.org/enigma#Cohort"/>
<rdfs:range rdf:resource="https://w3id.org/enigma#Location"/>
<rdfs:comment>The location of the cohort</rdfs:comment>
<rdfs:label>has location</rdfs:label>
</owl:ObjectProperty>



<!-- https://w3id.org/enigma#isPartOfCohort -->

<owl:ObjectProperty rdf:about="https://w3id.org/enigma#isPartOfCohort">
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<rdfs:comment xml:lang="en">Describes the ancestry of the participants of the cohort</rdfs:comment>
<rdfs:label xml:lang="en">has ancestry</rdfs:label>
</owl:DatatypeProperty>



<!-- https://w3id.org/enigma#hasBriefDescription -->
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</owl:DatatypeProperty>



<!-- https://w3id.org/enigma#hasExclusionCriteria -->

<owl:DatatypeProperty rdf:about="https://w3id.org/enigma#hasExclusionCriteria">
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<!-- https://w3id.org/enigma#has_city -->

<owl:DatatypeProperty rdf:about="https://w3id.org/enigma#has_city">
<rdfs:domain rdf:resource="https://w3id.org/enigma#Location"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
<rdfs:comment>City in which cohort is located</rdfs:comment>
<rdfs:label>has city</rdfs:label>
</owl:DatatypeProperty>



<!-- https://w3id.org/enigma#has_country -->

<owl:DatatypeProperty rdf:about="https://w3id.org/enigma#has_country">
<rdfs:domain rdf:resource="https://w3id.org/enigma#Location"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
<rdfs:comment>Country in which cohort is located</rdfs:comment>
<rdfs:label>has country</rdfs:label>
</owl:DatatypeProperty>



<!-- https://w3id.org/enigma#has_latitude -->

<owl:DatatypeProperty rdf:about="https://w3id.org/enigma#has_latitude">
<rdfs:domain rdf:resource="https://w3id.org/enigma#Location"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
<rdfs:comment>The latitude of the cohort</rdfs:comment>
<rdfs:label>has latitude</rdfs:label>
</owl:DatatypeProperty>



<!-- https://w3id.org/enigma#has_longitude -->

<owl:DatatypeProperty rdf:about="https://w3id.org/enigma#has_longitude">
<rdfs:domain rdf:resource="https://w3id.org/enigma#Location"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
<rdfs:comment>The longitude of the cohort</rdfs:comment>
<rdfs:label>has longitude</rdfs:label>
</owl:DatatypeProperty>



<!-- https://w3id.org/enigma#isOverallCohort -->

<owl:DatatypeProperty rdf:about="https://w3id.org/enigma#isOverallCohort">
Expand Down Expand Up @@ -1285,17 +1343,6 @@ NOTE: study design options are mutually exclusive for Cohort Groups but not Proj



<!-- https://w3id.org/enigma#City -->

<owl:Class rdf:about="https://w3id.org/enigma#City">
<rdfs:subClassOf rdf:resource="https://w3id.org/enigma#Location"/>
<vann:example xml:lang="en">Los Angeles</vann:example>
<rdfs:comment xml:lang="en">City in which a cohort is located</rdfs:comment>
<rdfs:label xml:lang="en">City</rdfs:label>
</owl:Class>



<!-- https://w3id.org/enigma#Cohort -->

<owl:Class rdf:about="https://w3id.org/enigma#Cohort">
Expand Down Expand Up @@ -1334,17 +1381,6 @@ Example: STELLENBOCH_proj_FS for the Freesurfer project</rdfs:comment>



<!-- https://w3id.org/enigma#Country -->

<owl:Class rdf:about="https://w3id.org/enigma#Country">
<rdfs:subClassOf rdf:resource="https://w3id.org/enigma#Location"/>
<vann:example xml:lang="en">United States</vann:example>
<rdfs:comment xml:lang="en">Country in which a cohort is located</rdfs:comment>
<rdfs:label xml:lang="en">Country</rdfs:label>
</owl:Class>



<!-- https://w3id.org/enigma#Covariates -->

<owl:Class rdf:about="https://w3id.org/enigma#Covariates">
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32 changes: 16 additions & 16 deletions development/MedicationOntology.owl
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<Prefix name="vaem" IRI="http://www.linkedmodel.org/schema/vaem#"/>
<Prefix name="vann" IRI="http://purl.org/vocab/vann/"/>
<Prefix name="terms" IRI="http://purl.org/dc/terms/"/>
<Annotation>
<AnnotationProperty abbreviatedIRI="terms:contributor"/>
<Literal>Aarya Vakharia</Literal>
</Annotation>
<Annotation>
<AnnotationProperty abbreviatedIRI="terms:contributor"/>
<Literal>Agnes McMahon</Literal>
Expand All @@ -40,10 +44,6 @@
<AnnotationProperty abbreviatedIRI="terms:contributor"/>
<Literal>Ryan Espiritu</Literal>
</Annotation>
<Annotation>
<AnnotationProperty abbreviatedIRI="terms:contributor"/>
<Literal>Aarya Vakharia</Literal>
</Annotation>
<Annotation>
<AnnotationProperty abbreviatedIRI="terms:creator"/>
<Literal>Daniel Garijo</Literal>
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<DataProperty IRI="#AtypicalAntipsychoticUseLifetime"/>
</Declaration>
<Declaration>
<DataProperty IRI="#CZP_Use_Current"/>
<DataProperty IRI="#CPZ_Use_Current"/>
</Declaration>
<Declaration>
<DataProperty IRI="#CZP_Use_Lifetime"/>
<DataProperty IRI="#CPZ_Use_Lifetime"/>
</Declaration>
<Declaration>
<DataProperty IRI="#LithiumUseCurrent"/>
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<Class IRI="#Medication"/>
</DataPropertyDomain>
<DataPropertyDomain>
<DataProperty IRI="#CZP_Use_Current"/>
<DataProperty IRI="#CPZ_Use_Current"/>
<Class IRI="#Medication"/>
</DataPropertyDomain>
<DataPropertyDomain>
<DataProperty IRI="#CZP_Use_Lifetime"/>
<DataProperty IRI="#CPZ_Use_Lifetime"/>
<Class IRI="#Medication"/>
</DataPropertyDomain>
<DataPropertyDomain>
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<Datatype abbreviatedIRI="xsd:boolean"/>
</DataPropertyRange>
<DataPropertyRange>
<DataProperty IRI="#CZP_Use_Current"/>
<DataProperty IRI="#CPZ_Use_Current"/>
<Datatype abbreviatedIRI="xsd:boolean"/>
</DataPropertyRange>
<DataPropertyRange>
<DataProperty IRI="#CZP_Use_Lifetime"/>
<DataProperty IRI="#CPZ_Use_Lifetime"/>
<Datatype abbreviatedIRI="xsd:boolean"/>
</DataPropertyRange>
<DataPropertyRange>
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</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:comment"/>
<IRI>#CZP_Use_Current</IRI>
<IRI>#CPZ_Use_Current</IRI>
<Literal>Chlorpromazine use (or its equivalents), a 1st generation antipsychotic at time of study</Literal>
</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:label"/>
<IRI>#CZP_Use_Current</IRI>
<Literal>CZP Use Current</Literal>
<IRI>#CPZ_Use_Current</IRI>
<Literal>CPZ Use Current</Literal>
</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:comment"/>
<IRI>#CZP_Use_Lifetime</IRI>
<IRI>#CPZ_Use_Lifetime</IRI>
<Literal>Chlorpromazine use (or its equivalents), a 1st generation antipsychotic during lifetime</Literal>
</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:label"/>
<IRI>#CZP_Use_Lifetime</IRI>
<Literal>CZP Use Lifetime</Literal>
<IRI>#CPZ_Use_Lifetime</IRI>
<Literal>CPZ Use Lifetime</Literal>
</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:comment"/>
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8 changes: 4 additions & 4 deletions development/Neuropsychiatric.owl
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Expand Up @@ -11,11 +11,11 @@
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="https://w3id.org/enigma">
<owl:versionIRI rdf:resource="https://w3id.org/enigma/neuropsychiatric/1.1.0"/>
<terms:contributor>Aarya Vakharia</terms:contributor>
<terms:contributor>Agnes McMahon</terms:contributor>
<terms:contributor>MiHyun Jang</terms:contributor>
<terms:contributor>Michael Bornstein</terms:contributor>
<terms:contributor>Ryan Espiritu</terms:contributor>
<terms:contributor>Aarya Vakharia</terms:contributor>
<terms:creator>Daniel Garijo</terms:creator>
<terms:creator>Haripriya Dharmala</terms:creator>
<terms:creator>Joanna Bright</terms:creator>
Expand Down Expand Up @@ -799,14 +799,14 @@



<!-- https://w3id.org/enigma#PANNS -->
<!-- https://w3id.org/enigma#PANSS -->

<owl:DatatypeProperty rdf:about="https://w3id.org/enigma#PANNS">
<owl:DatatypeProperty rdf:about="https://w3id.org/enigma#PANSS">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topDataProperty"/>
<rdfs:domain rdf:resource="https://w3id.org/enigma#Neuropsychiatric"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
<rdfs:comment>Positive and Negative Syndrome Scale</rdfs:comment>
<rdfs:label>PANNS</rdfs:label>
<rdfs:label>PANSS</rdfs:label>
</owl:DatatypeProperty>


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