Commit dfb9fa23 authored by Vasundra Touré's avatar Vasundra Touré
Browse files

fixes to the SPHN RDF schema 2021-1

parent fe2b1c92
......@@ -250,7 +250,7 @@
<Class IRI="#Substance"/>
</Declaration>
<Declaration>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
</Declaration>
<Declaration>
<Class IRI="#SystemicArterialBloodPressure"/>
......@@ -1552,7 +1552,7 @@
</EquivalentClasses>
<EquivalentClasses>
<Class IRI="http://snomed.info/id/118555000"/>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
</EquivalentClasses>
<EquivalentClasses>
<Class IRI="http://snomed.info/id/122869004"/>
......@@ -1670,10 +1670,6 @@
<Class IRI="http://snomed.info/id/386725007"/>
<Class IRI="#BodyTemperature"/>
</EquivalentClasses>
<EquivalentClasses>
<Class IRI="http://snomed.info/id/386725007"/>
<Class IRI="https://loinc.org/rdf/8310-5"/>
</EquivalentClasses>
<EquivalentClasses>
<Class IRI="http://snomed.info/id/394658006"/>
<Class IRI="#TherapeuticArea"/>
......@@ -1935,6 +1931,10 @@
<Class IRI="#BodySite"/>
<Class IRI="https://loinc.org/rdf/39111-0"/>
</EquivalentClasses>
<EquivalentClasses>
<Class IRI="#BodyTemperature"/>
<Class IRI="https://loinc.org/rdf/8310-5"/>
</EquivalentClasses>
<EquivalentClasses>
<Class IRI="#BodyWeight"/>
<Class IRI="https://loinc.org/rdf/29463-7"/>
......@@ -2422,7 +2422,7 @@
<Class IRI="#SPHNConcept"/>
</SubClassOf>
<SubClassOf>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
<Class IRI="#SPHNConcept"/>
</SubClassOf>
<SubClassOf>
......@@ -3973,7 +3973,7 @@
<Class IRI="#RadiotherapyProcedure"/>
<Class IRI="#RespiratoryRate"/>
<Class IRI="#SimpleScore"/>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
<Class IRI="#SystemicArterialBloodPressure"/>
<Class IRI="#TNMClassification"/>
<Class IRI="#TimePattern"/>
......@@ -4247,7 +4247,7 @@
<Class IRI="#RespiratoryRate"/>
<Class IRI="#SimpleScore"/>
<Class IRI="#SubjectPseudoIdentifier"/>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
<Class IRI="#SystemicArterialBloodPressure"/>
<Class IRI="#TNMClassification"/>
<Class IRI="#TimePattern"/>
......@@ -4541,7 +4541,7 @@
<Class IRI="#ProblemCondition"/>
<Class IRI="#RadiotherapyProcedure"/>
<Class IRI="#SimpleScore"/>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
<Class IRI="#TNMClassification"/>
<Class IRI="#TimePattern"/>
<Class IRI="#TumorGrade"/>
......@@ -4566,7 +4566,7 @@
</ObjectPropertyDomain>
<ObjectPropertyDomain>
<ObjectProperty IRI="#hasSubstanceAmountUnit"/>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
</ObjectPropertyDomain>
<ObjectPropertyDomain>
<ObjectProperty IRI="#hasSubstanceCode"/>
......@@ -4614,7 +4614,7 @@
<Class IRI="#LabResult"/>
<Class IRI="#Measurement"/>
<Class IRI="#RadiotherapyProcedure"/>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
<Class IRI="#TumorSpecimen"/>
</ObjectUnionOf>
</ObjectPropertyDomain>
......@@ -5174,6 +5174,10 @@
<ObjectProperty IRI="#hasDiagnosticRadiologicExaminationMethod"/>
<Class IRI="#DiagnosticRadiologicExamination_method"/>
</ObjectPropertyRange>
<ObjectPropertyRange>
<ObjectProperty IRI="#hasDiagnosticRadiologicExaminationUnit"/>
<Class IRI="#Unit"/>
</ObjectPropertyRange>
<ObjectPropertyRange>
<ObjectProperty IRI="#hasDrug"/>
<Class IRI="#Drug"/>
......@@ -5424,7 +5428,7 @@
</ObjectPropertyRange>
<ObjectPropertyRange>
<ObjectProperty IRI="#hasSubstanceAmount"/>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
</ObjectPropertyRange>
<ObjectPropertyRange>
<ObjectProperty IRI="#hasSubstanceAmountUnit"/>
......@@ -5972,7 +5976,7 @@
<Class IRI="#GestationalAgeAtBirth"/>
<Class IRI="#InhaledOxygenConcentration"/>
<Class IRI="#Measurement"/>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
<Class IRI="#TumorSpecimen"/>
</ObjectUnionOf>
</DataPropertyDomain>
......@@ -6026,7 +6030,7 @@
</DataPropertyDomain>
<DataPropertyDomain>
<DataProperty IRI="#hasSubstanceAmountValue"/>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
</DataPropertyDomain>
<DataPropertyDomain>
<DataProperty IRI="#hasSubstanceGenericName"/>
......@@ -6070,7 +6074,7 @@
<Class IRI="#Measurement"/>
<Class IRI="#ProblemCondition"/>
<Class IRI="#SimpleScore"/>
<Class IRI="#SustanceAmount"/>
<Class IRI="#SubstanceAmount"/>
<Class IRI="#TNMClassification"/>
<Class IRI="#TumorSpecimen"/>
</ObjectUnionOf>
......@@ -6251,6 +6255,10 @@
<DataProperty IRI="#hasMeanPressureValue"/>
<Datatype abbreviatedIRI="xsd:double"/>
</DataPropertyRange>
<DataPropertyRange>
<DataProperty IRI="#hasMeasuredValue"/>
<Datatype abbreviatedIRI="xsd:double"/>
</DataPropertyRange>
<DataPropertyRange>
<DataProperty IRI="#hasNPrefix"/>
<Datatype abbreviatedIRI="xsd:string"/>
......@@ -8039,21 +8047,21 @@
<IRI>#Substance</IRI>
<Literal>Substance</Literal>
</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:label"/>
<IRI>#Surgery</IRI>
<Literal>Surgery</Literal>
</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:comment"/>
<IRI>#SustanceAmount</IRI>
<IRI>#SubstanceAmount</IRI>
<Literal>amount and unit of a substance</Literal>
</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:label"/>
<IRI>#SustanceAmount</IRI>
<IRI>#SubstanceAmount</IRI>
<Literal>Substance Amount</Literal>
</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:label"/>
<IRI>#Surgery</IRI>
<Literal>Surgery</Literal>
</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:label"/>
<IRI>#SynovialFluid</IRI>
......@@ -9767,7 +9775,7 @@
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:comment"/>
<IRI>#hasMeasuredValue</IRI>
<Literal>measured value as double or integer</Literal>
<Literal>measured value</Literal>
</AnnotationAssertion>
<AnnotationAssertion>
<AnnotationProperty abbreviatedIRI="rdfs:label"/>
......
@prefix : <https://biomedit.ch/rdf/sphn-ontology/sphn#> .
@prefix : <https://biomedit.ch/rdf/sphn-ontology/sphn> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix atc: <https://biomedit.ch/rdf/sphn-resource/atc/> .
@prefix dct: <http://purl.org/dc/terms/> .
......@@ -116,7 +116,7 @@ sphn:hasAdministrativeCase rdf:type owl:ObjectProperty ;
sphn:RadiotherapyProcedure
sphn:RespiratoryRate
sphn:SimpleScore
sphn:SustanceAmount
sphn:SubstanceAmount
sphn:SystemicArterialBloodPressure
sphn:TNMClassification
sphn:TimePattern
......@@ -699,7 +699,7 @@ sphn:hasDataProviderInstitute rdf:type owl:ObjectProperty ;
sphn:RespiratoryRate
sphn:SimpleScore
sphn:SubjectPseudoIdentifier
sphn:SustanceAmount
sphn:SubstanceAmount
sphn:SystemicArterialBloodPressure
sphn:TNMClassification
sphn:TimePattern
......@@ -1050,6 +1050,7 @@ sphn:hasDiagnosticRadiologicExaminationMethod rdf:type owl:ObjectProperty ;
sphn:hasDiagnosticRadiologicExaminationUnit rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf sphn:hasUnit ;
rdfs:domain sphn:DiagnosticRadiologicExamination ;
rdfs:range sphn:Unit ;
rdfs:comment "unit of the amount of radiation applied" ;
rdfs:label "has diagnostic radiologic examination unit" ;
skos:note "unit must be 'Gy', 'cGy', 'mCi' or 'MBq'" .
......@@ -1629,7 +1630,7 @@ sphn:hasSubjectPseudoIdentifier rdf:type owl:ObjectProperty ;
sphn:ProblemCondition
sphn:RadiotherapyProcedure
sphn:SimpleScore
sphn:SustanceAmount
sphn:SubstanceAmount
sphn:TNMClassification
sphn:TimePattern
sphn:TumorGrade
......@@ -1664,7 +1665,7 @@ sphn:hasSubstanceAmount rdf:type owl:ObjectProperty ;
sphn:DrugPrescription
)
] ;
rdfs:range sphn:SustanceAmount ;
rdfs:range sphn:SubstanceAmount ;
rdfs:comment "quantity of a substance prescribed to an individual or administered to an individual at a given time point or over a given time span continuously" ;
rdfs:label "has substance amount" .
......@@ -1672,7 +1673,7 @@ sphn:hasSubstanceAmount rdf:type owl:ObjectProperty ;
### https://biomedit.ch/rdf/sphn-ontology/sphn#hasSubstanceAmountUnit
sphn:hasSubstanceAmountUnit rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf sphn:hasUnit ;
rdfs:domain sphn:SustanceAmount ;
rdfs:domain sphn:SubstanceAmount ;
rdfs:range sphn:Unit ;
rdfs:comment "unit of the amount of a substance, e.g. mL, mg" ;
rdfs:label "has substance amount unit" .
......@@ -1778,7 +1779,7 @@ sphn:hasUnit rdf:type owl:ObjectProperty ;
sphn:LabResult
sphn:Measurement
sphn:RadiotherapyProcedure
sphn:SustanceAmount
sphn:SubstanceAmount
sphn:TumorSpecimen
)
] ;
......@@ -2281,11 +2282,12 @@ sphn:hasMeasuredValue rdf:type owl:DatatypeProperty ;
sphn:GestationalAgeAtBirth
sphn:InhaledOxygenConcentration
sphn:Measurement
sphn:SustanceAmount
sphn:SubstanceAmount
sphn:TumorSpecimen
)
] ;
rdfs:comment "measured value as double or integer" ;
rdfs:range xsd:double ;
rdfs:comment "measured value" ;
rdfs:label "has measured value" .
......@@ -2393,7 +2395,7 @@ sphn:hasStartDateTime rdf:type owl:DatatypeProperty ;
### https://biomedit.ch/rdf/sphn-ontology/sphn#hasSubstanceAmountValue
sphn:hasSubstanceAmountValue rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf sphn:hasMeasuredValue ;
rdfs:domain sphn:SustanceAmount ;
rdfs:domain sphn:SubstanceAmount ;
rdfs:range xsd:double ;
rdfs:comment "amount of a substance, e.g. 300" ;
rdfs:label "has substance amount value" .
......@@ -2484,7 +2486,7 @@ sphn:hasValue rdf:type owl:DatatypeProperty ;
sphn:Measurement
sphn:ProblemCondition
sphn:SimpleScore
sphn:SustanceAmount
sphn:SubstanceAmount
sphn:TNMClassification
sphn:TumorSpecimen
)
......@@ -2523,7 +2525,7 @@ sphn:hasValue rdf:type owl:DatatypeProperty ;
### http://snomed.info/id/118555000
<http://snomed.info/id/118555000> owl:equivalentClass sphn:SustanceAmount .
<http://snomed.info/id/118555000> owl:equivalentClass sphn:SubstanceAmount .
### http://snomed.info/id/122869004
......@@ -2643,8 +2645,7 @@ sphn:hasValue rdf:type owl:DatatypeProperty ;
### http://snomed.info/id/386725007
<http://snomed.info/id/386725007> owl:equivalentClass sphn:BodyTemperature ,
<https://loinc.org/rdf/8310-5> .
<http://snomed.info/id/386725007> owl:equivalentClass sphn:BodyTemperature .
### http://snomed.info/id/394658006
......@@ -3005,6 +3006,7 @@ sphn:BodySite rdf:type owl:Class ;
### https://biomedit.ch/rdf/sphn-ontology/sphn#BodyTemperature
sphn:BodyTemperature rdf:type owl:Class ;
owl:equivalentClass <https://loinc.org/rdf/8310-5> ;
rdfs:subClassOf sphn:Measurement ;
rdfs:comment "body temperature of the individual" ;
rdfs:label "Body Temperature" .
......@@ -3441,11 +3443,11 @@ sphn:Substance rdf:type owl:Class ;
rdfs:label "Substance" .
### https://biomedit.ch/rdf/sphn-ontology/sphn#SustanceAmount
sphn:SustanceAmount rdf:type owl:Class ;
rdfs:subClassOf sphn:SPHNConcept ;
rdfs:comment "amount and unit of a substance" ;
rdfs:label "Substance Amount" .
### https://biomedit.ch/rdf/sphn-ontology/sphn#SubstanceAmount
sphn:SubstanceAmount rdf:type owl:Class ;
rdfs:subClassOf sphn:SPHNConcept ;
rdfs:comment "amount and unit of a substance" ;
rdfs:label "Substance Amount" .
### https://biomedit.ch/rdf/sphn-ontology/sphn#SystemicArterialBloodPressure
......
......@@ -9,6 +9,14 @@ The schema is provided in turtle (.ttl) and in OWL/XML (.owl) formats.
The external terminologies referenced in the SPHN RDF schema are accessible upon request to [dcc@sib.swiss](mailto:dcc@sib.swiss).
## Change notes
New update from the 02.06.2021:
* fixing typo in __https://biomedit.ch/rdf/sphn-ontology/sphn/SustanceAmount__ changed to __https://biomedit.ch/rdf/sphn-ontology/sphn/SubstanceAmount__
* fixing meaning binding of __Body temperature (https://loinc.org/rdf/8310-5)__ from __Body temperature (observable entity) (http://snomed.info/id/386725007)__ to __Body Temperature https://biomedit.ch/rdf/sphn-ontology/BodyTemperature__
* added Range to hasMeasuredValue: __xsd:double__
* updated description of hasMeasuredValue
* added Range to hasDiagnosticExaminationUnit: __Unit__
## Documentation
......
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