# $Id: core.ttl,v 1.17 2014/09/23 09:55:56 eric Exp $ # # ericP at the keyboard @prefix rdfs: . @prefix owl: . @prefix xsd: . @prefix skos: . @prefix foaf: . @prefix bridg: . @prefix bridg999: . @prefix data: . @prefix dt: . # really . @prefix : . a owl:Ontology ; owl:imports , . ############################################################################### # primitives # # clinical trial subject or clinical care patient # bridg:StudySubject is a participation of an individual (in this case) in a trial # TemporalProfile is one of: :Acute :Subacute :Chronic # @@ separated out 'cause it appeared thrice in MetaModel, but maybe they are different beasts. # :PrognosisProfile owl:disjointUnionOf ( # administrative, clinical, prognosisProfile # :Acute :Subacute :Chronic # ) . # :Acute rdfs:subClassOf :TemporalProfile . # :Subacute rdfs:subClassOf :TemporalProfile . # :Chronic rdfs:subClassOf :TemporalProfile . # :temporalProfile a owl:ObjectProperty ; # rdfs:range :TemporalProfile . ############################################################################### # Therapeutic Interventions (left, purple) # # TherapeuticIntervention is one of :BehaviorModification :TherapeuticProcedure :MedicationAdministration :TherapeuticIntervention a owl:Class ; owl:disjointUnionOf ( :BehaviorModification :TherapeuticProcedure :MedicationAdministration ) ; # rdfs:subClassOf [ # owl:onProperty :temporalProfile ; # owl:allValuesFrom :TemporalProfile # ] . :BehaviorModification a owl:Class ; rdfs:subClassOf :TherapeuticIntervention . :TherapeuticProcedure a owl:Class ; rdfs:subClassOf :TherapeuticIntervention , bridg:PerformedProcedure . :MedicationAdministration a owl:Class ; rdfs:subClassOf :TherapeuticIntervention , bridg:PerformedSubstanceAdministration , [ a owl:Restriction ; owl:onProperty :hasMedication ; owl:cardinality 1 ] . :hasInterventionTime a owl:DatatypeProperty ; rdfs:domain :TherapeuticIntervention ; rdfs:range xsd:dateTime ; rdfs:subPropertyOf bridg:PerformedActivity.dateRange . # :Prescription is a bridg:ScheduledSubstanceAdministration\ # bridg:ConcomitantAgent :MedicationPrescription a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty :hasDosagePlan ; owl:cardinality 1 ] ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty :hasMedication ; owl:cardinality 1 ] . :Medication a owl:Class ; rdfs:subClassOf bridg:Drug . # can revert to bridg:Drug if we never need to differentiate. # TI properties :hasIntervention a owl:ObjectProperty ; rdfs:range :TherapeuticIntervention . :hasMedication a owl:ObjectProperty ; # rdfs:domain :MedicationAdministration ; # :MedicationAdministration or :MedicationPrescription rdfs:range :Medication . :hasActiveIngredient a owl:ObjectProperty ; rdfs:domain :Medication ; rdfs:range :ActiveIngredient . :ActiveIngredient a owl:Class . # see drugs.ttl for members :hasConsentForIntervention a owl:ObjectProperty ; rdfs:domain :TherapeuticIntervention ; rdfs:range :ConsentForIntervention . # @@ BRIDG-ify :hasEncounterProfile a owl:ObjectProperty ; rdfs:domain :TherapeuticIntervention ; rdfs:range :EncounterProfile . :hasDosagePlan a owl:ObjectProperty ; # @@ move to BRIDG # rdfs:domain :MedicationAdministration ; rdfs:range :DosagePlan . :hasMedicationSchedule a owl:ObjectProperty ; rdfs:domain :DosagePlan ; rdfs:range :MedicationSchedule . # :medicationRoute a owl:ObjectProperty ; # ignoring route elides coded concept for now. # rdfs:domain :Dosage ; # rdfs:range :MedicationRoute . # :MedicationRoute rdfs:subClassOf :CodedConcept. :hasMedicationQuantity a owl:ObjectProperty ; rdfs:domain :Dosage ; rdfs:range :MedicationQuantity . :MedicationQuantity a owl:Class ; rdfs:subClassOf dt:PQ. :DosagePlan a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty :hasMedicationSchedule ; owl:cardinality 1 ] , # [ a owl:Restriction ; owl:onProperty :medicationRoute ; owl:cardinality 1 ] , [ a owl:Restriction ; owl:onProperty :hasMedicationQuantity ; owl:cardinality 1 ] . :hasMedicationFrequency a owl:DatatypeProperty ; rdfs:domain :Dosage ; rdfs:range xsd:integer . :hasMedicationDuration a owl:DatatypeProperty ; rdfs:domain :Dosage ; rdfs:range xsd:float . :hasMedicationUnits a owl:DatatypeProperty ; rdfs:domain :Dosage ; rdfs:range xsd:string . :MedicationSchedule a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty :hasMedicationFrequency ; owl:cardinality 1 ] , [ a owl:Restriction ; owl:onProperty :hasMedicationDuration ; owl:cardinality 1 ] , [ a owl:Restriction ; owl:onProperty :hasMedicationUnits ; owl:cardinality 1 ] . :EncounterProfile a owl:Class . # @@ elided schedule and emergency status ############################################################################### # Observations (middle, yellow) # :hasObservation a owl:ObjectProperty ; rdfs:range :Observation ; rdfs:seeAlso bridg:AssessedActivityRelationship . # ?s :hasObservation ?o -> [ a AAR: ; AAR:.assessedPerformedActivity ?s ; AAR:assessingPerformedObservation ?o ] . :Observation a owl:Class ; owl:disjointUnionOf ( :AdministrativeObservation :ClinicalObservation ) ; rdfs:subClassOf bridg:PerformedObservation , [ a owl:Restriction ; owl:onProperty :hasObservationTime ; owl:cardinality 1 ] . # , :AdministrativeObservation a owl:Class ; rdfs:subClassOf :Observation . :ClinicalObservation a owl:Class ; rdfs:subClassOf :Observation . # Don't apply cardinality constraints to properties defined as property # chains or you'll get a "reasoner died" dialgo with e.g. (from Fact++): # org.semanticweb.owlapi.reasoner.OWLReasonerRuntimeException: Non-simple object property 'http://www.w3.org/2013/12/FDA-TA/core#hasResultValue' is used as a simple one # [ a owl:Restriction ; owl:onProperty :hasResultValue ; owl:cardinality 1 ] . :AdministrativeObservation a owl:Class . :Disposition a owl:Class ; rdfs:subClassOf :AdministrativeObservation , [ a owl:Restriction ; owl:onProperty :hasResultValue ; owl:someValuesFrom :DispositionValue ] . :DispositionValue a owl:Class ; owl:equivalentClass [ a owl:Class ; owl:oneOf ( :Deceased :LostToFollowup :AdministrativeWithdrawl :ConsentWithdrawl ) ] . :DefinedAdministrativeEndpoint a owl:Class ; rdfs:subClassOf bridg:DefinedObservation . :AdministrativeEndpoint a owl:Class ; rdfs:subClassOf :Disposition , [ a owl:Restriction ; owl:onProperty :dependsOn ; owl:minCardinality 1 ] , [ a owl:Restriction ; owl:onProperty :sparqlQuery ; owl:cardinality 1 ] . # @@ Will we use this hierarchy from cUTI? ### :Disposition :includes :Prematurely_Withdrawn_from_Treatment . ### :Prematurely_Withdrawn_from_Treatment :includes :Unacceptable_or_Intolerable_AE . ### :Prematurely_Withdrawn_from_Treatment :includes :Lack_of_Efficacy . ### :Prematurely_Withdrawn_from_Treatment :includes :Investigator_Decision . ### :Disposition :includes :Prematurely_Withdrawn_from_Study . ### :Prematurely_Withdrawn_from_Study :includes :Lost_to_Follow-Up . ### :Prematurely_Withdrawn_from_Study :includes :Administrative_Reasons . ### :Prematurely_Withdrawn_from_Study :includes :Consent_Withdrawn . # A couple standard outcome queries for all TA-protocols to use: :Death a :AdministrativeEndpoint ; :sparqlQuery """ SELECT ("Death" AS ?endpoint) (COUNT(*) AS ?count) (GROUP_CONCAT(?name) AS ?labels) WHERE { BIND (1 AS ?g) [ bridg:Subject.performingBiologicEntity [ foaf:name ?name ] ; :hasDisposition [ :hasResultValue :Deceased ] ] } GROUP BY ?g """ . :LTFU a :AdministrativeEndpoint ; :sparqlQuery """ SELECT ("LTFU" AS ?endpoint) (COUNT(*) AS ?count) (GROUP_CONCAT(?name) AS ?labels) WHERE { BIND (1 AS ?g) [ bridg:Subject.performingBiologicEntity [ foaf:name ?name ] ; :hasDisposition [ :hasResultValue :LostToFollowUp ] ] } GROUP BY ?g """ . # ClinicalObservation is one of: :Assessment :DiagnosticProcedure :QuantitativeMeasurement :SignsAndSymptoms :ClinicalObservation owl:disjointUnionOf ( :Assessment :SingleObservation :InferrableDiagnosis ) . :Assessment a owl:Class ; rdfs:subClassOf :ClinicalObservation . :SingleObservation a owl:Class ; rdfs:subClassOf :ClinicalObservation . :InferrableDiagnosis a owl:Class ; rdfs:subClassOf :ClinicalObservation . # :Assessment described below :SingleObservation owl:unionOf ( :DiagnosticProcedure :QuantitativeMeasurement :SignsAndSymptoms ) . :DiagnosticProcedure a owl:Class ; rdfs:subClassOf :SingleObservation . :QuantitativeMeasurement a owl:Class ; rdfs:subClassOf :SingleObservation . :SignsAndSymptoms a owl:Class ; rdfs:subClassOf :SingleObservation . :isJustifiedBy a owl:ObjectProperty ; # @@reasonCode rdfs:domain :DiagnosticProcedure ; rdfs:range :ClinicalObservation . :hasLabReport a owl:ObjectProperty ; rdfs:domain :DiagnosticProcedure ; rdfs:range :LabReport . :specimentAccepability a owl:DatatypeProperty ; rdfs:range [ a owl:Class; owl:unionOf (true false) ] . :performedAtLocalOrCentralLab a owl:ObjectProperty ; rdfs:range [ a owl:Class ; owl:oneOf ( :LocalLab :CentralLab ) ] . :LabTest a owl:Class ; rdfs:subClassOf :QuantitativeMeasurement , # @@ subclass QuantitativeMeasurement for lab reports? [ a owl:Restriction ; owl:onProperty :specimentAccepability ; owl:maxCardinality 1 ] , [ a owl:Restriction ; owl:onProperty :performedAtLocalOrCentralLab ; owl:maxCardinality 1 ] . :LabReport a owl:Class ; rdfs:subClassOf bridg:PerformedObservationResult . :PathologyReport a owl:Class ; rdfs:subClassOf :QuantitativeMeasurement . :hasClassification a owl:ObjectProperty ; rdfs:domain :PathologyReport . # can have any value . :hasPathologyFinding a owl:ObjectProperty ; rdfs:domain :PathologyReport . # can have any value . :SignsAndSymptoms a owl:Class ; rdfs:subClassOf :SingleObservation . # [] a owl:AllDisjointClasses ; # @@ needed? # owl:members ( :Assessment :DiagnosticProcedure :QuantitativeMeasurement :SignsAndSymptoms ) . # Observation properties :monitorsEffectivenessOf a owl:ObjectProperty ; rdfs:domain :SingleOutcomeAssessment ; rdfs:range :TherapeuticIntervention . # Observation properties # :monitorsStateOf a owl:ObjectProperty ; # rdfs:domain :SingleOutcomeAssessment ; # rdfs:range :PhysiologicalProcess . # # :hasPlaceOfMeasurement a owl:ObjectProperty ; # rdfs:domain :ClinicalObservation ; # rdfs:range :PlaceOfMeasurement . # :PlaceOfMeasurement a owl:Class . # # :hasMeasurementMethodology a owl:ObjectProperty ; # rdfs:domain :ClinicalObservation ; # rdfs:range :MeasurementMethodology . # :MeasurementMethodology a owl:Class . # Information Model imposed on Observation. :hasObservationTime a owl:DatatypeProperty ; rdfs:domain :Observation ; rdfs:range xsd:dateTime . :Assessment a owl:Class ; rdfs:subClassOf :ClinicalObservation , [ a owl:Restriction ; owl:onProperty :hasObservation ; owl:minCardinality 1 ] . :hasObservation a owl:ObjectProperty ; # rdfs:domain :Assessment ; # lots of things have observations. rdfs:range :ClinicalObservation . # Outcome Assessment - a conclusions (disposition) based on a set of # observations before and after a clinical intervention. Outcome # assessments are themselves observations, permitting them to provide # (before/after) evidence for further assessments. :beforeIntervention a owl:ObjectProperty ; rdfs:subPropertyOf :hasObservation ; rdfs:domain :SingleOutcomeAssessment ; rdfs:range :ClinicalObservation . :afterIntervention a owl:ObjectProperty ; rdfs:subPropertyOf :hasObservation ; rdfs:domain :SingleOutcomeAssessment ; rdfs:range :ClinicalObservation . :hasResultValue a owl:ObjectProperty ; # BRIDG structure is # ?r a bridg:PerformedObservationResults ; # bridg:PerformedObservationResult.producingPerformedObservation ?o . # ?o a bridg:PerformedObservation ; # bridg:PerformedObservation.resultedPerformedObservationResult ?r . # !inv # # per DL Query: bridg:PerformedObservation.resultedPerformedObservationResult some bridg:PerformedClinicalResult # !!! uncomment for mapping to BRIDG ObservationResults. # commented because it makes Fact++ crawl. #owl:propertyChainAxiom ( bridg:PerformedObservation.resultedPerformedObservationResult bridg:PerformedObservationResult.value ) ; rdfs:domain :Observation ; rdfs:range :SingleOutcomeAssessmentValue . :SingleOutcomeAssessmentValue a owl:Class . :lastInterventionToAfterDuration a owl:DatatypeProperty ; rdfs:range xsd:string . # P10DT15H !! xsd:duration :hasOutcomeAssessment a owl:ObjectProperty ; # rdfs:domain :Subject ; or :EfficacyEndpoint rdfs:range :SingleOutcomeAssessment . :hasEndpoint a owl:ObjectProperty ; rdfs:domain :TAProtocol ; rdfs:range :EfficacyEndpoint . :TAProtocol a owl:Class ; rdfs:subClassOf bridg:StudyProtocol . :hasObservationType a owl:ObjectProperty . :hasInterventionType a owl:ObjectProperty . :DefinedSingleOutcomeAssessment a owl:Class ; rdfs:subClassOf bridg:DefinedObservation , [ a owl:Restriction ; owl:onProperty :hasObservationType ; owl:minCardinality 1 ] , [ a owl:Restriction ; owl:onProperty :hasInterventionType ; owl:minCardinality 1 ] , [ a owl:Restriction ; owl:onProperty :lastInterventionToAfterDuration ; owl:maxCardinality 1 ] . :SingleOutcomeAssessment a owl:Class ; rdfs:subClassOf :Assessment , [ a owl:Restriction ; owl:onProperty :beforeIntervention ; owl:minCardinality 1 ] , [ a owl:Restriction ; owl:onProperty :hasIntervention ; owl:minCardinality 1 ] , [ a owl:Restriction ; owl:onProperty :afterIntervention ; owl:minCardinality 1 ] . :DeathAssessment a owl:Class ; rdfs:subClassOf :SingleOutcomeAssessment ; rdfs:label "death assessment" ; skos:definition "attests that hasObservation identifies evidence of a subject's death." ; owl:equivalentClass [ a owl:Class ; owl:oneOf ( :CardioVascularDeath :NonCardioVascularDeath ) ] . :CardiacDeath a owl:Class ; rdfs:subClassOf :DeathAssessment ; skos:defintion "Death defined as the irreversible cessation of circulatory and respiratory functions. Death is declared in accordance with hospital policy and applicable state and local statues or regulation." . :CardioVascularDeath a owl:Class ; rdfs:subClassOf :DeathAssessment ; owl:equivalentClass [ a owl:Class ; owl:oneOf ( :HeartFailure :MyocardialInfarction :Stroke :CardiovascularHemorrhage :SuddenCardiacDeath :CardiovascularProcedures :Non-CNSSystemicEmbolism :CardiacTamponade :DocumentedAsystole :SystemicArterialEmbolicEvent :PulmonaryEmbolism :OtherCardiovascular ) ] . :HeartFailure a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :MyocardialInfarction a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :Stroke a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :CardiovascularHemorrhage a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :SuddenCardiacDeath a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :CardiovascularProcedures a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :Non-CNSSystemicEmbolism a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :CardiacTamponade a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :DocumentedAsystole a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :SystemicArterialEmbolicEvent a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :PulmonaryEmbolism a owl:Class ; rdfs:subClassOf :CardioVascularDeath . :OtherCardiovascular a owl:Class ; rdfs:subClassOf :CardioVascularDeath . #:OtherCardiac :NonCardioVascularDeath a owl:Class ; rdfs:subClassOf :DeathAssessment ; owl:equivalentClass [ a owl:Class ; owl:oneOf ( :PulmonaryDeath :RenalDeath :GastrointestinalDeath :HepatobiliaryDeath :PancreaticDeath :InfectionDeath :InflammatoryDeath :Hemorrhage_OtherDeath :CardiovascularBleedingOrStrokeDeath :Non-CVProcedureOrSurgeryDeath :TraumaDeath :SuicideDeath :NonPrescriptionDrugReactionOrOverdoseDeath :PrescriptionDrugReactionOverdoseOrAnaphylaxisDeath :Neurological_non-cardiovascularDeath :CancerDeath :TraumaDeath :InfectionDeath :RespiratoryFailureDeath :Non-bleedingStudyDrugToxicityDeath :Non-CNSBleedingDeath :CNSBleedingDeath :PeripheralEmbolismDeath :AorticDissectionOrRupture :OtherDeath ) ] . :PulmonaryDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :RenalDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :GastrointestinalDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :HepatobiliaryDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :PancreaticDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :InfectionDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :InflammatoryDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :Hemorrhage_OtherDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :CardiovascularBleedingOrStrokeDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :Non-CVProcedureOrSurgeryDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :TraumaDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :SuicideDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :NonPrescriptionDrugReactionOrOverdoseDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :PrescriptionDrugReactionOverdoseOrAnaphylaxisDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :Neurological_non-cardiovascularDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :CancerDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :TraumaDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :InfectionDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :RespiratoryFailureDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :Non-bleedingStudyDrugToxicityDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :Non-CNSBleedingDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :CNSBleedingDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :PeripheralEmbolismDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :AorticDissectionOrRuptureDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :OtherDeath a owl:Class ; rdfs:subClassOf :NonCardioVascularDeath . :FunctionOutcomeAssessment a owl:Class ; rdfs:subClassOf :SingleOutcomeAssessment . :DefinedEfficacyEndpoint a owl:Class ; rdfs:subClassOf bridg:DefinedObservation . :Endpoint a owl:Class ; owl:disjointUnionOf ( :SafetyEndpoint :EfficacyEndpoint ) ; rdfs:subClassOf :Assessment , [ a owl:Restriction ; owl:onProperty :hasObservation ; owl:allValuesFrom :SingleOutcomeAssessment ] , [ a owl:Restriction ; owl:onProperty :dependsOn ; owl:minCardinality 1 ] , [ a owl:Restriction ; owl:onProperty :sparqlQuery ; owl:cardinality 1 ] . :EfficacyEndpoint rdfs:subClassOf :Endpoint . :SafetyEndpoint rdfs:subClassOf :Endpoint . :dependsOn a owl:DatatypeProperty . :sparqlQuery a owl:DatatypeProperty ; rdfs:range xsd:string . :confirms a owl:DatatypeProperty ; rdfs:domain :SingleOutcomeAssessment . :PositiveOutcome a owl:Class ; rdfs:subClassOf :SingleOutcomeAssessment . :NegativeOutcome a owl:Class ; rdfs:subClassOf :SingleOutcomeAssessment . #:DeathOtherReasons rdfs:subClassOf :EfficacyEndpoint . # Diagnosis ############################################################################### # PhysiologicalProcess (right, blue) # # :PhysiologicalProcess a owl:Class . # :PhysiologicalProcess # owl:disjointUnionOf ( # :NormalPhysiologicalProcess :PathoPhysiologicalProcess # ) . # :NormalPhysiologicalProcess a owl:Class ; rdfs:subClassOf :PhysiologicalProcess . # :PathoPhysiologicalProcess a owl:Class ; rdfs:subClassOf :PhysiologicalProcess . :hasSpecimen a owl:ObjectProperty . :ScreenValue a owl:Class ; rdfs:subClassOf :SingleOutcomeAssessmentValue , [ a owl:Restriction ; owl:oneOf (:Positive :Negative :Unknown) ] . bridg999:StudySubject.involvingScheduledSubstanceAdministration a owl:ObjectProperty ; rdfs:domain bridg:StudySubject ; rdfs:range bridg:ScheduledSubstanceAdministration . bridg999:performedSpecimenCollection.material a owl:ObjectProperty ; rdfs:domain bridg:PerformedSpecimenCollection ; rdfs:range bridg:Biologic . bridg999:PerformedSubstanceExtraction.usedBiologic a owl:ObjectProperty ; rdfs:label "uses"^^xsd:string ; rdfs:domain bridg:PerformedSubstanceExtraction ; rdfs:range bridg:Biologic ; rdfs:subPropertyOf bridg:associationProperty ; # owl:inverseOf bridg999:Biologic.usingPerformedSubstanceExtraction . [ a owl:AllDisjointClasses ; owl:members ( bridg:PerformedObservation bridg:DefinedObservation ) ] . # @@ need to merge these ^v [ a owl:AllDisjointClasses ; owl:members ( bridg:PerformedObservationResult bridg:DefinedObservationResult ) ] .