Observation.shex

ShEx statement for observation

PREFIX fhir: <http://hl7.org/fhir/> 
PREFIX fhirvs: <http://hl7.org/fhir/ValueSet/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 

IMPORT <code.shex>
IMPORT <time.shex>
IMPORT <Group.shex>
IMPORT <Range.shex>
IMPORT <Ratio.shex>
IMPORT <Device.shex>
IMPORT <Period.shex>
IMPORT <Timing.shex>
IMPORT <string.shex>
IMPORT <Patient.shex>
IMPORT <instant.shex>
IMPORT <boolean.shex>
IMPORT <integer.shex>
IMPORT <Location.shex>
IMPORT <dateTime.shex>
IMPORT <Quantity.shex>
IMPORT <Specimen.shex>
IMPORT <markdown.shex>
IMPORT <CarePlan.shex>
IMPORT <Resource.shex>
IMPORT <CareTeam.shex>
IMPORT <canonical.shex>
IMPORT <Reference.shex>
IMPORT <Procedure.shex>
IMPORT <Substance.shex>
IMPORT <Encounter.shex>
IMPORT <Identifier.shex>
IMPORT <Medication.shex>
IMPORT <Attachment.shex>
IMPORT <Annotation.shex>
IMPORT <SampledData.shex>
IMPORT <Organization.shex>
IMPORT <Practitioner.shex>
IMPORT <DeviceMetric.shex>
IMPORT <GenomicStudy.shex>
IMPORT <ImagingStudy.shex>
IMPORT <Immunization.shex>
IMPORT <BodyStructure.shex>
IMPORT <DeviceRequest.shex>
IMPORT <RelatedPerson.shex>
IMPORT <DomainResource.shex>
IMPORT <NutritionOrder.shex>
IMPORT <ServiceRequest.shex>
IMPORT <CodeableConcept.shex>
IMPORT <BackboneElement.shex>
IMPORT <NutritionProduct.shex>
IMPORT <PractitionerRole.shex>
IMPORT <ImagingSelection.shex>
IMPORT <MolecularSequence.shex>
IMPORT <MedicationRequest.shex>
IMPORT <DocumentReference.shex>
IMPORT <MedicationDispense.shex>
IMPORT <MedicationStatement.shex>
IMPORT <QuestionnaireResponse.shex>
IMPORT <MedicationAdministration.shex>
IMPORT <BiologicallyDerivedProduct.shex>
IMPORT <ImmunizationRecommendation.shex>

start=@<Observation> AND {fhir:nodeRole [fhir:treeRoot]}

# Measurements and simple assertions
<Observation> EXTENDS @<DomainResource> CLOSED {   
    a [fhir:Observation]?;fhir:nodeRole [fhir:treeRoot]?;

    fhir:identifier @<OneOrMore_Identifier>?;  # Business Identifier for observation
    fhir:instantiates (@<canonical>  AND {fhir:link @<ObservationDefinition> })  OR 
    			(@<Reference>  AND {fhir:link @<ObservationDefinition> })  ?;  # Instantiates FHIR 
                                            # ObservationDefinition 
    fhir:basedOn @<OneOrMore_Reference_CarePlan_OR_DeviceRequest_OR_ImmunizationRecommendation_OR_MedicationRequest_OR_NutritionOrder_OR_ServiceRequest>?;  # Fulfills plan, proposal or order
    fhir:triggeredBy @<OneOrMore_Observation.triggeredBy>?;  # Triggering observation(s)
    fhir:partOf @<OneOrMore_Reference_GenomicStudy_OR_ImagingStudy_OR_Immunization_OR_MedicationAdministration_OR_MedicationDispense_OR_MedicationStatement_OR_Procedure>?;  # Part of referenced event
    fhir:status @<code> AND
    	{fhir:v @fhirvs:observation-status};  # registered | specimen-in-process | 
                                            # preliminary | final | amended | 
                                            # corrected | appended | cancelled | 
                                            # entered-in-error | unknown | 
                                            # cannot-be-obtained 
    fhir:category @<OneOrMore_CodeableConcept>?;  # Classification of  type of 
                                            # observation 
    fhir:code @<CodeableConcept>;           # Type of observation (code / type)
    fhir:subject @<Reference> AND {fhir:link 
    			@<BiologicallyDerivedProduct> OR 
    			@<Device> OR 
    			@<Group> OR 
    			@<Location> OR 
    			@<Medication> OR 
    			@<NutritionProduct> OR 
    			@<Organization> OR 
    			@<Patient> OR 
    			@<Practitioner> OR 
    			@<Procedure> OR 
    			@<Substance> ? }?;  # Who and/or what the observation is 
                                            # about 
    fhir:focus @<OneOrMore_Reference_Resource>?;  # What the observation is about, 
                                            # when it is not about the subject 
                                            # of record 
    fhir:encounter @<Reference> AND {fhir:link 
    			@<Encounter> ? }?;  # Healthcare event during which this 
                                            # observation is made 
    fhir:effective @<dateTime>  OR 
    			@<Period>  OR 
    			@<Timing>  OR 
    			@<instant>  ?;  # Clinically relevant 
                                            # time/time-period for observation 
    fhir:issued @<instant>?;                # Date/Time this version was made 
                                            # available 
    fhir:performer @<OneOrMore_Reference_CareTeam_OR_Organization_OR_Patient_OR_Practitioner_OR_PractitionerRole_OR_RelatedPerson>?;  # Who is responsible for the 
                                            # observation 
    fhir:value @<Quantity>  OR 
    			@<CodeableConcept>  OR 
    			@<string>  OR 
    			@<boolean>  OR 
    			@<integer>  OR 
    			@<Range>  OR 
    			@<Ratio>  OR 
    			@<SampledData>  OR 
    			@<time>  OR 
    			@<dateTime>  OR 
    			@<Period>  OR 
    			@<Attachment>  OR 
    			(@<Reference>  AND {fhir:link @<MolecularSequence> })  ?;  # Actual result
    fhir:dataAbsentReason @<CodeableConcept>?;  # Why the result value is missing
    fhir:interpretation @<OneOrMore_CodeableConcept>?;  # High, low, normal, etc
    fhir:note @<OneOrMore_Annotation>?;     # Comments about the observation
    fhir:bodySite @<CodeableConcept>?;      # Observed body part
    fhir:bodyStructure @<Reference> AND {fhir:link 
    			@<BodyStructure> ? }?;  # Observed body structure
    fhir:method @<CodeableConcept>?;        # How it was done
    fhir:specimen @<Reference> AND {fhir:link 
    			@<Group> OR 
    			@<Specimen> ? }?;  # Specimen used for this observation
    fhir:device @<Reference> AND {fhir:link 
    			@<Device> OR 
    			@<DeviceMetric> ? }?;  # A reference to the device that 
                                            # generates the measurements or the 
                                            # device settings for the device 
    fhir:referenceRange @<OneOrMore_Observation.referenceRange>?;  # Provides guide for interpretation
    fhir:hasMember @<OneOrMore_Reference_MolecularSequence_OR_Observation_OR_QuestionnaireResponse>?;  # Related resource that belongs to 
                                            # the Observation group 
    fhir:derivedFrom @<OneOrMore_Reference_DocumentReference_OR_GenomicStudy_OR_ImagingSelection_OR_ImagingStudy_OR_MolecularSequence_OR_Observation_OR_QuestionnaireResponse>?;  # Related resource from which the 
                                            # observation is made 
    fhir:component @<OneOrMore_Observation.component>?;  # Component results
}  

# Component results
<Observation.component> EXTENDS @<BackboneElement> CLOSED {   
    fhir:code @<CodeableConcept>;           # Type of component observation 
                                            # (code / type) 
    fhir:value @<Quantity>  OR 
    			@<CodeableConcept>  OR 
    			@<string>  OR 
    			@<boolean>  OR 
    			@<integer>  OR 
    			@<Range>  OR 
    			@<Ratio>  OR 
    			@<SampledData>  OR 
    			@<time>  OR 
    			@<dateTime>  OR 
    			@<Period>  OR 
    			@<Attachment>  OR 
    			(@<Reference>  AND {fhir:link @<MolecularSequence> })  ?;  # Actual component result
    fhir:dataAbsentReason @<CodeableConcept>?;  # Why the component result value is 
                                            # missing 
    fhir:interpretation @<OneOrMore_CodeableConcept>?;  # High, low, normal, etc
    fhir:referenceRange @<OneOrMore_Observation.referenceRange>?;  # Provides guide for interpretation 
                                            # of component result value 
}  

# Provides guide for interpretation
<Observation.referenceRange> EXTENDS @<BackboneElement> CLOSED {   
    fhir:low @<Quantity>?;                  # Low Range, if relevant
    fhir:high @<Quantity>?;                 # High Range, if relevant
    fhir:normalValue @<CodeableConcept>?;   # Normal value, if relevant
    fhir:type @<CodeableConcept>?;          # Reference range qualifier
    fhir:appliesTo @<OneOrMore_CodeableConcept>?;  # Reference range population
    fhir:age @<Range>?;                     # Applicable age range, if relevant
    fhir:text @<markdown>?;                 # Text based reference range in an 
                                            # observation 
}  

# Triggering observation(s)
<Observation.triggeredBy> EXTENDS @<BackboneElement> CLOSED {   
    fhir:observation @<Reference> AND {fhir:link 
    			@<Observation> ? };  # Triggering observation
    fhir:type @<code> AND
    	{fhir:v @fhirvs:observation-triggeredbytype};  # reflex | repeat | re-run
    fhir:reason @<string>?;                 # Reason that the observation was 
                                            # triggered 
}  

#---------------------- Cardinality Types (OneOrMore) -------------------
<OneOrMore_Identifier> CLOSED {
    rdf:first @<Identifier>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Identifier> 
}
<OneOrMore_Reference_CarePlan_OR_DeviceRequest_OR_ImmunizationRecommendation_OR_MedicationRequest_OR_NutritionOrder_OR_ServiceRequest> CLOSED {
    rdf:first @<Reference> AND {fhir:link 
			@<CarePlan> OR 
			@<DeviceRequest> OR 
			@<ImmunizationRecommendation> OR 
			@<MedicationRequest> OR 
			@<NutritionOrder> OR 
			@<ServiceRequest> } ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Reference_CarePlan_OR_DeviceRequest_OR_ImmunizationRecommendation_OR_MedicationRequest_OR_NutritionOrder_OR_ServiceRequest> 
}
<OneOrMore_Observation.triggeredBy> CLOSED {
    rdf:first @<Observation.triggeredBy>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Observation.triggeredBy> 
}
<OneOrMore_Reference_GenomicStudy_OR_ImagingStudy_OR_Immunization_OR_MedicationAdministration_OR_MedicationDispense_OR_MedicationStatement_OR_Procedure> CLOSED {
    rdf:first @<Reference> AND {fhir:link 
			@<GenomicStudy> OR 
			@<ImagingStudy> OR 
			@<Immunization> OR 
			@<MedicationAdministration> OR 
			@<MedicationDispense> OR 
			@<MedicationStatement> OR 
			@<Procedure> } ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Reference_GenomicStudy_OR_ImagingStudy_OR_Immunization_OR_MedicationAdministration_OR_MedicationDispense_OR_MedicationStatement_OR_Procedure> 
}
<OneOrMore_CodeableConcept> CLOSED {
    rdf:first @<CodeableConcept>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_CodeableConcept> 
}
<OneOrMore_Reference_Resource> CLOSED {
    rdf:first @<Reference> AND {fhir:link 
			@<Resource> } ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Reference_Resource> 
}
<OneOrMore_Reference_CareTeam_OR_Organization_OR_Patient_OR_Practitioner_OR_PractitionerRole_OR_RelatedPerson> CLOSED {
    rdf:first @<Reference> AND {fhir:link 
			@<CareTeam> OR 
			@<Organization> OR 
			@<Patient> OR 
			@<Practitioner> OR 
			@<PractitionerRole> OR 
			@<RelatedPerson> } ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Reference_CareTeam_OR_Organization_OR_Patient_OR_Practitioner_OR_PractitionerRole_OR_RelatedPerson> 
}
<OneOrMore_Annotation> CLOSED {
    rdf:first @<Annotation>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Annotation> 
}
<OneOrMore_Observation.referenceRange> CLOSED {
    rdf:first @<Observation.referenceRange>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Observation.referenceRange> 
}
<OneOrMore_Reference_MolecularSequence_OR_Observation_OR_QuestionnaireResponse> CLOSED {
    rdf:first @<Reference> AND {fhir:link 
			@<MolecularSequence> OR 
			@<Observation> OR 
			@<QuestionnaireResponse> } ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Reference_MolecularSequence_OR_Observation_OR_QuestionnaireResponse> 
}
<OneOrMore_Reference_DocumentReference_OR_GenomicStudy_OR_ImagingSelection_OR_ImagingStudy_OR_MolecularSequence_OR_Observation_OR_QuestionnaireResponse> CLOSED {
    rdf:first @<Reference> AND {fhir:link 
			@<DocumentReference> OR 
			@<GenomicStudy> OR 
			@<ImagingSelection> OR 
			@<ImagingStudy> OR 
			@<MolecularSequence> OR 
			@<Observation> OR 
			@<QuestionnaireResponse> } ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Reference_DocumentReference_OR_GenomicStudy_OR_ImagingSelection_OR_ImagingStudy_OR_MolecularSequence_OR_Observation_OR_QuestionnaireResponse> 
}
<OneOrMore_Observation.component> CLOSED {
    rdf:first @<Observation.component>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Observation.component> 
}

#---------------------- Value Sets ------------------------

# Codes providing the status of an observation.
fhirvs:observation-status ["registered" "specimen-in-process" "preliminary" "final" "amended" "corrected" "appended" "cancelled" "entered-in-error" "unknown" "cannot-be-obtained"]

# Codes providing the type of triggeredBy observation.
fhirvs:observation-triggeredbytype ["reflex" "repeat" "re-run"]