Clinical Research Core Implementation Guide 0.3 - Continuous Build

StructureDefinition: CRCoreResults

The official URL for this profile is: 

https://esource-consortium.github.io/fhir-clinical-research/cr-core-results

Overview

This FHIR profile sets minimum expectations for the Observation resource resource to search / fetch laboratory test results associated with a patient on a clinical trial. It identifies which core elements, extensions, vocabularies and value sets SHALL be present in the resource when using this profile.

FHIR servers must ensure that all lab results are associated with a protocol. Non protocol specific lab results SHOULD NOT be returned.

Example Usage Scenarios:

The following are example usage scenarios for the CR Core-Results profile:

  • Query for lab results belonging to all Patients on a clinical trial
  • Query for lab results belonging to a specific Patient on a clinical trial
  • Query for lab results belonging to a specific Patient on a clinical trial between two dates (in this example, between 6/20/2006 and 6/30/2006)

Mandatory Data Elements and Terminology

The following data-elements are mandatory (i.e data MUST be present). These are presented below in a simple human-readable explanation. Profile specific guidance and examples are provided as well. The Formal Profile Definition below provides the formal summary, definitions, and terminology requirements.

Each Observation must have:

  1. a status
  2. a category code of ‘laboratory’
  3. a LOINC code, if available, which tells you what is being measured
  4. a patient
  5. a result value

Each Observation should have:

  1. a time indicating when the measurement was taken
  2. a reference range if available

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

This structure is derived from Observation

Summary

Mandatory: 2 elements
Must-Support: 10 elements

Structures

This structure refers to these other structures:

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Measurements and simple assertions
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier SΣ0..*IdentifierBusiness Identifier for observation
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... use ?!Σ0..1codeusual | official | temp | secondary | old (If known)
Binding: IdentifierUse (required)
.... type Σ0..1CodeableConceptDescription of identifier
Binding: Identifier Type Codes (extensible)
.... system SΣ0..1uriThe namespace for the identifier value
Example General': http://www.acme.com/identifiers/patient
.... value SΣ0..1stringThe value that is unique
Example General': 123456
.... period Σ0..1PeriodTime period when id is/was valid for use
.... assigner Σ0..1Reference(Organization)Organization that issued id (may be just text)
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category SI1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred)
cr-core-1: Must have a category of 'laboratory' and a code system 'http://hl7.org/fhir/observation-category'
... code SΣ1..1CodeableConceptLaboratory Test Name
Binding: (unbound) (extensible)
... subject SΣ1..1Reference(CRCorePatient)Who and/or what the observation is about
... focus Σ0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SΣ0..1dateTime, Period, Timing, instantClinically relevant time/time-period for observation
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)Who is responsible for the observation
... value[x] SΣI0..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual result
... dataAbsentReason SI0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... note 0..*AnnotationComments about the observation
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example)
... method 0..1CodeableConceptHow it was done
Binding: ObservationMethods (example)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred)
.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... component ΣI0..*BackboneElementComponent results
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
.... value[x] Σ0..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

This structure is derived from Observation

Summary

Mandatory: 2 elements
Must-Support: 10 elements

Structures

This structure refers to these other structures:

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Measurements and simple assertions
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier SΣ0..*IdentifierBusiness Identifier for observation
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... use ?!Σ0..1codeusual | official | temp | secondary | old (If known)
Binding: IdentifierUse (required)
.... type Σ0..1CodeableConceptDescription of identifier
Binding: Identifier Type Codes (extensible)
.... system SΣ0..1uriThe namespace for the identifier value
Example General': http://www.acme.com/identifiers/patient
.... value SΣ0..1stringThe value that is unique
Example General': 123456
.... period Σ0..1PeriodTime period when id is/was valid for use
.... assigner Σ0..1Reference(Organization)Organization that issued id (may be just text)
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category SI1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred)
cr-core-1: Must have a category of 'laboratory' and a code system 'http://hl7.org/fhir/observation-category'
... code SΣ1..1CodeableConceptLaboratory Test Name
Binding: (unbound) (extensible)
... subject SΣ1..1Reference(CRCorePatient)Who and/or what the observation is about
... focus Σ0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SΣ0..1dateTime, Period, Timing, instantClinically relevant time/time-period for observation
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)Who is responsible for the observation
... value[x] SΣI0..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual result
... dataAbsentReason SI0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... note 0..*AnnotationComments about the observation
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example)
... method 0..1CodeableConceptHow it was done
Binding: ObservationMethods (example)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred)
.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... component ΣI0..*BackboneElementComponent results
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
.... value[x] Σ0..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

 

Other representations of profile: Schematron

Terminology Bindings

PathConformanceValueSet
Observation.languagepreferredCommonLanguages
Max Binding: AllLanguages
Observation.identifier.userequiredIdentifierUse
Observation.identifier.typeextensibleIdentifier Type Codes
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.codeextensible
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.interpretationextensibleObservationInterpretationCodes
Observation.bodySiteexampleSNOMEDCTBodyStructures
Observation.methodexampleObservationMethods
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationextensibleObservationInterpretationCodes

Constraints

IdPathDetailsRequirements
dom-2ObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-4ObservationIf a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-3ObservationIf the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-6ObservationA resource should have narrative for robust management
: text.div.exists()
dom-5ObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
obs-7ObservationIf Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
: value.empty() or component.code.where( (coding.code = %resource.code.coding.code) and (coding.system = %resource.code.coding.system)).empty()
obs-6ObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
cr-core-1Observation.categoryMust have a category of 'laboratory' and a code system 'http://hl7.org/fhir/observation-category'
: where(coding.system='http://hl7.org/fhir/observation-category' and coding.code='laboratory').exists()
ele-1Observation.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
obs-3Observation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())

Quick Start

Below is an overview of the required set of RESTful FHIR interactions - for example, search and read operations - for this profile. See the Conformance requirements for a complete list of supported RESTful interactions for this IG.

GET [base]/Observation?ResearchStudy=[study-id]&category=laboratory

Example: GET [base]/Observation?ResearchStudy=12-345&category=laboratory

Support: Mandatory to support search by Research Study and category code = ‘laboratory’.

Implementation Notes: Search based on a Research Study and laboratory category code = “laboratory”. This fetches a bundle of all Observation resources with laboratory categories for the specified ResearchStudy.

GET [base]/observations?ResearchStudy=[study-id]&category=laboratory&patient:_has:ResearchSubject:identifier=[subject-id]

Example: GET [base]/observations?ResearchStudy=12-345&category=laboratory&patient:_has:ResearchSubject:identifier=12345

Support: Mandatory to support search by Research Subject and category code = ‘laboratory’.

Implementation Notes: Search based on a Research Study and Research Subject with laboratory category code = “laboratory”. This fetches a bundle of all Observation resources with laboratory categories for the specified ResearchStudy / ResearchSubject.

GET [base]/observations?ResearchStudy=[study-id]&category=laboratory&date=[date]&date=[date]

Example: GET [base]/observations?ResearchStudy=17-238&category=laboratory&context:Encounter.date=le2006-06-30&context:Encounter.date=ge2006-06-20

Support: Mandatory to support search by Research Study, category code = ‘laboratory’, and date/period.

Implementation Notes: Search based on a Research Study and date with laboratory category code = “laboratory”. This fetches a bundle of all Observation resources with laboratory categories for the specified ResearchStudy for a specified time period.