Standard Health Record FHIR Implementation Guide

SHR Specimen Profile

 

The official URL for this profile is:

http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-Specimen

Sample for analysis

This profile builds on Specimen.

This profile was published on Wed Dec 20 00:00:00 EST 2017 as a draft by The MITRE Corporation: Standard Health Record Collaborative.

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

Summary

Mandatory: 0 element (1 nested mandatory element)

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

SHR Mapping Source

This structure represents the following SHR mapping definition:

shr.entity.Specimen maps to Specimen:
  AccessionIdentifier maps to accessionIdentifier
  Status maps to status
  Type maps to type
  Subject maps to subject
  SourceSpecimen maps to parent
  ReceivedTime maps to receivedTime
  SpecimenCollectionPerformed.AmountOrSize maps to collection.quantity
  SpecimenCollectionPerformed.BodySite maps to collection.bodySite
  SpecimenCollectionPerformed.PerformedContext.OccurrenceTimeOrPeriod maps to collection.collected[x]
  SpecimenCollectionPerformed.PerformedContext.Participant maps to collection.collector
  SpecimenCollectionPerformed.PerformedContext.Method maps to collection.method
  SpecimenCollectionPerformed.PerformedContext.RelatedRequest maps to request
  SpecimenContainer.Identifier maps to container.identifier
  SpecimenContainer.Details maps to container.description
  SpecimenContainer.Type maps to container.type
  SpecimenContainer.Capacity maps to container.capacity
  SpecimenContainer.SpecimenQuantity maps to container.specimenQuantity
  SpecimenContainer.Additive maps to container.additive[x]

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen SHR Specimen Profile
... accessionIdentifier SHR Identifier Profile
... type 1..1Binding: v2 Specimen Type (required)
... subject Reference(SHR Patient Profile), Reference(SHR Group Profile), Reference(SHR Device Profile)
... parent 0..1Reference(SHR Specimen Profile)
... collection
.... quantity SHR SimpleQuantity Profile
.... bodySite Binding: SHR BodySiteVS ValueSet (required)
... container
.... identifier SHR Identifier Profile
.... capacity SHR SimpleQuantity Profile
.... specimenQuantity SHR Quantity Profile
.... additive[x] CodeableConcept, Reference(SHR Substance Profile)
... shr-base-RelatedEncounter-extension 0..1Reference(SHR EncounterPerformed Profile)SHR RelatedEncounter Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-RelatedEncounter-extension
... shr-base-Author-extension 0..1(Complex)SHR Author Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-Author-extension
... shr-base-Informant-extension 0..1(Complex)SHR Informant Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-Informant-extension
... shr-entity-SpecimenTreatment-extension 0..*Reference(SHR SpecimenTreatment Profile)SHR SpecimenTreatment Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-SpecimenTreatment-extension
... shr-entity-HandlingRisk-extension 0..*CodeableConceptSHR HandlingRisk Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-HandlingRisk-extension
... shr-entity-SpecialHandling-extension 0..*CodeableConceptSHR SpecialHandling Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-SpecialHandling-extension

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen I0..*SHR Specimen Profile
... 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: Common Languages (extensible)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... shr-base-RelatedEncounter-extension 0..1Reference(SHR EncounterPerformed Profile)SHR RelatedEncounter Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-RelatedEncounter-extension
... shr-base-Author-extension 0..1(Complex)SHR Author Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-Author-extension
... shr-base-Informant-extension 0..1(Complex)SHR Informant Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-Informant-extension
... shr-entity-SpecimenTreatment-extension 0..*Reference(SHR SpecimenTreatment Profile)SHR SpecimenTreatment Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-SpecimenTreatment-extension
... shr-entity-HandlingRisk-extension 0..*CodeableConceptSHR HandlingRisk Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-HandlingRisk-extension
... shr-entity-SpecialHandling-extension 0..*CodeableConceptSHR SpecialHandling Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-SpecialHandling-extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierExternal Identifier
... accessionIdentifier Σ0..1SHR Identifier ProfileIdentifier assigned by the lab
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required)
... type Σ1..1CodeableConceptKind of material that forms the specimen
Binding: v2 Specimen Type (required)
... subject Σ1..1Reference(SHR Patient Profile), Reference(SHR Group Profile), Reference(SHR Device Profile)Where the specimen came from. This may be from the patient(s) or from the environment or a device
... receivedTime Σ0..1dateTimeThe time when specimen was received for processing
... parent 0..1Reference(SHR Specimen Profile)Specimen from which this specimen originated
... request 0..*Reference(ProcedureRequest)Why the specimen was collected
... collection I0..1BackboneElementCollection details
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... collector Σ0..1Reference(Practitioner)Who collected the specimen
.... collected[x] Σ0..1dateTime, PeriodCollection time
.... quantity 0..1SHR SimpleQuantity ProfileThe quantity of specimen collected
.... method 0..1CodeableConceptTechnique used to perform collection
Binding: FHIR Specimen Collection Method (example)
.... bodySite 0..1CodeableConceptAnatomical collection site
Binding: SHR BodySiteVS ValueSet (required)
... processing I0..*BackboneElementProcessing and processing step details
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... description 0..1stringTextual description of procedure
.... procedure 0..1CodeableConceptIndicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example)
.... additive 0..*Reference(Substance)Material used in the processing step
.... time[x] 0..1dateTime, PeriodDate and time of specimen processing
... container I0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... identifier Σ0..*SHR Identifier ProfileId for the container
.... description 0..1stringTextual description of the container
.... type 0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainer (example)
.... capacity 0..1SHR SimpleQuantity ProfileContainer volume or size
.... specimenQuantity 0..1SHR Quantity ProfileQuantity of specimen within container
.... additive[x] 0..1CodeableConcept, Reference(SHR Substance Profile)Additive associated with container
Binding: v2 Additive/Preservative (example)
... note 0..*AnnotationComments

doco Documentation for this format

Summary

Mandatory: 0 element (1 nested mandatory element)

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

SHR Mapping Source

This structure represents the following SHR mapping definition:

shr.entity.Specimen maps to Specimen:
  AccessionIdentifier maps to accessionIdentifier
  Status maps to status
  Type maps to type
  Subject maps to subject
  SourceSpecimen maps to parent
  ReceivedTime maps to receivedTime
  SpecimenCollectionPerformed.AmountOrSize maps to collection.quantity
  SpecimenCollectionPerformed.BodySite maps to collection.bodySite
  SpecimenCollectionPerformed.PerformedContext.OccurrenceTimeOrPeriod maps to collection.collected[x]
  SpecimenCollectionPerformed.PerformedContext.Participant maps to collection.collector
  SpecimenCollectionPerformed.PerformedContext.Method maps to collection.method
  SpecimenCollectionPerformed.PerformedContext.RelatedRequest maps to request
  SpecimenContainer.Identifier maps to container.identifier
  SpecimenContainer.Details maps to container.description
  SpecimenContainer.Type maps to container.type
  SpecimenContainer.Capacity maps to container.capacity
  SpecimenContainer.SpecimenQuantity maps to container.specimenQuantity
  SpecimenContainer.Additive maps to container.additive[x]

Differential View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen SHR Specimen Profile
... accessionIdentifier SHR Identifier Profile
... type 1..1Binding: v2 Specimen Type (required)
... subject Reference(SHR Patient Profile), Reference(SHR Group Profile), Reference(SHR Device Profile)
... parent 0..1Reference(SHR Specimen Profile)
... collection
.... quantity SHR SimpleQuantity Profile
.... bodySite Binding: SHR BodySiteVS ValueSet (required)
... container
.... identifier SHR Identifier Profile
.... capacity SHR SimpleQuantity Profile
.... specimenQuantity SHR Quantity Profile
.... additive[x] CodeableConcept, Reference(SHR Substance Profile)
... shr-base-RelatedEncounter-extension 0..1Reference(SHR EncounterPerformed Profile)SHR RelatedEncounter Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-RelatedEncounter-extension
... shr-base-Author-extension 0..1(Complex)SHR Author Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-Author-extension
... shr-base-Informant-extension 0..1(Complex)SHR Informant Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-Informant-extension
... shr-entity-SpecimenTreatment-extension 0..*Reference(SHR SpecimenTreatment Profile)SHR SpecimenTreatment Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-SpecimenTreatment-extension
... shr-entity-HandlingRisk-extension 0..*CodeableConceptSHR HandlingRisk Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-HandlingRisk-extension
... shr-entity-SpecialHandling-extension 0..*CodeableConceptSHR SpecialHandling Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-SpecialHandling-extension

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen I0..*SHR Specimen Profile
... 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: Common Languages (extensible)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... shr-base-RelatedEncounter-extension 0..1Reference(SHR EncounterPerformed Profile)SHR RelatedEncounter Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-RelatedEncounter-extension
... shr-base-Author-extension 0..1(Complex)SHR Author Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-Author-extension
... shr-base-Informant-extension 0..1(Complex)SHR Informant Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-base-Informant-extension
... shr-entity-SpecimenTreatment-extension 0..*Reference(SHR SpecimenTreatment Profile)SHR SpecimenTreatment Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-SpecimenTreatment-extension
... shr-entity-HandlingRisk-extension 0..*CodeableConceptSHR HandlingRisk Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-HandlingRisk-extension
... shr-entity-SpecialHandling-extension 0..*CodeableConceptSHR SpecialHandling Extension
URL: http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-SpecialHandling-extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierExternal Identifier
... accessionIdentifier Σ0..1SHR Identifier ProfileIdentifier assigned by the lab
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required)
... type Σ1..1CodeableConceptKind of material that forms the specimen
Binding: v2 Specimen Type (required)
... subject Σ1..1Reference(SHR Patient Profile), Reference(SHR Group Profile), Reference(SHR Device Profile)Where the specimen came from. This may be from the patient(s) or from the environment or a device
... receivedTime Σ0..1dateTimeThe time when specimen was received for processing
... parent 0..1Reference(SHR Specimen Profile)Specimen from which this specimen originated
... request 0..*Reference(ProcedureRequest)Why the specimen was collected
... collection I0..1BackboneElementCollection details
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... collector Σ0..1Reference(Practitioner)Who collected the specimen
.... collected[x] Σ0..1dateTime, PeriodCollection time
.... quantity 0..1SHR SimpleQuantity ProfileThe quantity of specimen collected
.... method 0..1CodeableConceptTechnique used to perform collection
Binding: FHIR Specimen Collection Method (example)
.... bodySite 0..1CodeableConceptAnatomical collection site
Binding: SHR BodySiteVS ValueSet (required)
... processing I0..*BackboneElementProcessing and processing step details
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... description 0..1stringTextual description of procedure
.... procedure 0..1CodeableConceptIndicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example)
.... additive 0..*Reference(Substance)Material used in the processing step
.... time[x] 0..1dateTime, PeriodDate and time of specimen processing
... container I0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... identifier Σ0..*SHR Identifier ProfileId for the container
.... description 0..1stringTextual description of the container
.... type 0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainer (example)
.... capacity 0..1SHR SimpleQuantity ProfileContainer volume or size
.... specimenQuantity 0..1SHR Quantity ProfileQuantity of specimen within container
.... additive[x] 0..1CodeableConcept, Reference(SHR Substance Profile)Additive associated with container
Binding: v2 Additive/Preservative (example)
... note 0..*AnnotationComments

doco Documentation for this format

Downloads: StructureDefinition: (XML, JSON, TTL), Schema: XML Schematron

 

Terminology Bindings

PathNameConformanceValueSet
Specimen.languageCommon LanguagesextensibleCommon Languages
Specimen.statusSpecimenStatusrequiredSpecimenStatus
Specimen.typev2 Specimen Typerequiredv2 Specimen Type
Specimen.collection.methodFHIR Specimen Collection MethodexampleFHIR Specimen Collection Method
Specimen.collection.bodySiteSHR BodySiteVS ValueSetrequiredSHR BodySiteVS ValueSet
Specimen.processing.procedureSpecimenProcessingProcedureexampleSpecimenProcessingProcedure
Specimen.container.typeSpecimenContainerexampleSpecimenContainer
Specimen.container.additive[x]v2 Additive/Preservativeexamplev2 Additive/Preservative

 

Constraints

IdPathDetailsRequirements
dom-2SpecimenIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-1SpecimenIf the resource is contained in another resource, it SHALL NOT contain any narrative
: contained.text.empty()
dom-4SpecimenIf 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-3SpecimenIf the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource
: contained.where(('#'+id in %resource.descendants().reference).not()).empty()
ele-1Specimen.collectionAll FHIR elements must have a @value or children
: hasValue() | (children().count() > id.count())
ele-1Specimen.processingAll FHIR elements must have a @value or children
: hasValue() | (children().count() > id.count())
ele-1Specimen.containerAll FHIR elements must have a @value or children
: hasValue() | (children().count() > id.count())