HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1
1.0.0 - STU1

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

StructureDefinition: GeneticSpecimen

A small sample of blood, hair, skin, amniotic fluid (the fluid that surrounds a fetus during pregnancy), or other tissue which is excised from a subject for the purposes of genomics testing or analysis.

The official URL for this profile is: 

http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genetic-specimen

Formal Views of Profile Content

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

This structure is derived from Specimen

Summary

Mandatory: 1 element
Must-Support: 3 elements

Extensions

This structure refers to these extensions:

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen I0..*SpecimenSample for analysis
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierExternal Identifier
... accessionIdentifier ΣI0..1IdentifierIdentifier assigned by the lab
... status ?!ΣI0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required)
... type SΣI1..1CodeableConceptKind of material that forms the specimen
Binding: Genetic Specimen Type Value Set (required)
... subject ΣI0..1Reference(Patient | Group | Device | Substance | Location)Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device
... receivedTime ΣI0..1dateTimeThe time when specimen was received for processing
... parent I0..*Reference(Specimen)Specimen from which this specimen originated
... request I0..*Reference(ServiceRequest)Why the specimen was collected
... collection I0..1BackboneElementCollection details
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... collector ΣI0..1Reference(Practitioner | PractitionerRole)Who collected the specimen
.... collected[x] ΣI0..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... duration ΣI0..1DurationHow long it took to collect specimen
.... quantity I0..1SimpleQuantityThe quantity of specimen collected
.... method I0..1CodeableConceptTechnique used to perform collection
Binding: FHIRSpecimenCollectionMethod (example)
.... bodySite SI0..1CodeableConceptAnatomical collection site
Binding: SNOMEDCTBodyStructures (example)
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... mcode-laterality SI0..1CodeableConceptOptional Extensions Element
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality
..... coding ΣI0..*CodingCode defined by a terminology system
..... text ΣI0..1stringPlain text representation of the concept
.... fastingStatus[x] ΣI0..1Whether or how long patient abstained from food and/or drink
Binding: v2 Relevant Clincial Information (extensible)
..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration
... processing I0..*BackboneElementProcessing and processing step details
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... description I0..1stringTextual description of procedure
.... procedure I0..1CodeableConceptIndicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example)
.... additive I0..*Reference(Substance)Material used in the processing step
.... time[x] I0..1Date and time of specimen processing
..... timeDateTimedateTime
..... timePeriodPeriod
... container I0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... identifier ΣI0..*IdentifierId for the container
.... description I0..1stringTextual description of the container
.... type I0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainerType (example)
.... capacity I0..1SimpleQuantityContainer volume or size
.... specimenQuantity I0..1SimpleQuantityQuantity of specimen within container
.... additive[x] I0..1Additive associated with container
Binding: v2 Additive (example)
..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(Substance)
... condition ΣI0..*CodeableConceptState of the specimen
Binding: v2 Specimen Condition (extensible)
... note I0..*AnnotationComments

doco Documentation for this format

This structure is derived from Specimen

Summary

Mandatory: 1 element
Must-Support: 3 elements

Extensions

This structure refers to these extensions:

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen I0..*SpecimenSample for analysis
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierExternal Identifier
... accessionIdentifier ΣI0..1IdentifierIdentifier assigned by the lab
... status ?!ΣI0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required)
... type SΣI1..1CodeableConceptKind of material that forms the specimen
Binding: Genetic Specimen Type Value Set (required)
... subject ΣI0..1Reference(Patient | Group | Device | Substance | Location)Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device
... receivedTime ΣI0..1dateTimeThe time when specimen was received for processing
... parent I0..*Reference(Specimen)Specimen from which this specimen originated
... request I0..*Reference(ServiceRequest)Why the specimen was collected
... collection I0..1BackboneElementCollection details
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... collector ΣI0..1Reference(Practitioner | PractitionerRole)Who collected the specimen
.... collected[x] ΣI0..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... duration ΣI0..1DurationHow long it took to collect specimen
.... quantity I0..1SimpleQuantityThe quantity of specimen collected
.... method I0..1CodeableConceptTechnique used to perform collection
Binding: FHIRSpecimenCollectionMethod (example)
.... bodySite SI0..1CodeableConceptAnatomical collection site
Binding: SNOMEDCTBodyStructures (example)
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... mcode-laterality SI0..1CodeableConceptOptional Extensions Element
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality
..... coding ΣI0..*CodingCode defined by a terminology system
..... text ΣI0..1stringPlain text representation of the concept
.... fastingStatus[x] ΣI0..1Whether or how long patient abstained from food and/or drink
Binding: v2 Relevant Clincial Information (extensible)
..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration
... processing I0..*BackboneElementProcessing and processing step details
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... description I0..1stringTextual description of procedure
.... procedure I0..1CodeableConceptIndicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example)
.... additive I0..*Reference(Substance)Material used in the processing step
.... time[x] I0..1Date and time of specimen processing
..... timeDateTimedateTime
..... timePeriodPeriod
... container I0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... identifier ΣI0..*IdentifierId for the container
.... description I0..1stringTextual description of the container
.... type I0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainerType (example)
.... capacity I0..1SimpleQuantityContainer volume or size
.... specimenQuantity I0..1SimpleQuantityQuantity of specimen within container
.... additive[x] I0..1Additive associated with container
Binding: v2 Additive (example)
..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(Substance)
... condition ΣI0..*CodeableConceptState of the specimen
Binding: v2 Specimen Condition (extensible)
... note I0..*AnnotationComments

doco Documentation for this format

 

Other representations of profile: Schematron

Terminology Bindings

Terminology Bindings

PathConformanceValueSet
Specimen.languagepreferredCommonLanguages
Max Binding: AllLanguages
Specimen.statusrequiredSpecimenStatus
Specimen.typerequiredGeneticSpecimenTypeVS
Specimen.collection.methodexampleFHIRSpecimenCollectionMethod
Specimen.collection.bodySiteexampleSNOMEDCTBodyStructures
Specimen.collection.fastingStatus[x]extensiblev2.0916
Specimen.processing.procedureexampleSpecimenProcessingProcedure
Specimen.container.typeexampleSpecimenContainerType
Specimen.container.additive[x]examplev2.0371
Specimen.conditionextensiblev2.0493

Constraints

Constraints

IdPathDetailsRequirements