minimal Common Oncology Data Elements (mCODE) Implementation Guide
2.0.0 - STU 2

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Resource Profile: Genomic Specimen Profile

Defining URL:http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-specimen
Version:2.0.0
Name:GenomicSpecimen
Title:Genomic Specimen Profile
Status:Active as of 1/18/22 3:17 AM
Definition:

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.

Publisher:HL7 International Clinical Interoperability Council
Source Resource:XML / JSON / Turtle

The official URL for this profile is: 

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

Usage

The specimen SHOULD be referenced by GenomicsReport. Multiple specimens are possible in the case of a tumor normal test where the variants found in a tumor specimen are compared with the variants in a normal specimen.

Conformance

Specimen resources associated with an in-scope patient with a Specimen.code in the value set GenomicSpecimenTypeVS MUST conform to this profile. Beyond this requirement, a producer of resources SHOULD ensure that any resource instance associated with an in-scope patient that would reasonably be expected to conform to this profile SHOULD be published in this form.

Formal Views of Profile Content

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

This structure is derived from Specimen

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*SpecimenSample for analysis
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... mcode-related-condition S0..1Reference(Condition)Cancer condition associated with this specimen.
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition
.... value[x] 1..1Reference(Primary Cancer Condition Profile | Secondary Cancer Condition Profile)Value of extension
... status S0..1codeavailable | unavailable | unsatisfactory | entered-in-error
... subject S0..1Reference(Cancer Patient Profile)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
... collection S0..1BackboneElementCollection details
.... bodySite S0..1CodeableConceptAnatomical collection site
..... extension S0..*ExtensionExtension
..... mcode-body-location-qualifier S0..*CodeableConceptBody Location Qualifier Extension
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier
Binding: Body Location Qualifier Value Set (required)
..... mcode-laterality-qualifier S0..1CodeableConceptLaterality Qualifier Extension
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier
Binding: Laterality Qualifier Value Set (required)

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*SpecimenSample for analysis
... id Σ0..1stringLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... mcode-related-condition S0..1Reference(Condition)Cancer condition associated with this specimen.
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition
.... id 0..1stringUnique id for inter-element referencing
.... Slices for extension 0..0
.... url 1..1uri"http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition"
.... value[x] 1..1Reference(Primary Cancer Condition Profile | Secondary Cancer Condition Profile)Value of extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierExternal Identifier
... accessionIdentifier Σ0..1IdentifierIdentifier assigned by the lab
... status ?!SΣ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣ1..1CodeableConceptKind of material that forms the specimen
Binding: Genomic Specimen Type Value Set (extensible)
... subject SΣ0..1Reference(Cancer Patient Profile)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 Σ0..1dateTimeThe time when specimen was received for processing
... parent 0..*Reference(Specimen)Specimen from which this specimen originated
... request 0..*Reference(ServiceRequest)Why the specimen was collected
... collection S0..1BackboneElementCollection details
.... 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
.... collector Σ0..1Reference(Practitioner | PractitionerRole)Who collected the specimen
.... collected[x] Σ0..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... duration Σ0..1DurationHow long it took to collect specimen
.... quantity 0..1SimpleQuantityThe quantity of specimen collected
.... method 0..1CodeableConceptTechnique used to perform collection
Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.

.... bodySite S0..1CodeableConceptAnatomical collection site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

..... id 0..1stringUnique id for inter-element referencing
..... Slices for extension S0..*ExtensionExtension
Slice: Unordered, Open by value:url
..... mcode-body-location-qualifier S0..*CodeableConceptBody Location Qualifier Extension
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier
Binding: Body Location Qualifier Value Set (required)
..... mcode-laterality-qualifier S0..1CodeableConceptLaterality Qualifier Extension
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier
Binding: Laterality Qualifier Value Set (required)
..... coding Σ0..*CodingCode defined by a terminology system
..... text Σ0..1stringPlain text representation of the concept
.... fastingStatus[x] Σ0..1Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.

..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration
... processing 0..*BackboneElementProcessing and processing step details
.... 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
.... description 0..1stringTextual description of procedure
.... procedure 0..1CodeableConceptIndicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.

.... additive 0..*Reference(Substance)Material used in the processing step
.... time[x] 0..1Date and time of specimen processing
..... timeDateTimedateTime
..... timePeriodPeriod
... container 0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... 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
.... identifier Σ0..*IdentifierId for the container
.... description 0..1stringTextual description of the container
.... type 0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainerType (example): Type of specimen container.

.... capacity 0..1SimpleQuantityContainer volume or size
.... specimenQuantity 0..1SimpleQuantityQuantity of specimen within container
.... additive[x] 0..1Additive associated with container
Binding: hl7VS-additivePreservative (example): Substance added to specimen container.

..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(Substance)
... condition Σ0..*CodeableConceptState of the specimen
Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.


... note 0..*AnnotationComments

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*SpecimenSample for analysis
... mcode-related-condition 0..1Reference(Condition)Cancer condition associated with this specimen.
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type Σ1..1CodeableConceptKind of material that forms the specimen
Binding: Genomic Specimen Type Value Set (extensible)
... collection 0..1BackboneElementCollection details
.... bodySite 0..1CodeableConceptAnatomical collection site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

..... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
..... mcode-body-location-qualifier 0..*CodeableConceptBody Location Qualifier Extension
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier
Binding: Body Location Qualifier Value Set (required)
..... mcode-laterality-qualifier 0..1CodeableConceptLaterality Qualifier Extension
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier
Binding: Laterality Qualifier Value Set (required)

doco Documentation for this format

Differential View

This structure is derived from Specimen

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*SpecimenSample for analysis
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... mcode-related-condition S0..1Reference(Condition)Cancer condition associated with this specimen.
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition
.... value[x] 1..1Reference(Primary Cancer Condition Profile | Secondary Cancer Condition Profile)Value of extension
... status S0..1codeavailable | unavailable | unsatisfactory | entered-in-error
... subject S0..1Reference(Cancer Patient Profile)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
... collection S0..1BackboneElementCollection details
.... bodySite S0..1CodeableConceptAnatomical collection site
..... extension S0..*ExtensionExtension
..... mcode-body-location-qualifier S0..*CodeableConceptBody Location Qualifier Extension
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier
Binding: Body Location Qualifier Value Set (required)
..... mcode-laterality-qualifier S0..1CodeableConceptLaterality Qualifier Extension
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier
Binding: Laterality Qualifier Value Set (required)

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*SpecimenSample for analysis
... id Σ0..1stringLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... mcode-related-condition S0..1Reference(Condition)Cancer condition associated with this specimen.
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition
.... id 0..1stringUnique id for inter-element referencing
.... Slices for extension 0..0
.... url 1..1uri"http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition"
.... value[x] 1..1Reference(Primary Cancer Condition Profile | Secondary Cancer Condition Profile)Value of extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierExternal Identifier
... accessionIdentifier Σ0..1IdentifierIdentifier assigned by the lab
... status ?!SΣ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣ1..1CodeableConceptKind of material that forms the specimen
Binding: Genomic Specimen Type Value Set (extensible)
... subject SΣ0..1Reference(Cancer Patient Profile)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 Σ0..1dateTimeThe time when specimen was received for processing
... parent 0..*Reference(Specimen)Specimen from which this specimen originated
... request 0..*Reference(ServiceRequest)Why the specimen was collected
... collection S0..1BackboneElementCollection details
.... 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
.... collector Σ0..1Reference(Practitioner | PractitionerRole)Who collected the specimen
.... collected[x] Σ0..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... duration Σ0..1DurationHow long it took to collect specimen
.... quantity 0..1SimpleQuantityThe quantity of specimen collected
.... method 0..1CodeableConceptTechnique used to perform collection
Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.

.... bodySite S0..1CodeableConceptAnatomical collection site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

..... id 0..1stringUnique id for inter-element referencing
..... Slices for extension S0..*ExtensionExtension
Slice: Unordered, Open by value:url
..... mcode-body-location-qualifier S0..*CodeableConceptBody Location Qualifier Extension
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier
Binding: Body Location Qualifier Value Set (required)
..... mcode-laterality-qualifier S0..1CodeableConceptLaterality Qualifier Extension
URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier
Binding: Laterality Qualifier Value Set (required)
..... coding Σ0..*CodingCode defined by a terminology system
..... text Σ0..1stringPlain text representation of the concept
.... fastingStatus[x] Σ0..1Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.

..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration
... processing 0..*BackboneElementProcessing and processing step details
.... 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
.... description 0..1stringTextual description of procedure
.... procedure 0..1CodeableConceptIndicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.

.... additive 0..*Reference(Substance)Material used in the processing step
.... time[x] 0..1Date and time of specimen processing
..... timeDateTimedateTime
..... timePeriodPeriod
... container 0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... 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
.... identifier Σ0..*IdentifierId for the container
.... description 0..1stringTextual description of the container
.... type 0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainerType (example): Type of specimen container.

.... capacity 0..1SimpleQuantityContainer volume or size
.... specimenQuantity 0..1SimpleQuantityQuantity of specimen within container
.... additive[x] 0..1Additive associated with container
Binding: hl7VS-additivePreservative (example): Substance added to specimen container.

..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(Substance)
... condition Σ0..*CodeableConceptState of the specimen
Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.


... note 0..*AnnotationComments

doco Documentation for this format

 

Other representations of profile: CSV, Excel, Schematron

Terminology Bindings

PathConformanceValueSet
Specimen.languagepreferredCommonLanguages
Max Binding: AllLanguages
Specimen.statusrequiredSpecimenStatus
Specimen.typeextensibleGenomicSpecimenTypeVS
Specimen.collection.methodexampleFHIRSpecimenCollectionMethod
Specimen.collection.bodySiteexampleSNOMEDCTBodyStructures
Specimen.collection.fastingStatus[x]extensibleHl7VSRelevantClincialInformation
Specimen.processing.procedureexampleSpecimenProcessingProcedure
Specimen.container.typeexampleSpecimenContainerType
Specimen.container.additive[x]exampleHl7VSAdditivePreservative
Specimen.conditionextensibleHl7VSSpecimenCondition