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: CancerGeneticVariant - Mappings

Mappings for the Profile.

Mappings for Argonaut-DQ-DSTU2 (http://unknown.org/Argonaut-DQ-DSTU2)

CancerGeneticVariant
ObservationObservation
   statusObservation.status
   categoryObservation.category
   category (Laboratory)Observation.category
   codeObservation.code
   subjectObservation.subject
   effective[x]Observation.effective[x]
   value[x]Observation.value[x]
   value[x] (valueCodeableConcept)Observation.value[x]
   dataAbsentReasonObservation.dataAbsentReason

Mappings for Workflow Pattern (http://hl7.org/fhir/workflow)

CancerGeneticVariant
ObservationEvent
   identifierEvent.identifier
   basedOnEvent.basedOn
   partOfEvent.partOf
   statusEvent.status
   codeEvent.code
   subjectEvent.subject
   encounterEvent.context
   effective[x]Event.occurrence[x]
   performerEvent.performer.actor

Mappings for SNOMED CT Concept Domain Binding (http://snomed.info/conceptdomain)

CancerGeneticVariant
Observation< 363787002 |Observable entity|
   status< 445584004 |Report by finality status|
   code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
   value[x]< 441742003 |Evaluation finding|
   value[x] (valueCodeableConcept)< 441742003 |Evaluation finding|
   interpretation< 260245000 |Findings values|
   specimen< 123038009 |Specimen|
   device< 49062001 |Device|
   component
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (GeneStudied)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      value[x] (valueCodeableConcept)363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (VariationCode)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      value[x] (valueCodeableConcept)363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (GenomicDNAChange)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      value[x] (valueCodeableConcept)363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (GenomicSourceClass)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      value[x] (valueCodeableConcept)363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (AminoAcidChange)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      value[x] (valueCodeableConcept)363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (AminoAcidChangeType)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      value[x] (valueCodeableConcept)363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (CytogeneticLocation)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (CytogeneticNomenclature)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      value[x] (valueCodeableConcept)363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|

Mappings for HL7 v2 Mapping (http://hl7.org/v2)

CancerGeneticVariant
ObservationOBX
   identifierOBX.21 For OBX segments from systems without OBX-21 support a combination of ORC/OBR and OBX must be negotiated between trading partners to uniquely identify the OBX segment. Depending on how V2 has been implemented each of these may be an option: 1) OBR-3 + OBX-3 + OBX-4 or 2) OBR-3 + OBR-4 + OBX-3 + OBX-4 or 2) some other way to uniquely ID the OBR/ORC + OBX-3 + OBX-4.
   basedOnORC
   partOfVaries by domain
   statusOBX-11
   codeOBX-3
   subjectPID-3
   focusOBX-3
   encounterPV1
   effective[x]OBX-14, and/or OBX-19 after v2.4 (depends on who observation made)
   issuedOBR.22 (or MSH.7), or perhaps OBX-19 (depends on who observation made)
   performerOBX.15 / (Practitioner) OBX-16, PRT-5:PRT-4='RO' / (Device) OBX-18 , PRT-10:PRT-4='EQUIP' / (Organization) OBX-23, PRT-8:PRT-4='PO'
   value[x]OBX.2, OBX.5, OBX.6
   value[x] (valueCodeableConcept)OBX.2, OBX.5, OBX.6
   dataAbsentReasonN/A
   interpretationOBX-8
   noteNTE.3 (partner NTE to OBX, or sometimes another (child?) OBX)
   methodOBX-17
   specimenSPM segment
   deviceOBX-17 / PRT -10
   derivedFromRelationships established by OBX-4 usage
   componentcontainment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (GeneStudied)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      value[x] (valueCodeableConcept)OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (VariationCode)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      value[x] (valueCodeableConcept)OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (GenomicDNAChange)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      value[x] (valueCodeableConcept)OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (GenomicSourceClass)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      value[x] (valueCodeableConcept)OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (AminoAcidChange)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      value[x] (valueCodeableConcept)OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (AminoAcidChangeType)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      value[x] (valueCodeableConcept)OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (CytogeneticLocation)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (CytogeneticNomenclature)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      value[x] (valueCodeableConcept)OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7

Mappings for RIM Mapping (http://hl7.org/v3)

CancerGeneticVariant
ObservationEntity. Role, or Act, Observation[classCode=OBS, moodCode=EVN]
   textAct.text?
   containedN/A
   extensionN/A
   modifierExtensionN/A
   identifierid
   basedOn.inboundRelationship[typeCode=COMP].source[moodCode=EVN]
   partOf.outboundRelationship[typeCode=FLFS].target
   statusstatus Amended & Final are differentiated by whether it is the subject of a ControlAct event with a type of "revise"
   category.outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code
   category (Laboratory).outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code
   codecode
   subjectparticipation[typeCode=RTGT]
   focusparticipation[typeCode=SBJ]
   encounterinboundRelationship[typeCode=COMP].source[classCode=ENC, moodCode=EVN]
   effective[x]effectiveTime
   issuedparticipation[typeCode=AUT].time
   performerparticipation[typeCode=PRF]
   value[x]value
   value[x] (valueCodeableConcept)value
   dataAbsentReasonvalue.nullFlavor
   interpretationinterpretationCode
   notesubjectOf.observationEvent[code="annotation"].value
   methodmethodCode
   specimenparticipation[typeCode=SPC].specimen
   deviceparticipation[typeCode=DEV]
   derivedFrom.targetObservation
   componentoutBoundRelationship[typeCode=COMP]
      idn/a
      extensionn/a
      modifierExtensionN/A
      codecode
      value[x]value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (GeneStudied)outBoundRelationship[typeCode=COMP]
      idn/a
      extensionn/a
      modifierExtensionN/A
      codecode
      value[x]value
      value[x] (valueCodeableConcept)value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (VariationCode)outBoundRelationship[typeCode=COMP]
      idn/a
      extensionn/a
      modifierExtensionN/A
      codecode
      value[x]value
      value[x] (valueCodeableConcept)value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (GenomicDNAChange)outBoundRelationship[typeCode=COMP]
      idn/a
      extensionn/a
      modifierExtensionN/A
      codecode
      value[x]value
      value[x] (valueCodeableConcept)value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (GenomicSourceClass)outBoundRelationship[typeCode=COMP]
      idn/a
      extensionn/a
      modifierExtensionN/A
      codecode
      value[x]value
      value[x] (valueCodeableConcept)value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (AminoAcidChange)outBoundRelationship[typeCode=COMP]
      idn/a
      extensionn/a
      modifierExtensionN/A
      codecode
      value[x]value
      value[x] (valueCodeableConcept)value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (AminoAcidChangeType)outBoundRelationship[typeCode=COMP]
      idn/a
      extensionn/a
      modifierExtensionN/A
      codecode
      value[x]value
      value[x] (valueCodeableConcept)value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (CytogeneticLocation)outBoundRelationship[typeCode=COMP]
      idn/a
      extensionn/a
      modifierExtensionN/A
      codecode
      value[x]value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (CytogeneticNomenclature)outBoundRelationship[typeCode=COMP]
      idn/a
      extensionn/a
      modifierExtensionN/A
      codecode
      value[x]value
      value[x] (valueCodeableConcept)value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

Mappings for FiveWs Pattern Mapping (http://hl7.org/fhir/fivews)

CancerGeneticVariant
Observation
   identifierFiveWs.identifier
   statusFiveWs.status
   categoryFiveWs.class
   category (Laboratory)FiveWs.class
   codeFiveWs.what[x]
   subjectFiveWs.subject[x], FiveWs.subject
   focusFiveWs.subject[x], FiveWs.subject
   encounterFiveWs.context
   effective[x]FiveWs.done[x]
   issuedFiveWs.recorded
   performerFiveWs.actor
   component
      codeFiveWs.what[x]
   component (GeneStudied)
      codeFiveWs.what[x]
   component (VariationCode)
      codeFiveWs.what[x]
   component (GenomicDNAChange)
      codeFiveWs.what[x]
   component (GenomicSourceClass)
      codeFiveWs.what[x]
   component (AminoAcidChange)
      codeFiveWs.what[x]
   component (AminoAcidChangeType)
      codeFiveWs.what[x]
   component (CytogeneticLocation)
      codeFiveWs.what[x]
   component (CytogeneticNomenclature)
      codeFiveWs.what[x]

Mappings for SNOMED CT Attribute Binding (http://snomed.org/attributebinding)

CancerGeneticVariant
Observation
   code116680003 |Is a|
   value[x]363714003 |Interprets|
   value[x] (valueCodeableConcept)363714003 |Interprets|
   interpretation363713009 |Has interpretation|
   specimen704319004 |Inherent in|
   device424226004 |Using device|
   component
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (GeneStudied)
      value[x]363714003 |Interprets|
      value[x] (valueCodeableConcept)363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (VariationCode)
      value[x]363714003 |Interprets|
      value[x] (valueCodeableConcept)363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (GenomicDNAChange)
      value[x]363714003 |Interprets|
      value[x] (valueCodeableConcept)363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (GenomicSourceClass)
      value[x]363714003 |Interprets|
      value[x] (valueCodeableConcept)363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (AminoAcidChange)
      value[x]363714003 |Interprets|
      value[x] (valueCodeableConcept)363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (AminoAcidChangeType)
      value[x]363714003 |Interprets|
      value[x] (valueCodeableConcept)363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (CytogeneticLocation)
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (CytogeneticNomenclature)
      value[x]363714003 |Interprets|
      value[x] (valueCodeableConcept)363714003 |Interprets|
      interpretation363713009 |Has interpretation|