Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 3.0.0. For a full list of available versions, see the Directory of published versions

Resource Profile: MolecularConsequence - Mappings

Active as of 2023-12-18

Mappings for the molecular-consequence resource profile.

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

MolecularConsequence
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)

MolecularConsequence
Observation< 363787002 |Observable entity|
   status< 445584004 |Report by finality status|
   code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
   interpretation< 260245000 |Findings values|
   bodySite< 123037004 |Body structure|
   specimen< 123038009 |Specimen|
   device< 49062001 |Device|
   referenceRange
      type< 260245000 |Findings values| OR < 365860008 |General clinical state finding| OR < 250171008 |Clinical history or observation findings| OR < 415229000 |Racial group| OR < 365400002 |Finding of puberty stage| OR < 443938003 |Procedure carried out on subject|
      appliesTo< 260245000 |Findings values| OR < 365860008 |General clinical state finding| OR < 250171008 |Clinical history or observation findings| OR < 415229000 |Racial group| OR < 365400002 |Finding of puberty stage| OR < 443938003 |Procedure carried out on subject|
   component
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (conclusion-string)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (evidence-level)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (coding-hgvs)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (transcript-ref-seq)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (protein-hgvs)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (protein-ref-seq)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (feature-consequence)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|
   component (functional-effect)
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      interpretation< 260245000 |Findings values|

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

MolecularConsequence
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
   category
   category (labCategory)
      codingC*E.1-8, C*E.10-22
      textC*E.9. But note many systems use C*E.2 for this
   category (geCategory)
      codingC*E.1-8, C*E.10-22
      textC*E.9. But note many systems use C*E.2 for this
   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'
   dataAbsentReasonN/A
   interpretationOBX-8
   noteN/A
   bodySiteOBX-20
   methodOBX-17
   specimenSPM segment
   deviceOBX-17 / PRT -10
   referenceRangeOBX.7
      lowOBX-7
      highOBX-7
      typeOBX-10
      appliesToOBX-10
      textOBX-7
   hasMemberRelationships established by OBX-4 usage
   derivedFromRelationships established by OBX-4 usage
   derivedFrom (variant)Relationships established by OBX-4 usage
   derivedFrom (genotype)Relationships established by OBX-4 usage
   derivedFrom (haplotype)Relationships established by OBX-4 usage
   derivedFrom (biomarker)Relationships 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 (conclusion-string)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (evidence-level)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (coding-hgvs)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (transcript-ref-seq)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (protein-hgvs)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (protein-ref-seq)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (feature-consequence)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7
   component (functional-effect)containment by OBX-4?
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7

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

MolecularConsequence
ObservationEntity. Role, or Act, Observation[classCode=OBS, moodCode=EVN]
   textAct.text?
   containedN/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 (labCategory).outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code
      idn/a
      extensionn/a
      codingunion(., ./translation)
      text./originalText[mediaType/code="text/plain"]/data
   category (geCategory).outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code
      idn/a
      extensionn/a
      codingunion(., ./translation)
      text./originalText[mediaType/code="text/plain"]/data
   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]
   dataAbsentReasonvalue.nullFlavor
   interpretationinterpretationCode
   noten/a, Act
   bodySitetargetSiteCode
   methodmethodCode
   specimenparticipation[typeCode=SPC].specimen
   deviceparticipation[typeCode=DEV]
   referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
      idn/a
      extensionn/a
      modifierExtensionN/A
      lowvalue:IVL_PQ.low
      highvalue:IVL_PQ.high
      typeinterpretationCode
      appliesTointerpretationCode
      ageoutboundRelationship[typeCode=PRCN].targetObservationCriterion[code="age"].value
      textvalue:ST
   hasMemberoutBoundRelationship
   derivedFrom.targetObservation
   derivedFrom (variant).targetObservation
   derivedFrom (genotype).targetObservation
   derivedFrom (haplotype).targetObservation
   derivedFrom (biomarker).targetObservation
   componentoutBoundRelationship[typeCode=COMP]
      idn/a
      modifierExtensionN/A
      codecode
      value[x]value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (conclusion-string)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 (evidence-level)outBoundRelationship[typeCode=COMP]
      idn/a
      modifierExtensionN/A
      codecode
      value[x]value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (coding-hgvs)outBoundRelationship[typeCode=COMP]
      idn/a
      modifierExtensionN/A
      codecode
      value[x]value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (transcript-ref-seq)outBoundRelationship[typeCode=COMP]
      idn/a
      modifierExtensionN/A
      codecode
      value[x]value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (protein-hgvs)outBoundRelationship[typeCode=COMP]
      idn/a
      modifierExtensionN/A
      codecode
      value[x]value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (protein-ref-seq)outBoundRelationship[typeCode=COMP]
      idn/a
      modifierExtensionN/A
      codecode
      value[x]value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (feature-consequence)outBoundRelationship[typeCode=COMP]
      idn/a
      modifierExtensionN/A
      codecode
      value[x]value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]
   component (functional-effect)outBoundRelationship[typeCode=COMP]
      idn/a
      modifierExtensionN/A
      codecode
      value[x]value
      dataAbsentReasonvalue.nullFlavor
      interpretationinterpretationCode
      referenceRangeoutboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

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

MolecularConsequence
Observation
   identifierFiveWs.identifier
   statusFiveWs.status
   categoryFiveWs.class
   category (labCategory)FiveWs.class
   category (geCategory)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 (conclusion-string)
      codeFiveWs.what[x]
   component (evidence-level)
      codeFiveWs.what[x]
   component (coding-hgvs)
      codeFiveWs.what[x]
   component (transcript-ref-seq)
      codeFiveWs.what[x]
   component (protein-hgvs)
      codeFiveWs.what[x]
   component (protein-ref-seq)
      codeFiveWs.what[x]
   component (feature-consequence)
      codeFiveWs.what[x]
   component (functional-effect)
      codeFiveWs.what[x]

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

MolecularConsequence
Observation
   code116680003 |Is a|
   interpretation363713009 |Has interpretation|
   bodySite718497002 |Inherent location|
   specimen704319004 |Inherent in|
   device424226004 |Using device|
   component
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (conclusion-string)
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (evidence-level)
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (coding-hgvs)
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (transcript-ref-seq)
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (protein-hgvs)
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (protein-ref-seq)
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (feature-consequence)
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|
   component (functional-effect)
      value[x]363714003 |Interprets|
      interpretation363713009 |Has interpretation|