Genomics Reporting Implementation Guide (STU1)

This page is part of the Genetic Reporting Implementation Guide (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: GenomicsReport - Mappings

Mappings for the Profile.

Mappings for V2-CG-Results (http://unknown.org/V2-CG-Results)

GenomicsReport
DiagnosticReport
   extension
   extension (RelatedArtifact)
   extension (RecommendedAction)N/A (from other CG FHIR work)
      value[x] (valueReference)N/A (from other CG FHIR work)
   extension (SupportingInfo)N/A (from other CG FHIR work)
      value[x] (valueReference)N/A (from other CG FHIR work)
   result (gen-grouper)TBD
   result (overall)A.8
   result (inh-dis-path)TBD
   result (som-diagnostic)TBD
   result (som-prognostic)TBD
   result (som-predictive)TBD
   result (med-metabolism)TDB
   result (med-efficacy)TDB
   result (med-high-risk)TDB
   result (genotype)TBD
   result (haplotype)TBD
   result (variant)TBD
   result (region-studied)TBD
   presentedFormA.10

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

GenomicsReport
DiagnosticReportEvent
   identifierEvent.identifier
   basedOnEvent.basedOn
   statusEvent.status
   codeEvent.code
   subjectEvent.subject
   encounterEvent.encounter
   effective[x]Event.occurrence[x]
   effective[x] (effectiveDateTime)Event.occurrence[x]
   performerEvent.performer.actor
   resultsInterpreterEvent.performer.actor

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

GenomicsReport
DiagnosticReportORU -> OBR
   identifierOBR-51/ for globally unique filler ID - OBR-3 , For non-globally unique filler-id the flller/placer number must be combined with the universal service Id - OBR-2(if present)+OBR-3+OBR-4
   basedOnORC? OBR-2/3?
   statusOBR-25 (not 1:1 mapping)
   categoryOBR-24
   codeOBR-4 (HL7 v2 doesn't provide an easy way to indicate both the ordered test and the performed panel)
      codingC*E.1-8, C*E.10-22
      coding (code)C*E.1-8, C*E.10-22
         systemC*E.3
         versionC*E.7
         codeC*E.1
         displayC*E.2 - but note this is not well followed
         userSelectedSometimes implied by being first
      textC*E.9. But note many systems use C*E.2 for this
   subjectPID-3 (no HL7 v2 mapping for Group or Device)
   encounterPV1-19
   effective[x]OBR-7
   effective[x] (effectiveDateTime)OBR-7
   issuedOBR-22
   performerPRT-8 (where this PRT-4-Participation = "PO")
   resultsInterpreterOBR-32, PRT-8 (where this PRT-4-Participation = "PI")
   specimenSPM
   resultOBXs
   result (gen-grouper)OBXs
   result (overall)OBXs
   result (inh-dis-path)OBXs
   result (som-diagnostic)OBXs
   result (som-prognostic)OBXs
   result (som-predictive)OBXs
   result (med-metabolism)OBXs
   result (med-efficacy)OBXs
   result (med-transporter)OBXs
   result (med-high-risk)OBXs
   result (genotype)OBXs
   result (haplotype)OBXs
   result (variant)OBXs
   result (sequence-phase-relation)OBXs
   result (region-studied)OBXs
   mediaOBX?
   conclusionOBX
   conclusionCodeOBX
   presentedFormOBX

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

GenomicsReport
DiagnosticReportEntity. Role, or Act
   textAct.text?
   containedN/A
   extension
   extension (RelatedArtifact)
   extension (RecommendedAction)
      idn/a
      extensionn/a
      urlN/A
      value[x] (valueReference)N/A
   extension (SupportingInfo)
      idn/a
      extensionn/a
      urlN/A
      value[x] (valueReference)N/A
   extension (risk)
      idn/a
      urlN/A
      value[x]N/A
      value[x] (valueReference)N/A
   modifierExtensionN/A
   identifierid
   basedOnoutboundRelationship[typeCode=FLFS].target
   statusstatusCode Note: final and amended are distinguished by whether observation is the subject of a ControlAct event of type "revise"
   categoryinboundRelationship[typeCode=COMP].source[classCode=LIST, moodCode=EVN, code < LabService].code
   codecode
      idn/a
      extensionn/a
      codingunion(., ./translation)
      coding (code)union(., ./translation)
         idn/a
         extensionn/a
         system./codeSystem
         version./codeSystemVersion
         code./code
         displayCV.displayName
         userSelectedCD.codingRationale
      text./originalText[mediaType/code="text/plain"]/data
   subjectparticipation[typeCode=SBJ]
   encounterinboundRelationship[typeCode=COMP].source[classCode=ENC, moodCode=EVN]
   effective[x]effectiveTime
   effective[x] (effectiveDateTime)effectiveTime
   issuedparticipation[typeCode=VRF or AUT].time
   performer.participation[typeCode=PRF]
   resultsInterpreter.participation[typeCode=PRF]
   specimenparticipation[typeCode=SBJ]
   resultoutboundRelationship[typeCode=COMP].target
   result (gen-grouper)outboundRelationship[typeCode=COMP].target
   result (overall)outboundRelationship[typeCode=COMP].target
   result (inh-dis-path)outboundRelationship[typeCode=COMP].target
   result (som-diagnostic)outboundRelationship[typeCode=COMP].target
   result (som-prognostic)outboundRelationship[typeCode=COMP].target
   result (som-predictive)outboundRelationship[typeCode=COMP].target
   result (med-metabolism)outboundRelationship[typeCode=COMP].target
   result (med-efficacy)outboundRelationship[typeCode=COMP].target
   result (med-transporter)outboundRelationship[typeCode=COMP].target
   result (med-high-risk)outboundRelationship[typeCode=COMP].target
   result (genotype)outboundRelationship[typeCode=COMP].target
   result (haplotype)outboundRelationship[typeCode=COMP].target
   result (variant)outboundRelationship[typeCode=COMP].target
   result (sequence-phase-relation)outboundRelationship[typeCode=COMP].target
   result (region-studied)outboundRelationship[typeCode=COMP].target
   mediaoutboundRelationship[typeCode=COMP].target
      idn/a
      extensionn/a
      modifierExtensionN/A
      comment.inboundRelationship[typeCode=COMP].source[classCode=OBS, moodCode=EVN, code="annotation"].value
      link.value.reference
   conclusioninboundRelationship[typeCode="SPRT"].source[classCode=OBS, moodCode=EVN, code=LOINC:48767-8].value (type=ST)
   conclusionCodeinboundRelationship[typeCode=SPRT].source[classCode=OBS, moodCode=EVN, code=LOINC:54531-9].value (type=CD)
   presentedFormtext (type=ED)

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

GenomicsReport
DiagnosticReport
   identifierFiveWs.identifier
   statusFiveWs.status
   categoryFiveWs.class
   codeFiveWs.what[x]
   subjectFiveWs.subject[x]
   encounterFiveWs.context
   effective[x]FiveWs.done[x]
   effective[x] (effectiveDateTime)FiveWs.done[x]
   issuedFiveWs.recorded
   performerFiveWs.actor
   resultsInterpreterFiveWs.actor