FHIR Release 3 (STU)

This page is part of the FHIR Specification (v3.0.2: STU 3). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R4B R4 R3

10.1.14.6.5 StructureDefinition: Observation-Genetics - Mappings

Mappings:

Workflow Mapping

SNOMED CT Concept Domain Binding

HL7 v2 Mapping

RIM Mapping

W5 Mapping

SNOMED CT Attribute Binding

Mappings for the observation-genetics Profile.

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

Observation-genetics
ObservationEvent
   id
   meta
   implicitRules
   language
   text
   contained
   extension
   extensionDNASequenceVariantName
   extensionDNAVariantId
   extensionDNASequenceVariantType
   extensionAminoAcidChangeName
   extensionAminoAcidChangeType
   extensionGeneSymbol
   extensionDNARegionName
   extensionAlleleName
   extensionAllelicState
   extensionAllelicFrequency
   extensionCopyNumberEvent
   extensionGenomicSourceClass
   extensionPhaseSet
   extensionSequence
   extensionInterpretation
   modifierExtension
   identifierEvent.identifier
   basedOnEvent.basedOn
   statusEvent.status
   category
   codeEvent.code
   subjectEvent.subject
   contextEvent.context
   effective[x]Event.occurrence[x]
   issued
   performerEvent.performer
   value[x]Event.notDone, Event.notDoneReason (maps to valeu[x] or dataAbsentReason)
   dataAbsentReasonEvent.notDone, Event.notDoneReason (maps to valeu[x] or dataAbsentReason)
   interpretation
   commentEvent.note
   bodySite
   method
   specimen
   device
   referenceRange
      id
      extension
      modifierExtension
      low
      high
      type
      appliesTo
      age
      text
   related
      id
      extension
      modifierExtension
      type
      target
   component
      id
      extension
      modifierExtension
      code
      value[x]
      dataAbsentReason
      interpretation
      referenceRange

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

Concept domain bindings link a resource or an element to a set of SNOMED CT concepts that represent the intended semantics of the instances (whether or not SNOMED CT is used to encode that data element). This set of concepts is represented using a SNOMED CT expression constraint. Note that the 'Concept domain binding' may be a superset of the 'value set binding'. These bindings help to support:

  • Quality checking FHIR resources by ensuring that (a) the intended semantics of the instances matches the valid range of the corresponding SNOMED CT attribute, and (b) the intended value set is appropriate for the intended semantics of the instances
  • Semantic checking of data instances by helping to detect potential inconsistencies caused by overlap between the semantics incorporated in two concept domains
Observation-genetics
Observation< 363787002 |Observable entity|
   id
   meta
   implicitRules
   language
   text
   contained
   extension
   extensionDNASequenceVariantName
   extensionDNAVariantId
   extensionDNASequenceVariantType
   extensionAminoAcidChangeName
   extensionAminoAcidChangeType
   extensionGeneSymbol
   extensionDNARegionName
   extensionAlleleName
   extensionAllelicState
   extensionAllelicFrequency
   extensionCopyNumberEvent
   extensionGenomicSourceClass
   extensionPhaseSet
   extensionSequence
   extensionInterpretation
   modifierExtension
   identifier
   basedOn
   status< 445584004 |Report by finality status|
   category
   code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
   subject
   context
   effective[x]
   issued
   performer
   value[x]< 441742003 |Evaluation finding|
   dataAbsentReason
   interpretation< 260245000 |Findings values|
   comment
   bodySite< 123037004 |Body structure|
   method
   specimen< 123038009 |Specimen|
   device< 49062001 |Device|
   referenceRange
      id
      extension
      modifierExtension
      low
      high
      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|
      age
      text
   related
      id
      extension
      modifierExtension
      type
      target
   component
      id
      extension
      modifierExtension
      code< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
      value[x]363714003 |Interprets| < 441742003 |Evaluation finding|
      dataAbsentReason
      interpretation< 260245000 |Findings values|
      referenceRange

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

Observation-genetics
ObservationOBX
   id
   meta
   implicitRules
   language
   text
   contained
   extension
   extensionDNASequenceVariantName
   extensionDNAVariantId
   extensionDNASequenceVariantType
   extensionAminoAcidChangeName
   extensionAminoAcidChangeType
   extensionGeneSymbol
   extensionDNARegionName
   extensionAlleleName
   extensionAllelicState
   extensionAllelicFrequency
   extensionCopyNumberEvent
   extensionGenomicSourceClass
   extensionPhaseSet
   extensionSequence
   extensionInterpretation
   modifierExtension
   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
   statusOBX-11
   category
   codeOBX-3
   subjectPID-3
   contextPV1
   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
   dataAbsentReasonN/A
   interpretationOBX-8
   commentNTE.3 (partner NTE to OBX, or sometimes another (child?) OBX)
   bodySiteOBX-20
   methodOBX-17
   specimenSPM segment
   deviceOBX-17 / PRT -10
   referenceRangeOBX.7
      id
      extension
      modifierExtension
      lowOBX-7
      highOBX-7
      typeOBX-10
      appliesToOBX-10
      age
      textOBX-7
   relatedRelationships established by OBX-4 usage
      id
      extension
      modifierExtension
      typeN/A
      target
   componentcontainment by OBX-4?
      id
      extension
      modifierExtension
      codeOBX-3
      value[x]OBX.2, OBX.5, OBX.6
      dataAbsentReasonN/A
      interpretationOBX-8
      referenceRangeOBX.7

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

Observation-genetics
ObservationEntity. Role, or Act
   id
   meta
   implicitRules
   language
   textAct.text?
   containedN/A
   extension
   extensionDNASequenceVariantName
   extensionDNAVariantId
   extensionDNASequenceVariantType
   extensionAminoAcidChangeName
   extensionAminoAcidChangeType
   extensionGeneSymbol
   extensionDNARegionName
   extensionAlleleName
   extensionAllelicState
   extensionAllelicFrequency
   extensionCopyNumberEvent
   extensionGenomicSourceClass
   extensionPhaseSet
   extensionSequence
   extensionInterpretation
   modifierExtensionN/A
   identifierid
   basedOn.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
   codecode
   subjectparticipation[typeCode=SBJ]
   contextinboundRelationship[typeCode=COMP].source[classCode=ENC, moodCode=EVN]
   effective[x]effectiveTime
   issuedparticipation[typeCode=AUT].time
   performerparticipation[typeCode=PRF]
   value[x]value
   dataAbsentReasonvalue.nullFlavor
   interpretationinterpretationCode
   commentsubjectOf.observationEvent[code="annotation"].value
   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
   relatedoutBoundRelationship
      idn/a
      extensionn/a
      modifierExtensionN/A
      type.typeCode
      target.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]

10.1.14.11 Mappings for W5 Mapping (http://hl7.org/fhir/w5)

Observation-genetics
Observationclinical.diagnostics
   id
   meta
   implicitRules
   language
   text
   contained
   extension
   extensionDNASequenceVariantName
   extensionDNAVariantId
   extensionDNASequenceVariantType
   extensionAminoAcidChangeName
   extensionAminoAcidChangeType
   extensionGeneSymbol
   extensionDNARegionName
   extensionAlleleName
   extensionAllelicState
   extensionAllelicFrequency
   extensionCopyNumberEvent
   extensionGenomicSourceClass
   extensionPhaseSet
   extensionSequence
   extensionInterpretation
   modifierExtension
   identifierid
   basedOn
   statusstatus
   categoryclass
   codewhat
   subjectwho.focus
   contextcontext
   effective[x]when.done
   issuedwhen.recorded
   performerwho.actor
   value[x]
   dataAbsentReason
   interpretation
   comment
   bodySite
   method
   specimen
   device
   referenceRange
      id
      extension
      modifierExtension
      low
      high
      type
      appliesTo
      age
      text
   related
      id
      extension
      modifierExtension
      type
      target
   component
      id
      extension
      modifierExtension
      codewhat
      value[x]
      dataAbsentReason
      interpretation
      referenceRange

10.1.14.12 Mappings for SNOMED CT Attribute Binding (http://snomed.info/sct)

Attribute bindings link coded data elements in FHIR resources to a corresponding attribute in the SNOMED CT concept model. These bindings help to support:

  • clarifying the intended meaning of the data element
  • Quality checking the alignment between FHIR resource design and any coresponding SNOMED CT concept model
  • Composition and decomposition of data instances by indicating the SNOMED CT concept model attribute whose value may be used to decompose a precoordinated concept into this data element
Observation-genetics
Observation
   id
   meta
   implicitRules
   language
   text
   contained
   extension
   extensionDNASequenceVariantName
   extensionDNAVariantId
   extensionDNASequenceVariantType
   extensionAminoAcidChangeName
   extensionAminoAcidChangeType
   extensionGeneSymbol
   extensionDNARegionName
   extensionAlleleName
   extensionAllelicState
   extensionAllelicFrequency
   extensionCopyNumberEvent
   extensionGenomicSourceClass
   extensionPhaseSet
   extensionSequence
   extensionInterpretation
   modifierExtension
   identifier
   basedOn
   status
   category
   code116680003 |Is a|
   subject
   context
   effective[x]
   issued
   performer
   value[x]363714003 |Interprets|
   dataAbsentReason
   interpretation363713009 |Has interpretation|
   comment
   bodySite718497002 |Inherent location|
   method
   specimen704319004 |Inherent in|
   device424226004 |Using device|
   referenceRange
      id
      extension
      modifierExtension
      low
      high
      type
      appliesTo
      age
      text
   related
      id
      extension
      modifierExtension
      type
      target
   component
      id
      extension
      modifierExtension
      code
      value[x]363714003 |Interprets|
      dataAbsentReason
      interpretation363713009 |Has interpretation|
      referenceRange