Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Resource Profile: GenomicBase - Mappings

Page standards status: Trial-use Maturity Level: 2

Mappings for the genomic-base resource profile.

Mappings to Structures in this Implementation Guide

No Mappings Found

Mappings to other Structures

No Mappings Found

Other Mappings

NameWorkflow PatternFiveWs Pattern MappingHL7 V2 MappingRIM MappingSNOMED CT Concept Domain BindingSNOMED CT Attribute Bindingdoco
.. Observation
Event
clinical.diagnostics
OBX
  • Entity
  • Role
  • or Act
  • Observation[classCode=OBS
  • moodCode=EVN]
< 363787002 |Observable entity|
... id
... meta
... implicitRules
... language
... text
Act.text?
... contained
N/A
... Slices for extension
.... extension:secondary-finding
.... extension:body-structure
... modifierExtension
N/A
... identifier
Event.identifier
FiveWs.identifier
1) OBR-3 + OBX-3 + OBX-4 or 2) OBR-3 + OBR-4 + OBX-3 + OBX-4 or 3) some other way to uniquely ID the OBR/ORC + OBX-3 + OBX-4.
id
... instantiates[x]
Event.instantiatesCanonical
.outboundRelationship[typeCode=DEFN].target
... basedOn
Event.basedOn
ORC
.inboundRelationship[typeCode=COMP].source[moodCode=EVN]
... triggeredBy
ORC
.inboundRelationship[typeCode=COMP].source[moodCode=EVN]
.... id
n/a
.... extension
n/a
.... modifierExtension
N/A
.... observation
outBoundRelationship
.... type
code
.... reason
annotation
... partOf
Event.partOf
Varies by domain
.outboundRelationship[typeCode=FLFS].target
... status
Event.status
FiveWs.status
OBX-11
status Amended & Final are differentiated by whether it is the subject of a ControlAct event with a type of "revise"
< 445584004 |Report by finality status|
... Slices for category
FiveWs.class
  • .outboundRelationship[typeCode="COMP].target[classCode="LIST"
  • moodCode="EVN"].code
.... category:labCategory
FiveWs.class
  • .outboundRelationship[typeCode="COMP].target[classCode="LIST"
  • moodCode="EVN"].code
..... id
n/a
..... extension
n/a
..... coding
  • C*E.1-8
  • C*E.10-22
  • union(.
  • ./translation)
..... text
C*E.9. But note many systems use C*E.2 for this
./originalText[mediaType/code="text/plain"]/data
.... category:geCategory
FiveWs.class
  • .outboundRelationship[typeCode="COMP].target[classCode="LIST"
  • moodCode="EVN"].code
..... id
n/a
..... extension
n/a
..... coding
  • C*E.1-8
  • C*E.10-22
  • union(.
  • ./translation)
..... text
C*E.9. But note many systems use C*E.2 for this
./originalText[mediaType/code="text/plain"]/data
... code
Event.code
FiveWs.what[x]
OBX-3
code
< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
116680003 |Is a|
... subject
Event.subject
FiveWs.subject[x]
PID-3
participation[typeCode=RTGT]
... focus
FiveWs.subject[x]
OBX-3
participation[typeCode=SBJ]
... organizer
... encounter
Event.encounter
FiveWs.context
PV1
  • inboundRelationship[typeCode=COMP].source[classCode=ENC
  • moodCode=EVN]
... effective[x]
Event.occurrence[x]
FiveWs.done[x]
  • OBX-14
  • and/or OBX-19 after v2.4 (depends on who observation made)
effectiveTime
... issued
FiveWs.recorded
  • OBR-22 (or MSH-7)
  • or perhaps OBX-19 (depends on who observation made)
participation[typeCode=AUT].time
... performer
Event.performer.actor
FiveWs.actor
  • OBX-15 / (Practitioner) OBX-16
  • PRT-4='RO' / (Device) OBX-18
  • PRT-4='EQUIP' / (Organization) OBX-23
  • PRT-4='PO'
participation[typeCode=PRF]
... value[x]
  • OBX-2
  • OBX-5
  • OBX-6
value
< 441742003 |Evaluation finding|
363714003 |Interprets|
... dataAbsentReason
N/A
value.nullFlavor
... interpretation
OBX-8
interpretationCode
< 260245000 |Findings values|
363713009 |Has interpretation|
... note
  • NTE-3 (partner NTE to OBX
  • or sometimes another (child?) OBX)
subjectOf.observationEvent[code="annotation"].value
... bodySite
OBX-20
targetSiteCode
< 123037004 |Body structure|
718497002 |Inherent location|
... bodyStructure
targetSiteCode
... method
OBX-17
methodCode
... specimen
SPM segment
participation[typeCode=SPC].specimen
< 123038009 |Specimen|
704319004 |Inherent in|
... device
OBX-17 / PRT -10
participation[typeCode=DEV]
< 49062001 |Device|
424226004 |Using device|
... referenceRange
OBX-7
  • outboundRelationship[typeCode=REFV]/target[classCode=OBS
  • moodCode=EVN]
.... id
n/a
.... extension
n/a
.... modifierExtension
N/A
.... low
OBX-7
IVL_PQ.low
.... high
OBX-7
IVL_PQ.high
.... normalValue
OBX-7
IVL_PQ.normal
.... type
OBX-10
interpretationCode
< 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
OBX-10
interpretationCode
< 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
outboundRelationship[typeCode=PRCN].targetObservationCriterion[code="age"].value
.... text
OBX-7
ST
... hasMember
Relationships established by OBX-4 usage
outBoundRelationship
... derivedFrom
Relationships established by OBX-4 usage
.targetObservation
... Slices for component
containment by OBX-4?
outBoundRelationship[typeCode=COMP]
.... component:All Slices
..... id
n/a
..... extension
n/a
..... modifierExtension
N/A
..... code
FiveWs.what[x]
OBX-3
code
< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
..... value[x]
  • OBX-2
  • OBX-5
  • OBX-6
value
363714003 |Interprets| < 441742003 |Evaluation finding|
363714003 |Interprets|
..... dataAbsentReason
N/A
value.nullFlavor
..... interpretation
OBX-8
interpretationCode
< 260245000 |Findings values|
363713009 |Has interpretation|
..... referenceRange
OBX-7
  • outboundRelationship[typeCode=REFV]/target[classCode=OBS
  • moodCode=EVN]
.... component:conclusion-string
containment by OBX-4?
outBoundRelationship[typeCode=COMP]
..... id
n/a
..... extension
n/a
..... modifierExtension
N/A
..... code
FiveWs.what[x]
OBX-3
code
< 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
..... value[x]
  • OBX-2
  • OBX-5
  • OBX-6
value
363714003 |Interprets| < 441742003 |Evaluation finding|
363714003 |Interprets|
..... dataAbsentReason
N/A
value.nullFlavor
..... interpretation
OBX-8
interpretationCode
< 260245000 |Findings values|
363713009 |Has interpretation|
..... referenceRange
OBX-7
  • outboundRelationship[typeCode=REFV]/target[classCode=OBS
  • moodCode=EVN]

doco Documentation for this format