Phenomics Exchange for Research and Diagnostics, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/phenomics-exchange-ig/ and changes regularly. See the Directory of published versions

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Resource Profile: Phenopacket - Mappings

Draft as of 2024-06-18

Mappings for the Phenopacket resource profile.

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

Phenopacket
Composition	Event
identifier	Event.identifier
status	Event.status
type	Event.code
category	Event.subject
encounter	Event.context
date	Event.occurrence[x]
author	Event.performer

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

Phenopacket
Composition	Entity. Role, or Act, Document[classCode="DOC" and moodCode="EVN" and isNormalAct()]
text	Act.text?
contained	N/A
extension	N/A
modifierExtension	N/A
identifier	Document.id / Document.setId
status	interim: .completionCode="IN" & ./statusCode[isNormalDatatype()]="active"; final: .completionCode="AU" && ./statusCode[isNormalDatatype()]="complete" and not(./inboundRelationship[typeCode="SUBJ" and isNormalActRelationship()]/source[subsumesCode("ActClass#CACT") and moodCode="EVN" and domainMember("ReviseComposition", code) and isNormalAct()]); amended: .completionCode="AU" && ./statusCode[isNormalDatatype()]="complete" and ./inboundRelationship[typeCode="SUBJ" and isNormalActRelationship()]/source[subsumesCode("ActClass#CACT") and moodCode="EVN" and domainMember("ReviseComposition", code) and isNormalAct() and statusCode="completed"]; withdrawn : .completionCode=NI && ./statusCode[isNormalDatatype()]="obsolete"
type	./code
category	.outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code
subject	.participation[typeCode="SBJ"].role[typeCode="PAT"]
encounter	unique(highest(./outboundRelationship[typeCode="SUBJ" and isNormalActRelationship()], priorityNumber)/target[moodCode="EVN" and classCode=("ENC", "PCPR") and isNormalAct])
date	.effectiveTime[type="TS"]
author	.participation[typeCode="AUT"].role[classCode="ASSIGNED"]
title	./title
confidentiality	.confidentialityCode
attester	.participation[typeCode="AUTHEN"].role[classCode="ASSIGNED"]
id	n/a
extension	n/a
modifierExtension	N/A
mode	unique(./modeCode)
time	./time[type="TS" and isNormalDatatype()]
party	./role[classCode="ASSIGNED" and isNormalRole]/player[determinerCode="INST" and classCode=("DEV", "PSN") and isNormalEntity()] or ./role[classCode="ASSIGNED" and isNormalRole and not(player)]/scoper[determinerCode="INST" and classCode="ORG" and isNormalEntity()]
custodian	.participation[typeCode="RCV"].role[classCode="CUST"].scoper[classCode="ORG" and determinerCode="INST"]
relatesTo	.outboundRelationship
id	n/a
extension	n/a
modifierExtension	N/A
code	.outboundRelationship.typeCode
target[x]	.target[classCode="DOC", moodCode="EVN"].id
event	outboundRelationship[typeCode="SUBJ"].target[classCode<'ACT']
id	n/a
extension	n/a
modifierExtension	N/A
code	.code
period	.effectiveTime
detail	.outboundRelationship[typeCode="SUBJ"].target
section	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
id	n/a
extension	n/a
modifierExtension	N/A
title	./title
code	./code
author	.participation[typeCode="AUT"].role[classCode="ASSIGNED"]
text	.text
mode	.outBoundRelationship[typeCode=COMP].target[classCode=OBS"].value
orderedBy	.outboundRelationship[typeCode=COMP].sequenceNumber > 1
entry	.outboundRelationship[typeCode=COMP] or .participation[typeCode=SBJ]
emptyReason	.inboundRelationship[typeCode=SUBJ,code<ListEmptyReason].value[type=CD]
section	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
section (phenotypic_features)	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
id	n/a
extension	n/a
modifierExtension	N/A
title	./title
code	./code
author	.participation[typeCode="AUT"].role[classCode="ASSIGNED"]
text	.text
mode	.outBoundRelationship[typeCode=COMP].target[classCode=OBS"].value
orderedBy	.outboundRelationship[typeCode=COMP].sequenceNumber > 1
entry	.outboundRelationship[typeCode=COMP] or .participation[typeCode=SBJ]
emptyReason	.inboundRelationship[typeCode=SUBJ,code<ListEmptyReason].value[type=CD]
section	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
section (measurements)	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
id	n/a
extension	n/a
modifierExtension	N/A
title	./title
code	./code
author	.participation[typeCode="AUT"].role[classCode="ASSIGNED"]
text	.text
mode	.outBoundRelationship[typeCode=COMP].target[classCode=OBS"].value
orderedBy	.outboundRelationship[typeCode=COMP].sequenceNumber > 1
entry	.outboundRelationship[typeCode=COMP] or .participation[typeCode=SBJ]
emptyReason	.inboundRelationship[typeCode=SUBJ,code<ListEmptyReason].value[type=CD]
section	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
section (biosamples)	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
id	n/a
extension	n/a
modifierExtension	N/A
title	./title
code	./code
author	.participation[typeCode="AUT"].role[classCode="ASSIGNED"]
text	.text
mode	.outBoundRelationship[typeCode=COMP].target[classCode=OBS"].value
orderedBy	.outboundRelationship[typeCode=COMP].sequenceNumber > 1
entry	.outboundRelationship[typeCode=COMP] or .participation[typeCode=SBJ]
emptyReason	.inboundRelationship[typeCode=SUBJ,code<ListEmptyReason].value[type=CD]
section	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
section (interpretations)	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
id	n/a
extension	n/a
modifierExtension	N/A
title	./title
code	./code
author	.participation[typeCode="AUT"].role[classCode="ASSIGNED"]
text	.text
mode	.outBoundRelationship[typeCode=COMP].target[classCode=OBS"].value
orderedBy	.outboundRelationship[typeCode=COMP].sequenceNumber > 1
entry	.outboundRelationship[typeCode=COMP] or .participation[typeCode=SBJ]
emptyReason	.inboundRelationship[typeCode=SUBJ,code<ListEmptyReason].value[type=CD]
section	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
section (diseases)	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
id	n/a
extension	n/a
modifierExtension	N/A
title	./title
code	./code
author	.participation[typeCode="AUT"].role[classCode="ASSIGNED"]
text	.text
mode	.outBoundRelationship[typeCode=COMP].target[classCode=OBS"].value
orderedBy	.outboundRelationship[typeCode=COMP].sequenceNumber > 1
entry	.outboundRelationship[typeCode=COMP] or .participation[typeCode=SBJ]
emptyReason	.inboundRelationship[typeCode=SUBJ,code<ListEmptyReason].value[type=CD]
section	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
section (files)	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
id	n/a
extension	n/a
modifierExtension	N/A
title	./title
code	./code
author	.participation[typeCode="AUT"].role[classCode="ASSIGNED"]
text	.text
mode	.outBoundRelationship[typeCode=COMP].target[classCode=OBS"].value
orderedBy	.outboundRelationship[typeCode=COMP].sequenceNumber > 1
entry	.outboundRelationship[typeCode=COMP] or .participation[typeCode=SBJ]
emptyReason	.inboundRelationship[typeCode=SUBJ,code<ListEmptyReason].value[type=CD]
section	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
section (medicalActions)	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]
id	n/a
extension	n/a
modifierExtension	N/A
title	./title
code	./code
author	.participation[typeCode="AUT"].role[classCode="ASSIGNED"]
text	.text
mode	.outBoundRelationship[typeCode=COMP].target[classCode=OBS"].value
orderedBy	.outboundRelationship[typeCode=COMP].sequenceNumber > 1
entry	.outboundRelationship[typeCode=COMP] or .participation[typeCode=SBJ]
emptyReason	.inboundRelationship[typeCode=SUBJ,code<ListEmptyReason].value[type=CD]
section	./outboundRelationship[typeCode="COMP" and isNormalActRelationship()]/target[moodCode="EVN" and classCode="DOCSECT" and isNormalAct]

Mappings for CDA (R2) (http://hl7.org/v3/cda)

Phenopacket
Composition	ClinicalDocument
identifier	.setId
status	n/a
type	.code
category	n/a
subject	.recordTarget
encounter	.componentOf.encompassingEncounter
date	.effectiveTime
author	.author.assignedAuthor
title	.title
confidentiality	.confidentialityCode
attester	.authenticator/.legalAuthenticator
mode	implied by .authenticator/.legalAuthenticator
time	.authenticator.time
party	.authenticator.assignedEnttty
custodian	.custodian.assignedCustodian
relatesTo	.relatedDocument
code	.relatedDocument.typeCode
target[x]	.relatedDocument.id
event	.documentationOf.serviceEvent
code	.code
period	.effectiveTime
detail	n/a
section	.component.structuredBody.component.section
title	.title
code	.code
author	.author.assignedAuthor
focus	.subject? (CDA did not differentiate between subject and focus)
text	.text
mode	n/a
orderedBy	n/a
entry	.entry
emptyReason	n/a
section	.component.section
section (phenotypic_features)	.component.structuredBody.component.section
title	.title
code	.code
author	.author.assignedAuthor
focus	.subject? (CDA did not differentiate between subject and focus)
text	.text
mode	n/a
orderedBy	n/a
entry	.entry
emptyReason	n/a
section	.component.section
section (measurements)	.component.structuredBody.component.section
title	.title
code	.code
author	.author.assignedAuthor
focus	.subject? (CDA did not differentiate between subject and focus)
text	.text
mode	n/a
orderedBy	n/a
entry	.entry
emptyReason	n/a
section	.component.section
section (biosamples)	.component.structuredBody.component.section
title	.title
code	.code
author	.author.assignedAuthor
focus	.subject? (CDA did not differentiate between subject and focus)
text	.text
mode	n/a
orderedBy	n/a
entry	.entry
emptyReason	n/a
section	.component.section
section (interpretations)	.component.structuredBody.component.section
title	.title
code	.code
author	.author.assignedAuthor
focus	.subject? (CDA did not differentiate between subject and focus)
text	.text
mode	n/a
orderedBy	n/a
entry	.entry
emptyReason	n/a
section	.component.section
section (diseases)	.component.structuredBody.component.section
title	.title
code	.code
author	.author.assignedAuthor
focus	.subject? (CDA did not differentiate between subject and focus)
text	.text
mode	n/a
orderedBy	n/a
entry	.entry
emptyReason	n/a
section	.component.section
section (files)	.component.structuredBody.component.section
title	.title
code	.code
author	.author.assignedAuthor
focus	.subject? (CDA did not differentiate between subject and focus)
text	.text
mode	n/a
orderedBy	n/a
entry	.entry
emptyReason	n/a
section	.component.section
section (medicalActions)	.component.structuredBody.component.section
title	.title
code	.code
author	.author.assignedAuthor
focus	.subject? (CDA did not differentiate between subject and focus)
text	.text
mode	n/a
orderedBy	n/a
entry	.entry
emptyReason	n/a
section	.component.section

Mappings for FHIR DocumentReference (http://hl7.org/fhir/documentreference)

Phenopacket
Composition	when described by DocumentReference
identifier	DocumentReference.masterIdentifier
status	DocumentReference.status
type	DocumentReference.type
category	DocumenttReference.category
subject	DocumentReference.subject
encounter	DocumentReference.context.encounter
date	DocumentReference.content.attachment.date, DocumentReference.created
author	DocumentReference.agent
title	DocumentReference.description, DocumentReference.content.attachment.title
confidentiality	DocumentReference.securityLabel
attester	DocumentReference.authenticator
custodian	DocumentReference.custodian
relatesTo	DocumentReference.relatesTo
code	DocumentReference.relatesTo.code
target[x]	DocumentReference.relatesTo.target
event	DocumentReference.event
code	DocumentReference.event.code
period	DocumentReference.event.period

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

Phenopacket
Composition
identifier	FiveWs.identifier
status	FiveWs.status
type	FiveWs.class
category	FiveWs.class
subject	FiveWs.subject[x], FiveWs.subject
encounter	FiveWs.context
date	FiveWs.done[x]
author	FiveWs.author
attester
party	FiveWs.witness
section
author	FiveWs.author
mode	FiveWs.class
section (phenotypic_features)
author	FiveWs.author
mode	FiveWs.class
section (measurements)
author	FiveWs.author
mode	FiveWs.class
section (biosamples)
author	FiveWs.author
mode	FiveWs.class
section (interpretations)
author	FiveWs.author
mode	FiveWs.class
section (diseases)
author	FiveWs.author
mode	FiveWs.class
section (files)
author	FiveWs.author
mode	FiveWs.class
section (medicalActions)
author	FiveWs.author
mode	FiveWs.class