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Resource Profile: BiologicalSample - Mappings

Draft as of 2025-04-03

Mappings for the onco-biological-sample resource profile.

Mappings for Fhir-osiris to osiris (Patient)

BiologicalSample
Specimen	BiologicalSample	Biological sample description
extension
extension (BiologicalSampleOrigin)
value[x] (valueCodeableConcept)	OSIRIS_pivot_BiologicalSample.BiologicalSample_Origin
extension (BasedOnCondition)
value[x] (valueReference)	OSIRIS_pivot_BiologicalSample.TumorPathologyEvent_Ref
identifier	OSIRIS_pivot_BiologicalSample.BiologicalSample_ExternalAccession
type	OSIRIS_pivot_BiologicalSample.BiologicalSample_Nature
subject	OSIRIS_pivot_BiologicalSample.Patient_Id
parent	OSIRIS_pivot_BiologicalSample.BiologicalSample_ParentExternalAccession
collection
collected[x] (collectedDateTime)	OSIRIS_pivot_BiologicalSample.BiologicalSample_CollectDate
quantity
value	OSIRIS_pivot_BiologicalSample.BiologicalSample_TumorCellularity
bodySite	OSIRIS_pivot_BiologicalSample.BiologicalSample_TopographyCode
condition	OSIRIS_pivot_BiologicalSample.BiologicalSample_StorageTemperature

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

BiologicalSample
Specimen	Entity. Role, or Act, Role[classCode=SPEC]
text	Act.text?
contained	N/A
extension
extension (BiologicalSampleOrigin)
id	n/a
url	N/A
value[x]	N/A
value[x] (valueCodeableConcept)	N/A
id	n/a
extension	n/a
coding	union(., ./translation)
text	./originalText[mediaType/code="text/plain"]/data
extension (BasedOnCondition)
id	n/a
url	N/A
value[x]	N/A
value[x] (valueReference)	N/A
modifierExtension	N/A
identifier	.id
accessionIdentifier	.participation[typeCode=SBJ].act[classCode=ACSN, moodCode=EVN].id
status	status
type	.code
subject	.scoper or .scoper.playsRole
receivedTime	.participation[typeCode=SBJ].act[code=SPCREC, moodCode=EVN].effectiveTime
parent	.scoper (if parent) .player.scopesRole[classCode=SPEC].player (if child)
request	outboundRelationship[typeCode=FLFS].target
collection	.participation[typeCode=SBJ].act[classCode=SPECCOLLECT, moodCode=EVN]
id	n/a
extension	n/a
modifierExtension	N/A
collector	.participation[typeCode=PFM].role
collected[x]	.effectiveTime
collected[x] (collectedDateTime)	.effectiveTime
quantity	.participation[typeCode=SBJ].role[classCode=SPEC].player.quantity
id	n/a
extension	n/a
value	PQ.value, CO.value, MO.value, IVL.high or IVL.low depending on the value
unit	PQ.unit
system	CO.codeSystem, PQ.translation.codeSystem
code	PQ.code, MO.currency, PQ.translation.code
method	.methodCode
bodySite	.targetSiteCode
processing	.participation[typeCode=SBJ].act[code=SPCTRT, moodCode=EVN]
id	n/a
extension	n/a
modifierExtension	N/A
description	.text
procedure	.code
additive	.participation[typeCode=CSM].role[classCode=ADTV].code
time[x]	.effectiveTime
container	.player.scopingRole[classCode=CONT].scoper
id	n/a
extension	n/a
modifierExtension	N/A
identifier	.id
description	.desc
type	.code
capacity	.quantity
specimenQuantity	.playedRole[classCode=CONT].quantity
additive[x]	.scopesRole[classCode=ADTV].player
condition
id	n/a
extension	n/a
coding	union(., ./translation)
text	./originalText[mediaType/code="text/plain"]/data
note	.inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code="annotation"].value

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

BiologicalSample
Specimen
identifier	FiveWs.identifier
accessionIdentifier	FiveWs.identifier
status	FiveWs.status
type	FiveWs.what[x]
subject	FiveWs.subject[x], FiveWs.subject
receivedTime	FiveWs.done[x]
request	FiveWs.why[x]
collection
collector	FiveWs.actor
collected[x]	FiveWs.init
collected[x] (collectedDateTime)	FiveWs.init
duration	FiveWs.init

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

BiologicalSample
Specimen
extension
extension (BiologicalSampleOrigin)
value[x]
value[x] (valueCodeableConcept)
coding	C*E.1-8, C*E.10-22
text	C*E.9. But note many systems use C*E.2 for this
identifier	SPM-2
accessionIdentifier	SPM-30 (v2.7+)
status	SPM-20
type	SPM-4 and possibly SPM-5
receivedTime	SPM-18
request	ORC? OBR-2/3?
collection	SPM-14
collector	PRT
collected[x]	SPM-17
collected[x] (collectedDateTime)	SPM-17
quantity	SPM-12
value	SN.2 / CQ - N/A
unit	(see OBX.6 etc.) / CQ.2
system	(see OBX.6 etc.) / CQ.2
code	(see OBX.6 etc.) / CQ.2
method	SPM-7
bodySite	SPM-8 and SPM-9
fastingStatus[x]	OBR-
processing
additive	SPM-6
container
identifier	SAC-3
type	SPM-27
capacity	one of: SAC 16, SAC17 and SAC 20, or SAC 21 and SAC 20
specimenQuantity	SAC-23 (value) SAC-24 (units
additive[x]	SAC-27
condition	SPM-24
coding	C*E.1-8, C*E.10-22
text	C*E.9. But note many systems use C*E.2 for this
note	OBX