FHIR Osiris Implementation Guide - Local Development build (v2.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

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Resource Profile: BiologicalSample - Mappings

Draft as of 2024-03-21

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]
meta	n/a, N/A
implicitRules	n/a
language	n/a
text	n/a, N/A, Act.text?
contained	Entity. Role, or Act, N/A
extension
extension (BiologicalSampleOrigin)
id	n/a
url	N/A
value[x]	n/a, N/A
value[x] (valueCodeableConcept)	n/a, N/A
id	n/a
extension	n/a, N/A
coding	n/a, CV, union(., ./translation)
text	n/a, ./originalText[mediaType/code="text/plain"]/data
extension (BasedOnCondition)
id	n/a
url	N/A
value[x]	n/a, N/A
value[x] (valueReference)	n/a, N/A
modifierExtension	n/a, N/A
identifier	n/a, II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT], .id
accessionIdentifier	n/a, II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT], .participation[typeCode=SBJ].act[classCode=ACSN, moodCode=EVN].id
status	n/a, status
type	n/a, CD, .code
subject	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity), .scoper or .scoper.playsRole
receivedTime	n/a, .participation[typeCode=SBJ].act[code=SPCREC, moodCode=EVN].effectiveTime
parent	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity), .scoper (if parent) .player.scopesRole[classCode=SPEC].player (if child)
request	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity), outboundRelationship[typeCode=FLFS].target
collection	n/a, .participation[typeCode=SBJ].act[classCode=SPECCOLLECT, moodCode=EVN]
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
collector	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity), .participation[typeCode=PFM].role
collected[x]	n/a, .effectiveTime
collected[x] (collectedDateTime)	n/a, .effectiveTime
duration	n/a, PQ, IVL<PQ>, MO, CO, depending on the values, PQ, IVL<PQ> depending on the values
quantity	n/a, PQ, IVL<PQ>, MO, CO, depending on the values, .participation[typeCode=SBJ].role[classCode=SPEC].player.quantity
id	n/a
extension	n/a, N/A
value	n/a, PQ.value, CO.value, MO.value, IVL.high or IVL.low depending on the value
unit	n/a, PQ.unit
system	n/a, CO.codeSystem, PQ.translation.codeSystem
code	n/a, PQ.code, MO.currency, PQ.translation.code
method	n/a, CD, .methodCode
bodySite	n/a, CD, .targetSiteCode
fastingStatus[x]	n/a
processing	n/a, .participation[typeCode=SBJ].act[code=SPCTRT, moodCode=EVN]
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
description	n/a, .text
procedure	n/a, CD, .code
additive	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity), .participation[typeCode=CSM].role[classCode=ADTV].code
time[x]	n/a, .effectiveTime
container	n/a, .player.scopingRole[classCode=CONT].scoper
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
identifier	n/a, II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT], .id
description	n/a, .desc
type	n/a, CD, .code
capacity	n/a, PQ, IVL<PQ>, MO, CO, depending on the values, .quantity
specimenQuantity	n/a, PQ, IVL<PQ>, MO, CO, depending on the values, .playedRole[classCode=CONT].quantity
additive[x]	n/a, .scopesRole[classCode=ADTV].player
condition	n/a, CD
id	n/a
extension	n/a, N/A
coding	n/a, CV, union(., ./translation)
text	n/a, ./originalText[mediaType/code="text/plain"]/data
note	n/a, Act, .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	CE/CNE/CWE subset one of the sets of component 1-3 or 4-6, C*E.1-8, C*E.10-22
text	C*E.9. But note many systems use C*E.2 for this
identifier	CX / EI (occasionally, more often EI maps to a resource id or a URL), SPM-2
accessionIdentifier	CX / EI (occasionally, more often EI maps to a resource id or a URL), SPM-30 (v2.7+)
status	SPM-20
type	CE/CNE/CWE, 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
duration	SN (see also Range) or CQ
quantity	SN (see also Range) or CQ, 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	CE/CNE/CWE, SPM-7
bodySite	CE/CNE/CWE, SPM-8 and SPM-9
fastingStatus[x]	OBR-
processing
procedure	CE/CNE/CWE
additive	SPM-6
container
identifier	CX / EI (occasionally, more often EI maps to a resource id or a URL), SAC-3
type	CE/CNE/CWE, SPM-27
capacity	SN (see also Range) or CQ, one of: SAC 16, SAC17 and SAC 20, or SAC 21 and SAC 20
specimenQuantity	SN (see also Range) or CQ, SAC-23 (value) SAC-24 (units
additive[x]	SAC-27
condition	CE/CNE/CWE, SPM-24
coding	CE/CNE/CWE subset one of the sets of component 1-3 or 4-6, C*E.1-8, C*E.10-22
text	C*E.9. But note many systems use C*E.2 for this
note	N/A, OBX