This page is part of the OSIRIS FHIR Implementation Guide (v1.1.0: Release) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

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Resource Profile: GenomeEntity - Mappings

Draft as of 2025-04-03

Mappings for the genome-entity resource profile.

Mappings for OSIRIS pivot files (Annotation)

GenomeEntity
MolecularSequence
extension (genomeentityType)	OSIRIS_pivot_Annotation.GenomeEntity_Type
patient	OSIRIS_pivot_Annotation.Patient_Id
repository
repository (genome-entity-db)
name	OSIRIS_pivot_Annotation.GenomeEntity_Database
datasetId	OSIRIS_pivot_Annotation.GenomeEntity_Id

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

GenomeEntity
MolecularSequence
identifier	FiveWs.identifier

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

GenomeEntity
MolecularSequence	Entity. Role, or Act
text	Act.text?
contained	N/A
modifierExtension	N/A
referenceSeq
id	n/a
extension	n/a
modifierExtension	N/A
variant
id	n/a
extension	n/a
modifierExtension	N/A
quality
id	n/a
extension	n/a
modifierExtension	N/A
roc
id	n/a
extension	n/a
modifierExtension	N/A
repository
id	n/a
extension	n/a
modifierExtension	N/A
repository (genome-entity-db)
id	n/a
extension	n/a
modifierExtension	N/A
structureVariant
id	n/a
extension	n/a
modifierExtension	N/A
outer
id	n/a
extension	n/a
modifierExtension	N/A
inner
id	n/a
extension	n/a
modifierExtension	N/A