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: GenomeEntity - Mappings

Draft as of 2024-03-21

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
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
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]
coordinateSystem	n/a
patient	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity)
specimen	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity)
device	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity)
performer	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity)
quantity	n/a, PQ, IVL<PQ>, MO, CO, depending on the values
referenceSeq	n/a
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
chromosome	n/a, CD
genomeBuild	n/a
orientation	n/a
referenceSeqId	n/a, CD
referenceSeqPointer	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity)
referenceSeqString	n/a
strand	n/a
windowStart	n/a
windowEnd	n/a
variant	n/a
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
start	n/a
end	n/a
observedAllele	n/a
referenceAllele	n/a
cigar	n/a
variantPointer	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity)
observedSeq	n/a
quality	n/a
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
type	n/a
standardSequence	n/a, CD
start	n/a
end	n/a
score	n/a, PQ, IVL<PQ>, MO, CO, depending on the values
method	n/a, CD
truthTP	n/a
queryTP	n/a
truthFN	n/a
queryFP	n/a
gtFP	n/a
precision	n/a
recall	n/a
fScore	n/a
roc	n/a
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
score	n/a
numTP	n/a
numFP	n/a
numFN	n/a
precision	n/a
sensitivity	n/a
fMeasure	n/a
readCoverage	n/a
repository	n/a
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
type	n/a
url	n/a
name	n/a
datasetId	n/a
variantsetId	n/a
readsetId	n/a
repository (genome-entity-db)	n/a
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
type	n/a
url	n/a
name	n/a
datasetId	n/a
variantsetId	n/a
readsetId	n/a
pointer	n/a, The target of a resource reference is a RIM entry point (Act, Role, or Entity)
structureVariant	n/a
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
variantType	n/a, CD
exact	n/a
length	n/a
outer	n/a
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
start	n/a
end	n/a
inner	n/a
id	n/a
extension	n/a, N/A
modifierExtension	n/a, N/A
start	n/a
end	n/a