Sequence - FHIR v3.5.0

R4 Ballot #2 (Mixed Normative/Trial use)

This page is part of the FHIR Specification (v3.5.0: R4 Ballot #2). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions

10.6.2 Resource Sequence - R3/R4 Conversions

Clinical Genomics

Work Group

Maturity Level: N/A

Ballot Status: Informative

Compartments: Not linked to any defined compartments

R3 : R4 Conversion maps for Sequence.

Functional status for this map: 16 tests that all execute ok. 16 fail round-trip testing and 16 r3 resources are invalid (0 errors). (see documentation)

10.6.2.1 R3 to R4

map "http://hl7.org/fhir/StructureMap/Sequence3to4" = "R3 to R4 Conversions for Sequence"


uses "http://hl7.org/fhir/3.0/StructureDefinition/Sequence" alias SequenceR3 as source
uses "http://hl7.org/fhir/StructureDefinition/Sequence" alias Sequence as target

imports "http://hl7.org/fhir/StructureMap/*3to4"



group Sequence extends DomainResource
  input src : SequenceR3 as source
  input tgt : Sequence as target

  "Sequence.identifier" : for src.identifier as vs make tgt.identifier as vt
  "Sequence.type" : for src.type as vs make tgt.type as vt
  "Sequence.coordinateSystem" : for src.coordinateSystem as vs make tgt.coordinateSystem as vt
  "Sequence.patient" : for src.patient as vs make tgt.patient as vt
  "Sequence.specimen" : for src.specimen as vs make tgt.specimen as vt
  "Sequence.device" : for src.device as vs make tgt.device as vt
  "Sequence.performer" : for src.performer as vs make tgt.performer as vt
  "Sequence.quantity" : for src.quantity as vs make tgt.quantity as vt
  "Sequence.referenceSeq" : for src.referenceSeq as vs0 make tgt.referenceSeq as vt0 then {
    "Sequence.referenceSeq.chromosome" : for vs0.chromosome as vs make vt0.chromosome as vt
    "Sequence.referenceSeq.genomeBuild" : for vs0.genomeBuild as vs make vt0.genomeBuild as vt
    "Sequence.referenceSeq.referenceSeqId" : for vs0.referenceSeqId as vs make vt0.referenceSeqId as vt
    "Sequence.referenceSeq.referenceSeqPointer" : for vs0.referenceSeqPointer as vs make vt0.referenceSeqPointer as vt
    "Sequence.referenceSeq.referenceSeqString" : for vs0.referenceSeqString as vs make vt0.referenceSeqString as vt
    "Sequence.referenceSeq.windowEnd" : for vs0.windowEnd as vs make vt0.windowEnd as vt
  }
  "Sequence.variant" : for src.variant as vs0 make tgt.variant as vt0 then {
    "Sequence.variant.start" : for vs0.start as vs make vt0.start as vt
    "Sequence.variant.end" : for vs0.end as vs make vt0.end as vt
    "Sequence.variant.observedAllele" : for vs0.observedAllele as vs make vt0.observedAllele as vt
    "Sequence.variant.referenceAllele" : for vs0.referenceAllele as vs make vt0.referenceAllele as vt
    "Sequence.variant.cigar" : for vs0.cigar as vs make vt0.cigar as vt
    "Sequence.variant.variantPointer" : for vs0.variantPointer as vs make vt0.variantPointer as vt
  }
  "Sequence.observedSeq" : for src.observedSeq as vs make tgt.observedSeq as vt
  "Sequence.quality" : for src.quality as vs0 make tgt.quality as vt0 then {
    "Sequence.quality.type" : for vs0.type as vs make vt0.type as vt
    "Sequence.quality.standardSequence" : for vs0.standardSequence as vs make vt0.standardSequence as vt
    "Sequence.quality.start" : for vs0.start as vs make vt0.start as vt
    "Sequence.quality.end" : for vs0.end as vs make vt0.end as vt
    "Sequence.quality.score" : for vs0.score as vs make vt0.score as vt
    "Sequence.quality.method" : for vs0.method as vs make vt0.method as vt
    "Sequence.quality.truthTP" : for vs0.truthTP as vs make vt0.truthTP as vt
    "Sequence.quality.queryTP" : for vs0.queryTP as vs make vt0.queryTP as vt
    "Sequence.quality.truthFN" : for vs0.truthFN as vs make vt0.truthFN as vt
    "Sequence.quality.queryFP" : for vs0.queryFP as vs make vt0.queryFP as vt
    "Sequence.quality.gtFP" : for vs0.gtFP as vs make vt0.gtFP as vt
    "Sequence.quality.precision" : for vs0.precision as vs make vt0.precision as vt
    "Sequence.quality.recall" : for vs0.recall as vs make vt0.recall as vt
    "Sequence.quality.fScore" : for vs0.fScore as vs make vt0.fScore as vt
  }
  "Sequence.readCoverage" : for src.readCoverage as vs make tgt.readCoverage as vt
  "Sequence.repository" : for src.repository as vs0 make tgt.repository as vt0 then {
    "Sequence.repository.type" : for vs0.type as vs make vt0.type as vt
    "Sequence.repository.url" : for vs0.url as vs make vt0.url as vt
    "Sequence.repository.name" : for vs0.name as vs make vt0.name as vt
    "Sequence.repository.datasetId" : for vs0.datasetId as vs make vt0.datasetId as vt
    "Sequence.repository.variantsetId" : for vs0.variantsetId as vs make vt0.variantsetId as vt
    "Sequence.repository.readsetId" : for vs0.readsetId as vs make vt0.readsetId as vt
  }
  "Sequence.pointer" : for src.pointer as vs make tgt.pointer as vt
endgroup

10.6.2.2 R4 to R3

map "http://hl7.org/fhir/StructureMap/Sequence4to3" = "R4 to R3 Conversion for Sequence"


uses "http://hl7.org/fhir/StructureDefinition/Sequence" alias Sequence as source
uses "http://hl7.org/fhir/3.0/StructureDefinition/Sequence" alias SequenceR3 as target

imports "http://hl7.org/fhir/StructureMap/*4to3"



group Sequence extends DomainResource
  input src : Sequence as source
  input tgt : SequenceR3 as target

  "Sequence.identifier" : for src.identifier as vs make tgt.identifier as vt
  "Sequence.type" : for src.type as vs make tgt.type as vt
  "Sequence.coordinateSystem" : for src.coordinateSystem as vs make tgt.coordinateSystem as vt
  "Sequence.patient" : for src.patient as vs make tgt.patient as vt
  "Sequence.specimen" : for src.specimen as vs make tgt.specimen as vt
  "Sequence.device" : for src.device as vs make tgt.device as vt
  "Sequence.performer" : for src.performer as vs make tgt.performer as vt
  "Sequence.quantity" : for src.quantity as vs make tgt.quantity as vt
  "Sequence.referenceSeq" : for src.referenceSeq as vs0 make tgt.referenceSeq as vt0 then {
    "Sequence.referenceSeq.chromosome" : for vs0.chromosome as vs make vt0.chromosome as vt
    "Sequence.referenceSeq.genomeBuild" : for vs0.genomeBuild as vs make vt0.genomeBuild as vt
    "Sequence.referenceSeq.referenceSeqId" : for vs0.referenceSeqId as vs make vt0.referenceSeqId as vt
    "Sequence.referenceSeq.referenceSeqPointer" : for vs0.referenceSeqPointer as vs make vt0.referenceSeqPointer as vt
    "Sequence.referenceSeq.referenceSeqString" : for vs0.referenceSeqString as vs make vt0.referenceSeqString as vt
    "Sequence.referenceSeq.windowEnd" : for vs0.windowEnd as vs make vt0.windowEnd as vt
  }
  "Sequence.variant" : for src.variant as vs0 make tgt.variant as vt0 then {
    "Sequence.variant.start" : for vs0.start as vs make vt0.start as vt
    "Sequence.variant.end" : for vs0.end as vs make vt0.end as vt
    "Sequence.variant.observedAllele" : for vs0.observedAllele as vs make vt0.observedAllele as vt
    "Sequence.variant.referenceAllele" : for vs0.referenceAllele as vs make vt0.referenceAllele as vt
    "Sequence.variant.cigar" : for vs0.cigar as vs make vt0.cigar as vt
    "Sequence.variant.variantPointer" : for vs0.variantPointer as vs make vt0.variantPointer as vt
  }
  "Sequence.observedSeq" : for src.observedSeq as vs make tgt.observedSeq as vt
  "Sequence.quality" : for src.quality as vs0 make tgt.quality as vt0 then {
    "Sequence.quality.type" : for vs0.type as vs make vt0.type as vt
    "Sequence.quality.standardSequence" : for vs0.standardSequence as vs make vt0.standardSequence as vt
    "Sequence.quality.start" : for vs0.start as vs make vt0.start as vt
    "Sequence.quality.end" : for vs0.end as vs make vt0.end as vt
    "Sequence.quality.score" : for vs0.score as vs make vt0.score as vt
    "Sequence.quality.method" : for vs0.method as vs make vt0.method as vt
    "Sequence.quality.truthTP" : for vs0.truthTP as vs make vt0.truthTP as vt
    "Sequence.quality.queryTP" : for vs0.queryTP as vs make vt0.queryTP as vt
    "Sequence.quality.truthFN" : for vs0.truthFN as vs make vt0.truthFN as vt
    "Sequence.quality.queryFP" : for vs0.queryFP as vs make vt0.queryFP as vt
    "Sequence.quality.gtFP" : for vs0.gtFP as vs make vt0.gtFP as vt
    "Sequence.quality.precision" : for vs0.precision as vs make vt0.precision as vt
    "Sequence.quality.recall" : for vs0.recall as vs make vt0.recall as vt
    "Sequence.quality.fScore" : for vs0.fScore as vs make vt0.fScore as vt
  }
  "Sequence.readCoverage" : for src.readCoverage as vs make tgt.readCoverage as vt
  "Sequence.repository" : for src.repository as vs0 make tgt.repository as vt0 then {
    "Sequence.repository.type" : for vs0.type as vs make vt0.type as vt
    "Sequence.repository.url" : for vs0.url as vs make vt0.url as vt
    "Sequence.repository.name" : for vs0.name as vs make vt0.name as vt
    "Sequence.repository.datasetId" : for vs0.datasetId as vs make vt0.datasetId as vt
    "Sequence.repository.variantsetId" : for vs0.variantsetId as vs make vt0.variantsetId as vt
    "Sequence.repository.readsetId" : for vs0.readsetId as vs make vt0.readsetId as vt
  }
  "Sequence.pointer" : for src.pointer as vs make tgt.pointer as vt
endgroup

10.6.2.3 R4 Validation Errors