This page is part of the FHIR Specification (v5.0.0: R5 - STU). This is the current published version in it's permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4
Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative | Security Category: Patient | Compartments: Patient |
R4 : R5 Conversion maps for MolecularSequence.
Functional status for this map: See Conversions Summary. (see documentation)
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/MolecularSequence" alias MolecularSequence as target imports "http://hl7.org/fhir/StructureMap/*3to4" group Sequence(source src : SequenceR3, target tgt : MolecularSequence) extends DomainResource <<type+>> { src.identifier -> tgt.identifier; src.type -> tgt.type; src.coordinateSystem -> tgt.coordinateSystem; src.patient -> tgt.patient; src.specimen -> tgt.specimen; src.device -> tgt.device; src.performer -> tgt.performer; src.quantity -> tgt.quantity; src.referenceSeq as vs0 -> tgt.referenceSeq as vt0 then referenceSeq(vs0, vt0); src.variant as vs0 -> tgt.variant as vt0 then variant(vs0, vt0); src.observedSeq -> tgt.observedSeq; src.quality as vs0 -> tgt.quality as vt0 then quality(vs0, vt0); src.readCoverage -> tgt.readCoverage; src.repository as vs0 -> tgt.repository as vt0 then repository(vs0, vt0); src.pointer -> tgt.pointer; } group referenceSeq(source src, target tgt) extends BackboneElement { src.chromosome -> tgt.chromosome; src.genomeBuild -> tgt.genomeBuild; src.referenceSeqId -> tgt.referenceSeqId; src.referenceSeqPointer -> tgt.referenceSeqPointer; src.referenceSeqString -> tgt.referenceSeqString; src.strand where value = 1 -> tgt.strand = 'watson'; src.strand where value = -1 -> tgt.strand = 'crick'; src.windowStart -> tgt.windowStart; src.windowEnd -> tgt.windowEnd; } group variant(source src, target tgt) extends BackboneElement { src.start -> tgt.start; src.end -> tgt.end; src.observedAllele -> tgt.observedAllele; src.referenceAllele -> tgt.referenceAllele; src.cigar -> tgt.cigar; src.variantPointer -> tgt.variantPointer; } group quality(source src, target tgt) extends BackboneElement { src.type -> tgt.type; src.standardSequence -> tgt.standardSequence; src.start -> tgt.start; src.end -> tgt.end; src.score -> tgt.score; src.method -> tgt.method; src.truthTP -> tgt.truthTP; src.queryTP -> tgt.queryTP; src.truthFN -> tgt.truthFN; src.queryFP -> tgt.queryFP; src.gtFP -> tgt.gtFP; src.precision -> tgt.precision; src.recall -> tgt.recall; src.fScore -> tgt.fScore; } group repository(source src, target tgt) extends BackboneElement { src.type -> tgt.type; src.url -> tgt.url; src.name -> tgt.name; src.datasetId -> tgt.datasetId; src.variantsetId -> tgt.variantsetId; src.readsetId -> tgt.readsetId; }
map "http://hl7.org/fhir/StructureMap/MolecularSequence4to3" = "R4 to R3 Conversions forSequence" uses "http://hl7.org/fhir/3.0/StructureDefinition/Sequence" alias SequenceR3 as target uses "http://hl7.org/fhir/StructureDefinition/MolecularSequence" alias MolecularSequence as source imports "http://hl7.org/fhir/StructureMap/*4to3" group Sequence(source src : MolecularSequence, target tgt : SequenceR3) extends DomainResource <<type+>> { src.identifier -> tgt.identifier; src.type -> tgt.type; src.coordinateSystem -> tgt.coordinateSystem; src.patient -> tgt.patient; src.specimen -> tgt.specimen; src.device -> tgt.device; src.performer -> tgt.performer; src.quantity -> tgt.quantity; src.referenceSeq as vs0 -> tgt.referenceSeq as vt0 then referenceSeq(vs0, vt0); src.variant as vs0 -> tgt.variant as vt0 then variant(vs0, vt0); src.observedSeq -> tgt.observedSeq; src.quality as vs0 -> tgt.quality as vt0 then quality(vs0, vt0); src.readCoverage -> tgt.readCoverage; src.repository as vs0 -> tgt.repository as vt0 then repository(vs0, vt0); src.pointer -> tgt.pointer; } group referenceSeq(source src, target tgt) extends BackboneElement { src.chromosome -> tgt.chromosome; src.genomeBuild -> tgt.genomeBuild; src.referenceSeqId -> tgt.referenceSeqId; src.referenceSeqPointer -> tgt.referenceSeqPointer; src.referenceSeqString -> tgt.referenceSeqString; src.strand where value = 'watson' -> tgt.strand = 1; src.strand where value = 'crick' -> tgt.strand = -1; src.windowStart -> tgt.windowStart; src.windowEnd -> tgt.windowEnd; } group variant(source src, target tgt) extends BackboneElement { src.start -> tgt.start; src.end -> tgt.end; src.observedAllele -> tgt.observedAllele; src.referenceAllele -> tgt.referenceAllele; src.cigar -> tgt.cigar; src.variantPointer -> tgt.variantPointer; } group quality(source src, target tgt) extends BackboneElement { src.type -> tgt.type; src.standardSequence -> tgt.standardSequence; src.start -> tgt.start; src.end -> tgt.end; src.score -> tgt.score; src.method -> tgt.method; src.truthTP -> tgt.truthTP; src.queryTP -> tgt.queryTP; src.truthFN -> tgt.truthFN; src.queryFP -> tgt.queryFP; src.gtFP -> tgt.gtFP; src.precision -> tgt.precision; src.recall -> tgt.recall; src.fScore -> tgt.fScore; } group repository(source src, target tgt) extends BackboneElement { src.type -> tgt.type; src.url -> tgt.url; src.name -> tgt.name; src.datasetId -> tgt.datasetId; src.variantsetId -> tgt.variantsetId; src.readsetId -> tgt.readsetId; }
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No validation errors - all conversions are clean