This page is part of the FHIR Specification (v4.3.0: R4B - STU). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4
R3 : R4 Conversion maps for MolecularSequence.
Functional status for this map: 14 tests that all execute ok. All tests pass round-trip testing and all r3 resources are valid. (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/Sequence4to3" = "R4 to R3 Conversion for Sequence"
uses "http://hl7.org/fhir/StructureDefinition/MolecularSequence" 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(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 as vvv where value = 'crick' -> tgt.strand = create('') as vvv "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;
}