R5 Final QA

This page is part of the FHIR Specification (v5.0.0-draft-final: Final QA Preview for R5 - see ballot notes). 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

10.7.11 Resource MolecularSequence - R4/R5 Conversions

Clinical Genomics icon Work GroupMaturity Level: N/AStandards Status: InformativeSecurity Category: Patient Compartments: Patient

R4 : R5 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)

10.7.11.1 R4 to R5 

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;
}

10.7.11.2 R5 to R4 

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;
}

This script does not compile: java.lang.NumberFormatException: For input string: "-"

10.7.11.3 R4 Validation Errors

<p>No validation errors - all conversions are clean</p>