Sequence-complex-variant.ttl

Example of representing complex variants in Sequence Resource

@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

<http://hl7.org/fhir/Sequence/sequence-complex-variant> a fhir:Sequence;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "sequence-complex-variant"];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: sequence-complex-variant</p><p><b>type</b>: DNA</p><p><b>coordinateSystem</b>: 1</p><h3>ReferenceSeqs</h3><table><tr><td>-</td><td><b>ReferenceSeqId</b></td><td><b>Strand</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>NC_000002.12 <span>(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NC_000002.12' = 'NC_000002.12)</span></td><td>1</td><td>128273724</td><td>128273754</td></tr></table><h3>Variants</h3><table><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ObservedAllele</b></td><td><b>ReferenceAllele</b></td><td><b>Cigar</b></td></tr><tr><td>*</td><td>128273724</td><td>128273736</td><td>CTCATTGT</td><td>CTCCATTGCATGCGTT</td><td>3M1D4M6N2M</td></tr></table></div>"
  ];
  fhir:Sequence.type [ fhir:value "DNA"];
  fhir:Sequence.coordinateSystem [ fhir:value "1"^^xsd:int];
  fhir:Sequence.referenceSeq [
     fhir:Sequence.referenceSeq.referenceSeqId [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore" ];
         fhir:Coding.code [ fhir:value "NC_000002.12" ]
       ]
     ];
     fhir:Sequence.referenceSeq.strand [ fhir:value "1"^^xsd:int ];
     fhir:Sequence.referenceSeq.windowStart [ fhir:value "128273724"^^xsd:int ];
     fhir:Sequence.referenceSeq.windowEnd [ fhir:value "128273754"^^xsd:int ]
  ];
  fhir:Sequence.variant [
     fhir:index 0;
     fhir:Sequence.variant.start [ fhir:value "128273724"^^xsd:int ];
     fhir:Sequence.variant.end [ fhir:value "128273736"^^xsd:int ];
     fhir:Sequence.variant.observedAllele [ fhir:value "CTCATTGT" ];
     fhir:Sequence.variant.referenceAllele [ fhir:value "CTCCATTGCATGCGTT" ];
     fhir:Sequence.variant.cigar [ fhir:value "3M1D4M6N2M" ]
  ] .

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