Sequence-complex-variant.ttl

Example of representing complex variants in MolecularSequence 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/MolecularSequence/sequence-complex-variant> a fhir:MolecularSequence;
  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</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource &quot;sequence-complex-variant&quot; </p></div><p><b>identifier</b>: id: ?ngen-9? (OFFICIAL)</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 1</p><p><b>specimen</b>: <a href=\"todo.html\">Specimen/genetics-example1-somatic: Molecular Specimen ID: MLD45-Z4-1234</a></p><p><b>device</b>: <span>: 12 lead EKG Device Metric</span></p><p><b>performer</b>: <a href=\"organization-hl7.html\">Organization/hl7: HL7</a> &quot;Health Level Seven International&quot;</p><p><b>quantity</b>: 25</p><h3>ReferenceSeqs</h3><table class=\"grid\"><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 style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NC_000002.12)</span></td><td>watson</td><td>128273724</td><td>128273754</td></tr></table><h3>Variants</h3><table class=\"grid\"><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><p><b>readCoverage</b>: 1</p><h3>Repositories</h3><table class=\"grid\"><tr><td>-</td><td><b>Type</b></td><td><b>DatasetId</b></td><td><b>ReadsetId</b></td></tr><tr><td>*</td><td>other</td><td>Ensembl</td><td>v1beta2</td></tr></table></div>"
  ];
  fhir:MolecularSequence.identifier [
     fhir:index 0;
     fhir:Identifier.use [ fhir:value "official" ]
  ];
  fhir:MolecularSequence.type [ fhir:value "dna"];
  fhir:MolecularSequence.coordinateSystem [ fhir:value "1"^^xsd:integer];
  fhir:MolecularSequence.specimen [
     fhir:link <http://hl7.org/fhir/Specimen/genetics-example1-somatic>;
     fhir:Reference.reference [ fhir:value "Specimen/genetics-example1-somatic" ];
     fhir:Reference.display [ fhir:value "Molecular Specimen ID: MLD45-Z4-1234" ]
  ];
  fhir:MolecularSequence.device [
     fhir:Reference.display [ fhir:value "12 lead EKG Device Metric" ]
  ];
  fhir:MolecularSequence.performer [
     fhir:link <http://hl7.org/fhir/Organization/hl7>;
     fhir:Reference.reference [ fhir:value "Organization/hl7" ];
     fhir:Reference.display [ fhir:value "HL7" ]
  ];
  fhir:MolecularSequence.quantity [
     fhir:Quantity.value [ fhir:value "25"^^xsd:decimal ]
  ];
  fhir:MolecularSequence.referenceSeq [
     fhir:MolecularSequence.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:MolecularSequence.referenceSeq.strand [ fhir:value "watson" ];
     fhir:MolecularSequence.referenceSeq.windowStart [ fhir:value "128273724"^^xsd:integer ];
     fhir:MolecularSequence.referenceSeq.windowEnd [ fhir:value "128273754"^^xsd:integer ]
  ];
  fhir:MolecularSequence.variant [
     fhir:index 0;
     fhir:MolecularSequence.variant.start [ fhir:value "128273724"^^xsd:integer ];
     fhir:MolecularSequence.variant.end [ fhir:value "128273736"^^xsd:integer ];
     fhir:MolecularSequence.variant.observedAllele [ fhir:value "CTCATTGT" ];
     fhir:MolecularSequence.variant.referenceAllele [ fhir:value "CTCCATTGCATGCGTT" ];
     fhir:MolecularSequence.variant.cigar [ fhir:value "3M1D4M6N2M" ]
  ];
  fhir:MolecularSequence.readCoverage [ fhir:value "1"^^xsd:integer];
  fhir:MolecularSequence.repository [
     fhir:index 0;
     fhir:MolecularSequence.repository.type [ fhir:value "other" ];
     fhir:MolecularSequence.repository.datasetId [ fhir:value "Ensembl" ];
     fhir:MolecularSequence.repository.readsetId [ fhir:value "v1beta2" ]
  ] .

<http://hl7.org/fhir/Specimen/genetics-example1-somatic> a fhir:Specimen .

<http://hl7.org/fhir/Organization/hl7> a fhir:Organization .

# - ontology header ------------------------------------------------------------

<http://hl7.org/fhir/MolecularSequence/sequence-complex-variant.ttl> a owl:Ontology;
  owl:imports fhir:fhir.ttl;
  owl:versionIRI <http://build.fhir.org/MolecularSequence/sequence-complex-variant.ttl> .

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