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Example MolecularSequence/sequence-example-fusion (Turtle)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: Patient

Raw Turtle (+ also see Turtle/RDF Format Specification)

BCR-ABL1 fusion (COSMIC https://cancer.sanger.ac.uk/cosmic/fusion/summary?id=1755). 5-prime end comprised of BCR exons 1-14. 3-prime end comprised of ABL1 exons 2-11.

@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <http://loinc.org/rdf#> .
@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 -------------------------------------------------------------------

[a fhir:MolecularSequence;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "sequence-example-fusion"];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"sequence-example-fusion\"> </a></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 MolecularSequence &quot;sequence-example-fusion&quot; </p></div><p><b>type</b>: rna</p><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 1-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30102-0)</span></p><p><b>ordinalPosition</b>: 1</p><p><b>sequenceRange</b>: 1-3234</p><h3>StartingSequences</h3><table class=\"grid\"><tr><td>-</td><td><b>Sequence[x]</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>NM_004327.4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NM_004327.4)</span></td><td>1</td><td>3234</td></tr></table></blockquote><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 1-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30102-0)</span></p><p><b>ordinalPosition</b>: 2</p><p><b>sequenceRange</b>: 3235-8367</p><h3>StartingSequences</h3><table class=\"grid\"><tr><td>-</td><td><b>Sequence[x]</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>NM_005157.6 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NM_005157.6)</span></td><td>174</td><td>5306</td></tr></table></blockquote></div>"
  ];
  fhir:MolecularSequence.type [ fhir:value "rna"];
  fhir:MolecularSequence.relative [
     fhir:index 0;
     fhir:MolecularSequence.relative.coordinateSystem [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA30102-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA30102-0" ];
         fhir:Coding.display [ fhir:value "1-based character counting" ]
       ]
     ];
     fhir:MolecularSequence.relative.ordinalPosition [ fhir:value "1"^^xsd:integer ];
     fhir:MolecularSequence.relative.sequenceRange [
       fhir:Range.low [
         fhir:Quantity.value [ fhir:value "1"^^xsd:decimal ]
       ];
       fhir:Range.high [
         fhir:Quantity.value [ fhir:value "3234"^^xsd:decimal ]
       ]
     ];
     fhir:MolecularSequence.relative.startingSequence [
       fhir:MolecularSequence.relative.startingSequence.sequenceCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore" ];
           fhir:Coding.code [ fhir:value "NM_004327.4" ]
         ]
       ];
       fhir:MolecularSequence.relative.startingSequence.windowStart [ fhir:value "1"^^xsd:integer ];
       fhir:MolecularSequence.relative.startingSequence.windowEnd [ fhir:value "3234"^^xsd:integer ]
     ]
  ], [
     fhir:index 1;
     fhir:MolecularSequence.relative.coordinateSystem [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA30102-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA30102-0" ];
         fhir:Coding.display [ fhir:value "1-based character counting" ]
       ]
     ];
     fhir:MolecularSequence.relative.ordinalPosition [ fhir:value "2"^^xsd:integer ];
     fhir:MolecularSequence.relative.sequenceRange [
       fhir:Range.low [
         fhir:Quantity.value [ fhir:value "3235"^^xsd:decimal ]
       ];
       fhir:Range.high [
         fhir:Quantity.value [ fhir:value "8367"^^xsd:decimal ]
       ]
     ];
     fhir:MolecularSequence.relative.startingSequence [
       fhir:MolecularSequence.relative.startingSequence.sequenceCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore" ];
           fhir:Coding.code [ fhir:value "NM_005157.6" ]
         ]
       ];
       fhir:MolecularSequence.relative.startingSequence.windowStart [ fhir:value "174"^^xsd:integer ];
       fhir:MolecularSequence.relative.startingSequence.windowEnd [ fhir:value "5306"^^xsd:integer ]
     ]
  ]] .

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

[a owl:Ontology;
  owl:imports fhir:fhir.ttl] .

# -------------------------------------------------------------------------------------


Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.