Release 5

This page is part of the FHIR Specification (v5.0.0: R5 - STU). This is the current published version in it's permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4

Example MolecularSequence/breastcancer (Turtle)

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

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

MolecularSequence example for patient with breast cancer gene variant

@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <https://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:id [ fhir:v "breastcancer"] ; # 
  fhir:text [
     fhir:status [ fhir:v "generated" ] ;
     fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"breastcancer\"> </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;breastcancer&quot; </p></div><p><b>type</b>: rna</p><p><b>subject</b>: <a href=\"broken-link.html\">Patient/brcapat</a></p><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 0-based interval counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30100-4)</span></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>Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#NM_000059.3)</span></td><td>101488058</td><td>101499444</td></tr></table><h3>Edits</h3><table class=\"grid\"><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ReplacementSequence</b></td><td><b>ReplacedSequence</b></td></tr><tr><td>*</td><td>32316186</td><td>32316187</td><td>A</td><td>C</td></tr></table></blockquote></div>"
  ] ; # 
  fhir:type [ fhir:v "rna"] ; # 
  fhir:subject [
     fhir:reference [ fhir:v "Patient/brcapat" ]
  ] ; # 
  fhir:relative ( [
     fhir:coordinateSystem [
       fhir:coding ( [
         a loinc:LA30100-4 ;
         fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
         fhir:code [ fhir:v "LA30100-4" ] ;
         fhir:display [ fhir:v "0-based interval counting" ]
       ] )
     ] ;
     fhir:startingSequence [
       fhir:sequence [
         a fhir:CodeableConcept ;
         fhir:coding ( [
           fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/nuccore/"^^xsd:anyURI ] ;
           fhir:code [ fhir:v "NM_000059.3" ] ;
           fhir:display [ fhir:v "Homo sapiens BRCA2, DNA repair associated (BRCA2), mRNA" ]
         ] )
       ] ;
       fhir:windowStart [ fhir:v "101488058"^^xsd:integer ] ;
       fhir:windowEnd [ fhir:v "101499444"^^xsd:integer ]
     ] ;
     fhir:edit ( [
       fhir:start [ fhir:v "32316186"^^xsd:integer ] ;
       fhir:end [ fhir:v "32316187"^^xsd:integer ] ;
       fhir:replacementSequence [ fhir:v "A" ] ;
       fhir:replacedSequence [ fhir:v "C" ]
     ] )
  ] )] . # 

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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.