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

Example MolecularSequence/seq-ordinal (Turtle)

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

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

MolecularSequence example for long fusion RNA molecule of FGFR and MET

@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 "seq-ordinal"] ; # 
  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=\"seq-ordinal\"> </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;seq-ordinal&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>: 1-2194</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_000141.5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#NM_000141.5)</span></td><td>1</td><td>2194</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>: 2194-4899</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_000245.4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#NM_000245.4)</span></td><td>1923</td><td>6822</td></tr></table></blockquote></div>"
  ] ; # 
  fhir:type [ fhir:v "rna"] ; # 
  fhir:relative ( [
     fhir:coordinateSystem [
       fhir:coding ( [
         a loinc:LA30102-0 ;
         fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
         fhir:code [ fhir:v "LA30102-0" ] ;
         fhir:display [ fhir:v "1-based character counting" ]
       ] )
     ] ;
     fhir:ordinalPosition [ fhir:v "1"^^xsd:integer ] ;
     fhir:sequenceRange [
       fhir:low [
         fhir:value [ fhir:v "1"^^xsd:decimal ]
       ] ;
       fhir:high [
         fhir:value [ fhir:v "2194"^^xsd:decimal ]
       ]
     ] ;
     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_000141.5" ]
         ] )
       ] ;
       fhir:windowStart [ fhir:v "1"^^xsd:integer ] ;
       fhir:windowEnd [ fhir:v "2194"^^xsd:integer ]
     ]
  ] [
     fhir:coordinateSystem [
       fhir:coding ( [
         a loinc:LA30102-0 ;
         fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
         fhir:code [ fhir:v "LA30102-0" ] ;
         fhir:display [ fhir:v "1-based character counting" ]
       ] )
     ] ;
     fhir:ordinalPosition [ fhir:v "2"^^xsd:integer ] ;
     fhir:sequenceRange [
       fhir:low [
         fhir:value [ fhir:v "2194"^^xsd:decimal ]
       ] ;
       fhir:high [
         fhir:value [ fhir:v "4899"^^xsd:decimal ]
       ]
     ] ;
     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_000245.4" ]
         ] )
       ] ;
       fhir:windowStart [ fhir:v "1923"^^xsd:integer ] ;
       fhir:windowEnd [ fhir:v "6822"^^xsd:integer ]
     ]
  ] )] . #    specific edits would be here   

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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.