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Example MolecularDefinition/example (XML)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: No defined compartments

Raw XML (canonical form + also see XML Format Specification)

Simple sequence example (id = "example")

<?xml version="1.0" encoding="UTF-8"?>

<MolecularDefinition xmlns="http://hl7.org/fhir">
  <id value="example"/> 
  <moleculeType> 
    <coding> 
      <system value="http://hl7.org/fhir/sequence-type"/> 
      <code value="dna"/> 
      <display value="DNA Sequence"/> 
    </coding> 
  </moleculeType> 
  <representation> 
    <literal> 
      <value value="ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAAATACC
      AGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGAC
      CCCAAAGATCTCATGTTAAGTGGAG AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTAT
      GG CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATT
      TGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCA
      CAGTCGGGAAACAAGCATAGAAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGC
      TCYG TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACTT
      TTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGG
      TTGGTCAGAAAGA"/> 
    </literal> 
    <resolvable> 
      <reference value="DocumentReference/example-genomicFile-mw7162561"/> 
    </resolvable> 
    <extracted> 
      <startingMolecule> 
        <reference value="MolecularDefinition/example-starting-sequence-2b-extracted"/> 
        <type value="MolecularDefinition"/> 
        <display value="Starting Sequence Resource"/> 
      </startingMolecule> 
      <coordinateInterval> 
        <coordinateSystem> 
          <system> 
            <coding> 
              <system value="http://loinc.org"/> 
              <code value="LA30100-4"/> 
              <display value="0-based interval counting"/> 
            </coding> 
            <text value="0-based interval counting"/> 
          </system> 
        </coordinateSystem> 
      </coordinateInterval> 
      <reverseComplement value="false"/> 
    </extracted> 
    <concatenated> 
      <sequenceElement> 
        <sequence> 
          <reference value="MolecularDefinition/example-sequence0-2b-concatenated"/> 
          <type value="MolecularDefinition"/> 
          <display value="Sequence-of index 0-Resource for concatenated sequence example"/> 
        </sequence> 
        <ordinalIndex value="0"/> 
      </sequenceElement> 
      <sequenceElement> 
        <sequence> 
          <reference value="MolecularDefinition/example-sequence1-2b-concatenated"/> 
          <type value="MolecularDefinition"/> 
          <display value="Sequence-of index 1-Resource for concatenated sequence example"/> 
        </sequence> 
        <ordinalIndex value="1"/> 
      </sequenceElement> 
      <sequenceElement> 
        <sequence> 
          <reference value="MolecularDefinition/example-sequence2-2b-concatenated"/> 
          <type value="MolecularDefinition"/> 
          <display value="Sequence-of index 2-Resource for concatenated sequence example"/> 
        </sequence> 
        <ordinalIndex value="2"/> 
      </sequenceElement> 
    </concatenated> 
    <relative> 
      <startingMolecule> 
        <reference value="MolecularDefinition/example-starting-sequence-2b-relative"/> 
        <type value="MolecularDefinition"/> 
        <display value="Starting Sequence Resource"/> 
      </startingMolecule> 
      <edit> 
        <coordinateInterval> 
          <coordinateSystem> 
            <system> 
              <coding> 
                <system value="http://loinc.org"/> 
                <code value="LA30100-4"/> 
                <display value="0-based interval counting"/> 
              </coding> 
              <text value="0-based interval counting"/> 
            </system> 
          </coordinateSystem> 
        </coordinateInterval> 
        <replacementMolecule> 
          <reference value="MolecularDefinition/example-replacement-sequence"/> 
          <type value="MolecularDefinition"/> 
          <display value="Replacement Sequence Resource"/> 
        </replacementMolecule> 
        <replacedMolecule> 
          <reference value="MolecularDefinition/example-replaced-sequence"/> 
          <type value="MolecularDefinition"/> 
          <display value="Replaced Sequence Resource"/> 
        </replacedMolecule> 
      </edit> 
    </relative> 
  </representation> 
</MolecularDefinition> 

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.