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Example MolecularDefinition/example-sequence1 (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 1 (id = "example-sequence1")

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

<MolecularDefinition xmlns="http://hl7.org/fhir">
  <id value="example-sequence1"/> 
  <meta> 
    <profile value="http://hl7.org/fhir/StructureDefinition/sequence"/> 
  </meta> 
  <type value="dna"/> 
  <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> 
      <contentType value="text/html"/> 
      <url value="https://www.ncbi.nlm.nih.gov/nuccore/MW716256.1?report=fasta"/> 
    </resolvable> 
    <extracted> 
      <startingMolecule> 
        <reference value="MolecularDefinition/example-starting-sequence-2b-extracted"/> 
        <type value="MolecularDefinition"/> 
        <display value="Starting Sequence Resource:                 ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAA
        GTTAACAAATGCACCTGGTTC                 TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTC
        CAAGAGAAGAAAAA                 GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTA
        AGTGGAG                 AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG
                         CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT
                         GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG
                         ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA
                         AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG
                         TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC
                         AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA
                         GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGAGCCTGTACAGACAGTT
                         AATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA"/> 
      </startingMolecule> 
      <start value="0"/> 
      <end value="754"/> 
      <coordinateSystem> 
        <coding> 
          <system value="http://loinc.org"/> 
          <code value="LA30100-4"/> 
          <display value="0-based interval counting"/> 
        </coding> 
        <text value="0-based interval counting"/> 
      </coordinateSystem> 
      <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:               
                ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAA
          ATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTG
          AAGACCCCAAAGATCTCATGTTAAGTGGAG"/> 
        </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:               
                AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG CACTCAGGAAAGTATCT
          CGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAA
          TTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAG
          AAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG"/> 
        </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:               
                TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACT
          TTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTG
          GTTGGTCAGAAAGA"/> 
        </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> 
        <coordinateSystem> 
          <coding> 
            <system value="http://loinc.org"/> 
            <code value="LA30100-4"/> 
            <display value="0-based interval counting"/> 
          </coding> 
          <text value="0-based interval counting"/> 
        </coordinateSystem> 
        <start value="0"/> 
        <end value="5"/> 
        <replacementMolecule> 
          <reference value="MolecularDefinition/example-replacement-sequence"/> 
          <type value="MolecularDefinition"/> 
          <display value="Replacement Sequence Resource: ATGAA"/> 
        </replacementMolecule> 
        <replacedMolecule> 
          <reference value="MolecularDefinition/example-replaced-sequence"/> 
          <type value="MolecularDefinition"/> 
          <display value="Replaced Sequence Resource: CCCCC"/> 
        </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.