R6 Ballot (2nd Draft)

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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"/> 
  <type value="dna"/> 
  <!--      <subject>
            <reference value="Patient/example"/>
        </subject>  -->
  <!--      <formatted>
            <contentType value="application/json"/>
            <url value="http://grch37.rest.ensembl.org/ga4gh/variants/3:rs1333049?content-typ
  e=application/json"/>
            <title value="GA4GH API"/>
        </formatted>  -->
  <!--      <repeated>
            <sequenceMotif>
                <reference value="MolecularDefinition/SequenceMotifExample"/>
                <type value="MolecularDefinition"/>
                <display value="Sequence Motif Resource"/>
            </sequenceMotif>
            <copyCount value="5"/>
        </repeated>  -->
  <representation> 
    <!--      <encoding>
        <coding>
            <system value="http://terminology.hl7.org/CodeSystem/..."/>
            <code value=""/>
            <display value=""/>
        </coding>
        <text value=""/>
    </encoding>  -->
    <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"/> 
      </startingMolecule> 
      <start value="0"/> 
      <end value="745"/> 
      <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"/> 
        </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> 
        <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="725"/> 
        <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.