Clinical Genomics Resource Incubator
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Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

: Molecular Definition Example

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<MolecularDefinition xmlns="http://hl7.org/fhir">
  <id value="example"/>
  <language value="en"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><p class="res-header-id"><b>Generated Narrative: MolecularDefinition example</b></p><a name="example"> </a><a name="hcexample"> </a><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">Language: en</p></div><p><b>moleculeType</b>: <span title="Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/moleculardefinition-moleculetype dna}">DNA sequence</span></p><blockquote><p><b>representation</b></p><h3>Literals</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Value</b></td></tr><tr><td style="display: none">*</td><td>ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA</td></tr></table><p><b>resolvable</b>: <a href="DocumentReference-example-genomicFile-mw7162561.html">DocumentReference: identifier = http://example.org/identifiers/files#11111; status = current; docStatus = preliminary; description = A sample Document Reference instance representing Homo sapiens isolate 7 BRCA1 (BRCA1) gene, exon 10 and partial cds.</a></p><blockquote><p><b>extracted</b></p><p><b>startingMolecule</b>: <a href="MolecularDefinition-example-starting-sequence-2b-extracted.html">Starting Sequence Resource</a></p><blockquote><p><b>coordinateInterval</b></p><h3>CoordinateSystems</h3><table class="grid"><tr><td style="display: none">-</td><td><b>System</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://loinc.org LA30100-4}">0-based interval counting</span></td></tr></table><p><b>start</b>: 0</p><p><b>end</b>: 745</p></blockquote><p><b>reverseComplement</b>: false</p></blockquote><blockquote><p><b>concatenated</b></p><blockquote><p><b>sequenceElement</b></p><p><b>sequence</b>: <a href="MolecularDefinition-example-sequence0-2b-concatenated.html">Sequence-of index 0-Resource for concatenated sequence example</a></p><p><b>ordinalIndex</b>: 0</p></blockquote><blockquote><p><b>sequenceElement</b></p><p><b>sequence</b>: <a href="MolecularDefinition-example-sequence1-2b-concatenated.html">Sequence-of index 1-Resource for concatenated sequence example</a></p><p><b>ordinalIndex</b>: 1</p></blockquote><blockquote><p><b>sequenceElement</b></p><p><b>sequence</b>: <a href="MolecularDefinition-example-sequence2-2b-concatenated.html">Sequence-of index 2-Resource for concatenated sequence example</a></p><p><b>ordinalIndex</b>: 2</p></blockquote></blockquote><blockquote><p><b>relative</b></p><p><b>startingMolecule</b>: <a href="MolecularDefinition-example-starting-sequence-2b-relative.html">Starting Sequence Resource</a></p><blockquote><p><b>edit</b></p><blockquote><p><b>coordinateInterval</b></p><h3>CoordinateSystems</h3><table class="grid"><tr><td style="display: none">-</td><td><b>System</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://loinc.org LA30100-4}">0-based interval counting</span></td></tr></table><p><b>start</b>: 0</p><p><b>end</b>: 745</p></blockquote><p><b>replacementMolecule</b>: <a href="MolecularDefinition-example-replacement-sequence.html">Replacement Sequence Resource</a></p><p><b>replacedMolecule</b>: <a href="MolecularDefinition-example-replaced-sequence.html">Replaced Sequence Resource</a></p></blockquote></blockquote></blockquote></div>
  </text>
  <moleculeType>
    <coding>
      <system
              value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/moleculardefinition-moleculetype"/>
      <code value="dna"/>
      <display value="DNA sequence"/>
    </coding>
  </moleculeType>
  <representation>
    <literal>
      <value
             value="ATGAACAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA"/>
    </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>
        <startQuantity>
          <value value="0"/>
        </startQuantity>
        <endQuantity>
          <value value="745"/>
        </endQuantity>
      </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>
          <startQuantity>
            <value value="0"/>
          </startQuantity>
          <endQuantity>
            <value value="745"/>
          </endQuantity>
        </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>