Molecular Definition Implementation Guide for Molecular Data Types
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Molecular Definition Implementation Guide for Molecular Data Types, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 1.0.0-ballot1 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/molecular-definition-data-types/ and changes regularly. See the Directory of published versions

: example-allelesliced-cyp2c19-1016-cont - XML Representation

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<MolecularDefinition xmlns="http://hl7.org/fhir">
  <id value="example-allelesliced-cyp2c19-1016-cont"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/molecular-definition-data-types/StructureDefinition/allele"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: MolecularDefinition example-allelesliced-cyp2c19-1016-cont</b></p><a name="example-allelesliced-cyp2c19-1016-cont"> </a><a name="hcexample-allelesliced-cyp2c19-1016-cont"> </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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-allele.html">Allele</a></p></div><p><b>moleculeType</b>: <span title="Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type rna}">RNA Sequence</span></p><p><b>type</b>: <span title="Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type dna}">DNA Sequence</span></p><blockquote><p><b>location</b></p><blockquote><p><b>sequenceLocation</b></p><p><b>sequenceContext</b>: <a href="#hcexample-allelesliced-cyp2c19-1016-cont/example-sequence-nm0007694-acc">Starting Sequence Resource: (CYP2C19), mRNA, NM_000769.4</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 LA30102-0}">1-based character counting</span></td></tr></table><p><b>start</b>: 1016</p><p><b>end</b>: 1016</p></blockquote></blockquote></blockquote><blockquote><p><b>representation</b></p><p><b>focus</b>: <span title="Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus allele-state}">Allele State</span></p><p><b>code</b>: <span title="Codes:{http://www.pharmvar.org PV00076}">CYP2C19*1.002</span></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>G</td></tr></table></blockquote><blockquote><p><b>representation</b></p><p><b>focus</b>: <span title="Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus context-state}">Context State</span></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>A</td></tr></table></blockquote><hr/><blockquote><p class="res-header-id"><b>Generated Narrative: MolecularDefinition #example-sequence-nm0007694-acc</b></p><a name="example-allelesliced-cyp2c19-1016-cont/example-sequence-nm0007694-acc"> </a><a name="hcexample-allelesliced-cyp2c19-1016-cont/example-sequence-nm0007694-acc"> </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"/><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-sequence.html">Sequence</a></p></div><p><b>moleculeType</b>: <span title="Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type rna}">RNA Sequence</span></p><p><b>type</b>: <span title="Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type dna}">DNA Sequence</span></p><h3>Representations</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000769.4}">Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), mRNA</span></td></tr></table></blockquote></div>
  </text>
  <contained>
    <MolecularDefinition>
      <id value="example-sequence-nm0007694-acc"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/molecular-definition-data-types/StructureDefinition/sequence"/>
      </meta>
      <moleculeType>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type"/>
          <code value="rna"/>
          <display value="RNA Sequence"/>
        </coding>
      </moleculeType>
      <type>
        <coding>
          <system
                  value="http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type"/>
          <code value="dna"/>
          <display value="DNA Sequence"/>
        </coding>
      </type>
      <representation>
        <code>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
            <code value="NM_000769.4"/>
            <display
                     value="Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), mRNA"/>
          </coding>
        </code>
      </representation>
    </MolecularDefinition>
  </contained>
  <moleculeType>
    <coding>
      <system
              value="http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type"/>
      <code value="rna"/>
      <display value="RNA Sequence"/>
    </coding>
  </moleculeType>
  <type>
    <coding>
      <system
              value="http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type"/>
      <code value="dna"/>
      <display value="DNA Sequence"/>
    </coding>
  </type>
  <location>
    <sequenceLocation>
      <sequenceContext>
        <reference value="#example-sequence-nm0007694-acc"/>
        <type value="MolecularDefinition"/>
        <display
                 value="Starting Sequence Resource: (CYP2C19), mRNA, NM_000769.4"/>
      </sequenceContext>
      <coordinateInterval>
        <coordinateSystem>
          <system>
            <coding>
              <system value="http://loinc.org"/>
              <code value="LA30102-0"/>
              <display value="1-based character counting"/>
            </coding>
          </system>
        </coordinateSystem>
        <startQuantity>
          <value value="1016"/>
        </startQuantity>
        <endQuantity>
          <value value="1016"/>
        </endQuantity>
      </coordinateInterval>
    </sequenceLocation>
  </location>
  <representation>
    <focus>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus"/>
        <code value="allele-state"/>
        <display value="Allele State"/>
      </coding>
    </focus>
    <code>
      <coding>
        <system value="http://www.pharmvar.org"/>
        <code value="PV00076"/>
        <display value="CYP2C19*1.002"/>
      </coding>
    </code>
    <literal>
      <value value="G"/>
    </literal>
  </representation>
  <representation>
    <focus>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus"/>
        <code value="context-state"/>
        <display value="Context State"/>
      </coding>
    </focus>
    <literal>
      <value value="A"/>
    </literal>
  </representation>
</MolecularDefinition>