R6 Ballot (2nd Draft)

Publish-box (todo)

Example MolecularDefinition/example-allelesliced1 (XML)

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

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

Example of Allele profile including slices (id = "example-allelesliced1")

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

<MolecularDefinition xmlns="http://hl7.org/fhir">
  <id value="example-allelesliced1"/> 
  <meta> 
    <profile value="http://hl7.org/fhir/StructureDefinition/allelesliced"/> 
  </meta> 
  <type value="dna"/> 
  <location> 
    <sequenceLocation> 
      <sequenceContext> 
        <reference value="MolecularDefinition/example-sequence-lrg584"/> 
        <type value="MolecularDefinition"/> 
        <display value="Starting Sequence Resource: LRG_584"/> 
      </sequenceContext> 
      <coordinateInterval> 
        <numberingSystem> 
          <coding> 
            <system value="http://loinc.org"/> 
            <code value="LA30100-4"/> 
            <display value="0-based interval counting"/> 
          </coding> 
          <text value="0-based interval counting"/> 
        </numberingSystem> 
        <startQuantity> 
          <value value="5001"/> 
        </startQuantity> 
        <endQuantity> 
          <value value="97867"/> 
        </endQuantity> 
      </coordinateInterval> 
    </sequenceLocation> 
  </location> 
  <representation> 
    <focus> 
      <coding> 
        <system value="http://hl7.org/fhir/moleculardefinition-focus"/> 
        <code value="allele-state"/> 
        <display value="Allele State"/> 
      </coding> 
    </focus> 
    <resolvable> 
      <url value="https://www.ncbi.nlm.nih.gov/nuccore/NG_008384.3"/> 
    </resolvable> 
  </representation> 
  <representation> 
    <focus> 
      <coding> 
        <system value="http://hl7.org/fhir/moleculardefinition-focus"/> 
        <code value="context-state"/> 
        <display value="Context State"/> 
      </coding> 
    </focus> 
    <relative> 
      <startingMolecule> 
        <reference value="MolecularDefinition/example-sequence-lrg584"/> 
        <type value="MolecularDefinition"/> 
        <display value="Starting Sequence Resource: LRG_584"/> 
      </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="5123"/> 
        <end value="5124"/> 
        <replacementMolecule> 
          <reference value="MolecularDefinition/example-sequence-t"/> 
          <type value="MolecularDefinition"/> 
          <display value="Replacement Sequence Resource: T"/> 
        </replacementMolecule> 
        <replacedMolecule> 
          <reference value="MolecularDefinition/example-sequence-c"/> 
          <type value="MolecularDefinition"/> 
          <display value="Replaced Sequence Resource: C"/> 
        </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.