NCPI FHIR Implementation Guide v2 - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

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: Example file metadata for a BAM-CRAM file from GREGoR - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="gregor-example-metadata"/>
  <meta>
    <profile
             value="https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-bamcram"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Observation gregor-example-metadata</b></p><a name="gregor-example-metadata"> </a><a name="hcgregor-example-metadata"> </a><a name="gregor-example-metadata-en-US"> </a><p><b>status</b>: Final</p><p><b>code</b>: <span title="Codes:{http://edamontology.org format_2572}">format_2572</span></p><p><b>focus</b>: <a href="Patient-GSS123456.html">Anonymous Patient (no stated gender), DoB Unknown ( https://anvil.terra.bio/#GSS123456)</a></p><p><b>specimen</b>: <a href="Specimen-GSS123456-01-010.html">Specimen: identifier = GSS123456-s1; type = </a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:">AssayStrategy</span></p><p><b>value</b>: <span title="Codes:">WGS</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:">PlatformInstrument</span></p><p><b>value</b>: <span title="Codes:">IlluminaHiSeq2000</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:">LibraryPrep</span></p><p><b>value</b>: <span title="Codes:">polyA</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:">LibrarySelection</span></p><p><b>value</b>: <span title="Codes:">PolyTEnrichment</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:">TargetRegion</span></p><p><b>value</b>: <span title="Codes:">Not Applicable</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:">Strandedness</span></p><p><b>value</b>: <span title="Codes:">stranded</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:">ReferenceGenome</span></p><p><b>value</b>: <span title="Codes:">GRCh38</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:">IsPairedEnd</span></p><p><b>value</b>: false</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:">WorkflowTool</span></p><p><b>value</b>: <span title="Codes:">bammem</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:">WorkflowType</span></p><p><b>value</b>: <span title="Codes:">alignment</span></p></blockquote></div>
  </text>
  <status value="final"/>
  <code>
    <coding>
      <system value="http://edamontology.org"/>
      <code value="format_2572"/>
    </coding>
  </code>
  <focus>🔗 
    <reference value="Patient/GSS123456"/>
  </focus>
  <specimen>🔗 
    <reference value="Specimen/GSS123456-01-010"/>
  </specimen>
  <component>
    <code>
      <coding>
        <code value="AssayStrategy"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <code value="WGS"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <code value="PlatformInstrument"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <code value="IlluminaHiSeq2000"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <code value="LibraryPrep"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <code value="polyA"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <code value="LibrarySelection"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <code value="PolyTEnrichment"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <code value="TargetRegion"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <text value="Not Applicable"/>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <code value="Strandedness"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <code value="stranded"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <code value="ReferenceGenome"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <code value="GRCh38"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <code value="IsPairedEnd"/>
      </coding>
    </code>
    <valueBoolean value="false"/>
  </component>
  <component>
    <code>
      <coding>
        <code value="WorkflowTool"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <code value="bammem"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <code value="WorkflowType"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <code value="alignment"/>
      </coding>
    </valueCodeableConcept>
  </component>
</Observation>