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: Ferlab.bio Example/cqdg-task-multi-omic - XML Representation

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<Task xmlns="http://hl7.org/fhir">
  <id value="CQDGTaskMultiOmicExample"/>
  <meta>
    <profile value="https://fhir.cqdg.ca/StructureDefinition/CQDGTask"/>
  </meta>
  <text>
    <status value="extensions"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Task CQDGTaskMultiOmicExample</b></p><a name="CQDGTaskMultiOmicExample"> </a><a name="hcCQDGTaskMultiOmicExample"> </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="https://simplifier.net/resolve?scope=hl7.fhir.ca.baseline@1.0.2&amp;canonical=https://fhir.cqdg.ca/StructureDefinition/CQDGTask">https://fhir.cqdg.ca/StructureDefinition/CQDGTask</a></p></div><blockquote><p><b>Ferlab.bio StructureDefinition/workflow</b></p><ul><li>genomeBuild: <a href="CodeSystem-genome-build.html#genome-build-GRCh38">Ferlab.bio CodeSystem/genome-build: GRCh38</a> (GRCh38)</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sequencing-experiment</b></p><ul><li>experimentalStrategy: <a href="CodeSystem-experimental-strategy.html#experimental-strategy-RNAS">Ferlab.bio CodeSystem/experimental-strategy: RNAS</a> (RNA-Seq)</li><li>platform: <a href="CodeSystem-sequencing-experiment-platform.html#sequencing-experiment-platform-Chromium">Ferlab.bio CodeSystem/sequencing-experiment-platform: Chromium</a> (Chromium)</li><li>selection: <a href="CodeSystem-sequencing-experiment-selection.html#sequencing-experiment-selection-TN5">Ferlab.bio CodeSystem/sequencing-experiment-selection: TN5</a> (Tn5)</li><li>source: <a href="CodeSystem-sequencing-experiment-source.html#sequencing-experiment-source-MUL">Ferlab.bio CodeSystem/sequencing-experiment-source: MUL</a> (Multi-omic)</li><li>experimentalStrategy: <a href="CodeSystem-experimental-strategy.html#experimental-strategy-ATACS">Ferlab.bio CodeSystem/experimental-strategy: ATACS</a> (ATAC-Seq)</li><li>profilingResolution: <a href="CodeSystem-profiling-resolution.html#profiling-resolution-Single-Nucleus">Ferlab.bio CodeSystem/profiling-resolution: Single-Nucleus</a> (Single Nucleus)</li><li>profilingResolution: <a href="CodeSystem-profiling-resolution.html#profiling-resolution-Single-Nucleus">Ferlab.bio CodeSystem/profiling-resolution: Single-Nucleus</a> (Single Nucleus)</li><li>platform: <a href="CodeSystem-sequencing-experiment-platform.html#sequencing-experiment-platform-Illumina">Ferlab.bio CodeSystem/sequencing-experiment-platform: Illumina</a> (Illumina)</li><li>instrumentModel: Chromium X</li><li>instrumentModel: NovaSeq X</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sample</b></p><ul><li>ldmSampleId: LDM67890</li><li>labAliquotId: AliquotID3</li></ul></blockquote><p><b>status</b>: Completed</p><p><b>intent</b>: order</p><p><b>priority</b>: Routine</p><p><b>code</b>: <span title="Codes:{https://fhir.cqdg.ca/CodeSystem/bioinfo-analysis-code MOA}">Multi-omic Analysis</span></p><p><b>requester</b>: <a href="Organization-OrganizationExample.html">Organization CQDG</a></p><p><b>owner</b>: <a href="Organization-OrganizationExample.html">Organization CQDG</a></p><h3>Inputs</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Type</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td><span title="Codes:">Analysed sample</span></td><td><a href="Specimen-SpecimenExample.html">Submitter Sample ID: SpecimenExample</a></td></tr></table><blockquote><p><b>output</b></p><p><b>type</b>: <span title="Codes:{https://fhir.cqdg.ca/CodeSystem/data-type Filtered-Feature-Count-Matrix}">Filtered Feature Count Matrix</span></p><p><b>value</b>: <a href="DocumentReference-DocumentReferenceExample1.html">DocumentReference: status = current; type = Sequencing Data Supplement; category = Genomics; securityLabel = test</a></p></blockquote><blockquote><p><b>output</b></p><p><b>type</b>: <span title="Codes:{https://fhir.cqdg.ca/CodeSystem/data-type Filtered-Peak-Barcode-Matrix}">Filtered Peak Barcode Matrix</span></p><p><b>value</b>: <a href="DocumentReference-DocumentReferenceExample2.html">DocumentReference: status = current; type = Aligned Reads; category = Genomics; securityLabel = test</a></p></blockquote></div>
  </text>
  <extension
             url="https://fhir.cqdg.ca/StructureDefinition/workflowExtension">
    <extension url="genomeBuild">
      <valueCoding>
        <system value="https://fhir.cqdg.ca/CodeSystem/genome-build"/>
        <code value="GRCh38"/>
        <display value="GRCh38"/>
      </valueCoding>
    </extension>
  </extension>
  <extension
             url="https://fhir.cqdg.ca/StructureDefinition/sequencingExperimentExtension">
    <extension url="experimentalStrategy">
      <valueCoding>
        <system
                value="https://fhir.cqdg.ca/CodeSystem/experimental-strategy"/>
        <code value="RNAS"/>
        <display value="RNA-Seq"/>
      </valueCoding>
    </extension>
    <extension url="platform">
      <valueCoding>
        <system
                value="https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-platform"/>
        <code value="Chromium"/>
        <display value="Chromium"/>
      </valueCoding>
    </extension>
    <extension url="selection">
      <valueCoding>
        <system
                value="https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-selection"/>
        <code value="TN5"/>
        <display value="Tn5"/>
      </valueCoding>
    </extension>
    <extension url="source">
      <valueCoding>
        <system
                value="https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-source"/>
        <code value="MUL"/>
        <display value="Multi-omic"/>
      </valueCoding>
    </extension>
    <extension url="experimentalStrategy">
      <valueCoding>
        <system
                value="https://fhir.cqdg.ca/CodeSystem/experimental-strategy"/>
        <code value="ATACS"/>
        <display value="ATAC-Seq"/>
      </valueCoding>
    </extension>
    <extension url="profilingResolution">
      <valueCoding>
        <system value="https://fhir.cqdg.ca/CodeSystem/profiling-resolution"/>
        <code value="Single-Nucleus"/>
        <display value="Single Nucleus"/>
      </valueCoding>
    </extension>
    <extension url="profilingResolution">
      <valueCoding>
        <system value="https://fhir.cqdg.ca/CodeSystem/profiling-resolution"/>
        <code value="Single-Nucleus"/>
        <display value="Single Nucleus"/>
      </valueCoding>
    </extension>
    <extension url="platform">
      <valueCoding>
        <system
                value="https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-platform"/>
        <code value="Illumina"/>
        <display value="Illumina"/>
      </valueCoding>
    </extension>
    <extension url="instrumentModel">
      <valueString value="Chromium X"/>
    </extension>
    <extension url="instrumentModel">
      <valueString value="NovaSeq X"/>
    </extension>
  </extension>
  <extension url="https://fhir.cqdg.ca/StructureDefinition/sampleExtension">
    <extension url="ldmSampleId">
      <valueString value="LDM67890"/>
    </extension>
    <extension url="labAliquotId">
      <valueString value="AliquotID3"/>
    </extension>
  </extension>
  <status value="completed"/>
  <intent value="order"/>
  <priority value="routine"/>
  <code>
    <coding>
      <system value="https://fhir.cqdg.ca/CodeSystem/bioinfo-analysis-code"/>
      <code value="MOA"/>
      <display value="Multi-omic Analysis"/>
    </coding>
  </code>
  <requester>🔗 
    <reference value="Organization/OrganizationExample"/>
  </requester>
  <owner>🔗 
    <reference value="Organization/OrganizationExample"/>
  </owner>
  <input>
    <type>
      <text value="Analysed sample"/>
    </type>
    <valueReference>🔗 
      <reference value="Specimen/SpecimenExample"/>
      <display value="Submitter Sample ID: SpecimenExample"/>
    </valueReference>
  </input>
  <output>
    <type>
      <coding>
        <system value="https://fhir.cqdg.ca/CodeSystem/data-type"/>
        <code value="Filtered-Feature-Count-Matrix"/>
        <display value="Filtered Feature Count Matrix"/>
      </coding>
    </type>
    <valueReference>🔗 
      <reference value="DocumentReference/DocumentReferenceExample1"/>
    </valueReference>
  </output>
  <output>
    <type>
      <coding>
        <system value="https://fhir.cqdg.ca/CodeSystem/data-type"/>
        <code value="Filtered-Peak-Barcode-Matrix"/>
        <display value="Filtered Peak Barcode Matrix"/>
      </coding>
    </type>
    <valueReference>🔗 
      <reference value="DocumentReference/DocumentReferenceExample2"/>
    </valueReference>
  </output>
</Task>