0.1.0 - ci-build

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

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

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<Task xmlns="http://hl7.org/fhir">
  <id value="CQDGTaskExample"/>
  <meta>
    <profile
             value="https://fhir.cqdg.ca/StructureDefinition/cqgc-analysis-task"/>
  </meta>
  <text>
    <status value="extensions"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Task CQDGTaskExample</b></p><a name="CQDGTaskExample"> </a><a name="hcCQDGTaskExample"> </a><a name="CQDGTaskExample-en-US"> </a><blockquote><p><b>Ferlab.bio StructureDefinition/workflow</b></p><ul><li>workflowName: Dragen</li><li>genomeBuild: <a href="CodeSystem-genome-build.html#genome-build-GRCh38">Ferlab.bio CodeSystem/genome-build GRCh38</a>: GRCh38</li><li>workflowVersion: SW null</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sequencing-experiment</b></p><ul><li>runName: 1898</li><li>platform: Illumina NovaSeq 6000 S4 PE150</li><li>isPairedEnd: true</li><li>readLength: 151,8,8,151</li><li>experimentalStrategy: <a href="CodeSystem-experimental-strategy.html#experimental-strategy-WXS">Ferlab.bio CodeSystem/experimental-strategy WXS</a>: Whole Exome Sequencing</li><li>runDate: 2020-11-06</li><li>labAliquotId: MPS12348274-B04</li><li>ldmSampleId: S03344</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 RABA}">Reads Alignement Bioinformatic 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 Aligned-reads}">Aligned Reads</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 SNV}">SNV</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 Germline-CNV}">Germline CNV</span></p><p><b>value</b>: <a href="DocumentReference-DocumentReferenceExample2.html">DocumentReference: status = current; type = Aligned Reads; 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 Sequencing-data-supplement}">Sequencing-data-supplement</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="workflowName">
      <valueString value="Dragen"/>
    </extension>
    <extension url="genomeBuild">
      <valueCoding>
        <system value="https://fhir.cqdg.ca/CodeSystem/genome-build"/>
        <code value="GRCh38"/>
        <display value="GRCh38"/>
      </valueCoding>
    </extension>
    <extension url="workflowVersion">
      <valueString value="SW null"/>
    </extension>
  </extension>
  <extension
             url="https://fhir.cqdg.ca/StructureDefinition/sequencingExperimentExtension">
    <extension url="runName">
      <valueString value="1898"/>
    </extension>
    <extension url="platform">
      <valueString value="Illumina NovaSeq 6000 S4 PE150"/>
    </extension>
    <extension url="isPairedEnd">
      <valueBoolean value="true"/>
    </extension>
    <extension url="readLength">
      <valueString value="151,8,8,151"/>
    </extension>
    <extension url="experimentalStrategy">
      <valueCoding>
        <system
                value="https://fhir.cqdg.ca/CodeSystem/experimental-strategy"/>
        <code value="WXS"/>
        <display value="Whole Exome Sequencing"/>
      </valueCoding>
    </extension>
    <extension url="runDate">
      <valueDateTime value="2020-11-06"/>
    </extension>
    <extension url="labAliquotId">
      <valueString value="MPS12348274-B04"/>
    </extension>
    <extension url="ldmSampleId">
      <valueString value="S03344"/>
    </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="RABA"/>
      <display value="Reads Alignement Bioinformatic 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="Aligned-reads"/>
        <display value="Aligned Reads"/>
      </coding>
    </type>
    <valueReference>🔗 
      <reference value="DocumentReference/DocumentReferenceExample1"/>
    </valueReference>
  </output>
  <output>
    <type>
      <coding>
        <system value="https://fhir.cqdg.ca/CodeSystem/data-type"/>
        <code value="SNV"/>
        <display value="SNV"/>
      </coding>
    </type>
    <valueReference>🔗 
      <reference value="DocumentReference/DocumentReferenceExample1"/>
    </valueReference>
  </output>
  <output>
    <type>
      <coding>
        <system value="https://fhir.cqdg.ca/CodeSystem/data-type"/>
        <code value="Germline-CNV"/>
        <display value="Germline CNV"/>
      </coding>
    </type>
    <valueReference>🔗 
      <reference value="DocumentReference/DocumentReferenceExample2"/>
    </valueReference>
  </output>
  <output>
    <type>
      <coding>
        <system value="https://fhir.cqdg.ca/CodeSystem/data-type"/>
        <code value="Sequencing-data-supplement"/>
        <display value="Sequencing-data-supplement"/>
      </coding>
    </type>
    <valueReference>🔗 
      <reference value="DocumentReference/DocumentReferenceExample2"/>
    </valueReference>
  </output>
</Task>