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-long-read - XML Representation

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<Task xmlns="http://hl7.org/fhir">
  <id value="CQDGTaskLongReadExample"/>
  <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 CQDGTaskLongReadExample</b></p><a name="CQDGTaskLongReadExample"> </a><a name="hcCQDGTaskLongReadExample"> </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>pipeline: dorado 0.7.2</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sequencing-experiment</b></p><ul><li>experimentalStrategy: <a href="CodeSystem-experimental-strategy.html#experimental-strategy-ADAS">Ferlab.bio CodeSystem/experimental-strategy: ADAS</a> (Adaptive Sampling)</li><li>platform: <a href="CodeSystem-sequencing-experiment-platform.html#sequencing-experiment-platform-ONT">Ferlab.bio CodeSystem/sequencing-experiment-platform: ONT</a> (ONT)</li><li>selection: <a href="CodeSystem-sequencing-experiment-selection.html#sequencing-experiment-selection-DIRECT">Ferlab.bio CodeSystem/sequencing-experiment-selection: DIRECT</a> (Direct)</li><li>source: <a href="CodeSystem-sequencing-experiment-source.html#sequencing-experiment-source-GEN">Ferlab.bio CodeSystem/sequencing-experiment-source: GEN</a> (Genomics)</li><li>profilingResolution: <a href="CodeSystem-profiling-resolution.html#profiling-resolution-Bulk">Ferlab.bio CodeSystem/profiling-resolution: Bulk</a> (Bulk)</li><li>instrumentModel: PromethION 24</li><li>poreType: R10.4.1</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sample</b></p><ul><li>ldmSampleId: LDM24680</li><li>labAliquotId: AliquotID4</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 GBVA}">Germline Variant 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 De-Novo-Assembly-Aligned-Reads}">De Novo Assembly 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 Methylation-Calls}">Methylation Calls</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 Tandem-Repeats}">Tandem Repeats (TRs)</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="pipeline">
      <valueString value="dorado 0.7.2"/>
    </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="ADAS"/>
        <display value="Adaptive Sampling"/>
      </valueCoding>
    </extension>
    <extension url="platform">
      <valueCoding>
        <system
                value="https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-platform"/>
        <code value="ONT"/>
        <display value="ONT"/>
      </valueCoding>
    </extension>
    <extension url="selection">
      <valueCoding>
        <system
                value="https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-selection"/>
        <code value="DIRECT"/>
        <display value="Direct"/>
      </valueCoding>
    </extension>
    <extension url="source">
      <valueCoding>
        <system
                value="https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-source"/>
        <code value="GEN"/>
        <display value="Genomics"/>
      </valueCoding>
    </extension>
    <extension url="profilingResolution">
      <valueCoding>
        <system value="https://fhir.cqdg.ca/CodeSystem/profiling-resolution"/>
        <code value="Bulk"/>
        <display value="Bulk"/>
      </valueCoding>
    </extension>
    <extension url="instrumentModel">
      <valueString value="PromethION 24"/>
    </extension>
    <extension url="poreType">
      <valueString value="R10.4.1"/>
    </extension>
  </extension>
  <extension url="https://fhir.cqdg.ca/StructureDefinition/sampleExtension">
    <extension url="ldmSampleId">
      <valueString value="LDM24680"/>
    </extension>
    <extension url="labAliquotId">
      <valueString value="AliquotID4"/>
    </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="GBVA"/>
      <display value="Germline Variant 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="De-Novo-Assembly-Aligned-Reads"/>
        <display value="De Novo Assembly 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="Methylation-Calls"/>
        <display value="Methylation Calls"/>
      </coding>
    </type>
    <valueReference>🔗 
      <reference value="DocumentReference/DocumentReferenceExample2"/>
    </valueReference>
  </output>
  <output>
    <type>
      <coding>
        <system value="https://fhir.cqdg.ca/CodeSystem/data-type"/>
        <code value="Tandem-Repeats"/>
        <display value="Tandem Repeats (TRs)"/>
      </coding>
    </type>
    <valueReference>🔗 
      <reference value="DocumentReference/DocumentReferenceExample2"/>
    </valueReference>
  </output>
</Task>