Genomics Reporting Implementation Guide
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Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: Find Subject Structural Subsuming Variants - XML Representation

Active as of 2024-11-19

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<OperationDefinition xmlns="http://hl7.org/fhir">
  <id value="find-subject-structural-subsuming-variants"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: OperationDefinition find-subject-structural-subsuming-variants</b></p><a name="find-subject-structural-subsuming-variants"> </a><a name="hcfind-subject-structural-subsuming-variants"> </a><a name="find-subject-structural-subsuming-variants-en-US"> </a><h3>Parameters</h3><table class="grid"><tr><td><b>Use</b></td><td><b>Name</b></td><td><b>Scope</b></td><td><b>Cardinality</b></td><td><b>Type</b></td><td><b>Binding</b></td><td><b>Documentation</b></td></tr><tr><td>IN</td><td>subject</td><td/><td>1..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a><br/>(<a href="http://hl7.org/fhir/R4/search.html#reference">reference</a>)</td><td/><td><div><p>The subject of interest.</p>
</div></td></tr><tr><td>IN</td><td>ranges</td><td/><td>1..*</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a><br/>(<a href="http://hl7.org/fhir/R4/search.html#special">special</a>)</td><td/><td><div><p>List of regions to be searched for variants. Must be in zero-based RefSeq:Integer-range format (e.g. 'NC_000007.14:55174721-55174820').</p>
</div></td></tr><tr><td>IN</td><td>testIdentifiers</td><td/><td>0..*</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a><br/>(<a href="http://hl7.org/fhir/R4/search.html#token">token</a>)</td><td/><td><div><p>Supply a list of test identifiers. Only results originating from one of these tests will be returned.</p>
</div></td></tr><tr><td>IN</td><td>testDateRange</td><td/><td>0..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#Period">Period</a></td><td/><td><div><p>Supply a date range. Only results generated during this range will be returned.</p>
</div></td></tr><tr><td>IN</td><td>specimenIdentifiers</td><td/><td>0..*</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a><br/>(<a href="http://hl7.org/fhir/R4/search.html#token">token</a>)</td><td/><td><div><p>Supply a list of specimen identifiers. Only results derived from one of these specimens will be returned.</p>
</div></td></tr><tr><td>IN</td><td>genomicSourceClass</td><td/><td>0..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a><br/>(<a href="http://hl7.org/fhir/R4/search.html#token">token</a>)</td><td/><td><div><p>Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include variants irrespective of genomic source class.</p>
</div></td></tr><tr><td>IN</td><td>includeVariants</td><td/><td>0..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#boolean">boolean</a></td><td/><td><div><p>Include variants in response if set to true. Default=false.</p>
</div></td></tr><tr><td>OUT</td><td>variants</td><td/><td>1..*</td><td></td><td/><td><div><p>(one for each range in rangeList)</p>
</div></td></tr><tr><td>OUT</td><td>variants.rangeItem</td><td/><td>1..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a></td><td/><td><div><p>range from rangeList</p>
</div></td></tr><tr><td>OUT</td><td>variants.presence</td><td/><td>1..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#boolean">boolean</a></td><td/><td><div><p>True if as least one variant is identified that subsumes the range</p>
</div></td></tr><tr><td>OUT</td><td>variants.variant</td><td/><td>0..*</td><td><a href="http://hl7.org/fhir/R4/observation.html">Observation</a></td><td/><td><div><p>If includeVariants=true then include variants that subsume the range. Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] and minimally include valueCodeableConcept; component:coding-change-type; component:genomic-ref-seq; component:coordinate-system (valued with '0-based interval counting'); components outer-start-end and/or inner-start-end.</p>
</div></td></tr></table></div>
  </text>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <url
       value="http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-structural-subsuming-variants"/>
  <version value="3.0.0"/>
  <name value="FindSubjectStructuralSubsumingVariants"/>
  <title value="Find Subject Structural Subsuming Variants"/>
  <status value="active"/>
  <kind value="operation"/>
  <date value="2024-11-19T22:01:39+00:00"/>
  <publisher value="HL7 International / Clinical Genomics"/>
  <contact>
    <name value="HL7 International / Clinical Genomics"/>
    <telecom>
      <system value="url"/>
      <value value="http://www.hl7.org/Special/committees/clingenomics"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="cg@lists.HL7.org"/>
    </telecom>
  </contact>
  <description
               value="Determine if structural variants are present that fully subsume a range."/>
  <jurisdiction>
    <coding>
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
      <code value="001"/>
      <display value="World"/>
    </coding>
  </jurisdiction>
  <code value="match"/>
  <system value="false"/>
  <type value="true"/>
  <instance value="false"/>
  <parameter>
    <name value="subject"/>
    <use value="in"/>
    <min value="1"/>
    <max value="1"/>
    <documentation value="The subject of interest."/>
    <type value="string"/>
    <searchType value="reference"/>
  </parameter>
  <parameter>
    <name value="ranges"/>
    <use value="in"/>
    <min value="1"/>
    <max value="*"/>
    <documentation
                   value="List of regions to be searched for variants. Must be in zero-based RefSeq:Integer-range format (e.g. 'NC_000007.14:55174721-55174820')."/>
    <type value="string"/>
    <searchType value="special"/>
  </parameter>
  <parameter>
    <name value="testIdentifiers"/>
    <use value="in"/>
    <min value="0"/>
    <max value="*"/>
    <documentation
                   value="Supply a list of test identifiers. Only results originating from one of these tests will be returned."/>
    <type value="string"/>
    <searchType value="token"/>
  </parameter>
  <parameter>
    <name value="testDateRange"/>
    <use value="in"/>
    <min value="0"/>
    <max value="1"/>
    <documentation
                   value="Supply a date range. Only results generated during this range will be returned."/>
    <type value="Period"/>
  </parameter>
  <parameter>
    <name value="specimenIdentifiers"/>
    <use value="in"/>
    <min value="0"/>
    <max value="*"/>
    <documentation
                   value="Supply a list of specimen identifiers. Only results derived from one of these specimens will be returned."/>
    <type value="string"/>
    <searchType value="token"/>
  </parameter>
  <parameter>
    <name value="genomicSourceClass"/>
    <use value="in"/>
    <min value="0"/>
    <max value="1"/>
    <documentation
                   value="Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include variants irrespective of genomic source class."/>
    <type value="string"/>
    <searchType value="token"/>
  </parameter>
  <parameter>
    <name value="includeVariants"/>
    <use value="in"/>
    <min value="0"/>
    <max value="1"/>
    <documentation
                   value="Include variants in response if set to true. Default=false."/>
    <type value="boolean"/>
  </parameter>
  <parameter>
    <name value="variants"/>
    <use value="out"/>
    <min value="1"/>
    <max value="*"/>
    <documentation value="(one for each range in rangeList)"/>
    <part>
      <name value="rangeItem"/>
      <use value="out"/>
      <min value="1"/>
      <max value="1"/>
      <documentation value="range from rangeList"/>
      <type value="string"/>
    </part>
    <part>
      <name value="presence"/>
      <use value="out"/>
      <min value="1"/>
      <max value="1"/>
      <documentation
                     value="True if as least one variant is identified that subsumes the range"/>
      <type value="boolean"/>
    </part>
    <part>
      <extension
                 url="http://hl7.org/fhir/StructureDefinition/operationdefinition-profile">
        <valueUri
                  value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
      </extension>
      <name value="variant"/>
      <use value="out"/>
      <min value="0"/>
      <max value="*"/>
      <documentation
                     value="If includeVariants=true then include variants that subsume the range. Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] and minimally include valueCodeableConcept; component:coding-change-type; component:genomic-ref-seq; component:coordinate-system (valued with '0-based interval counting'); components outer-start-end and/or inner-start-end."/>
      <type value="Observation"/>
    </part>
  </parameter>
</OperationDefinition>