Genomics Reporting Implementation Guide
3.0.0 - release International flag

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 Population Specific Haplotypes - XML Representation

Active as of 2024-11-19

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<OperationDefinition xmlns="http://hl7.org/fhir">
  <id value="find-population-specific-haplotypes"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: OperationDefinition find-population-specific-haplotypes</b></p><a name="find-population-specific-haplotypes"> </a><a name="hcfind-population-specific-haplotypes"> </a><a name="find-population-specific-haplotypes-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>haplotypes</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#token">token</a>)</td><td/><td><div><p>List of haplotypes and/or genotypes being sought. Must be in token or codesystem|code format.</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>includePatientList</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 list of matching patients if set to true. Default=false.</p>
</div></td></tr><tr><td>OUT</td><td>haplotypes</td><td/><td>1..*</td><td></td><td/><td><div><p>(one for each haplotype in haplotypeList)</p>
</div></td></tr><tr><td>OUT</td><td>haplotypes.haplotypeItem</td><td/><td>1..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a></td><td/><td><div><p>haplotype/genotype from haplotypeList</p>
</div></td></tr><tr><td>OUT</td><td>haplotypes.numerator</td><td/><td>1..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#Quantity">Quantity</a></td><td/><td><div><p>Count of patients having this variant</p>
</div></td></tr><tr><td>OUT</td><td>haplotypes.denominator</td><td/><td>0..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#Quantity">Quantity</a></td><td/><td><div><p>Count of patients in the cohort searched</p>
</div></td></tr><tr><td>OUT</td><td>haplotypes.subject</td><td/><td>0..*</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a></td><td/><td><div><p>Patient ID. Include if includePatientList=true</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-population-specific-haplotypes"/>
  <version value="3.0.0"/>
  <name value="FindPopulationSpecificHaplotypes"/>
  <title value="Find Population Specific Haplotypes"/>
  <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="Retrieve count or list of patients having specified genotypes/haplotypes."/>
  <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="haplotypes"/>
    <use value="in"/>
    <min value="1"/>
    <max value="*"/>
    <documentation
                   value="List of haplotypes and/or genotypes being sought. Must be in token or codesystem|code format."/>
    <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="includePatientList"/>
    <use value="in"/>
    <min value="0"/>
    <max value="1"/>
    <documentation
                   value="Include list of matching patients if set to true. Default=false."/>
    <type value="boolean"/>
  </parameter>
  <parameter>
    <name value="haplotypes"/>
    <use value="out"/>
    <min value="1"/>
    <max value="*"/>
    <documentation value="(one for each haplotype in haplotypeList)"/>
    <part>
      <name value="haplotypeItem"/>
      <use value="out"/>
      <min value="1"/>
      <max value="1"/>
      <documentation value="haplotype/genotype from haplotypeList"/>
      <type value="string"/>
    </part>
    <part>
      <name value="numerator"/>
      <use value="out"/>
      <min value="1"/>
      <max value="1"/>
      <documentation value="Count of patients having this variant"/>
      <type value="Quantity"/>
    </part>
    <part>
      <name value="denominator"/>
      <use value="out"/>
      <min value="0"/>
      <max value="1"/>
      <documentation value="Count of patients in the cohort searched"/>
      <type value="Quantity"/>
    </part>
    <part>
      <name value="subject"/>
      <use value="out"/>
      <min value="0"/>
      <max value="*"/>
      <documentation value="Patient ID. Include if includePatientList=true"/>
      <type value="string"/>
    </part>
  </parameter>
</OperationDefinition>