Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: Find Subject Molecular Consequences - XML Representation

Active as of 2023-12-18

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<OperationDefinition xmlns="http://hl7.org/fhir">
  <id value="find-subject-molecular-consequences"/>
  <text>
    <status value="extensions"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p>Parameters</p><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>variants</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#string">string</a>)</td><td/><td><div><p>List of variants from which consequences are derived. Must be in HGVS or SPDI format.</p>
</div></td></tr><tr><td>IN</td><td>ranges</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#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>featureConsequences</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>List of consequences sought. Must be in token or codesystem|code format. (These will generally be coded with Sequence Ontology codes under SO:0001537)</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>OUT</td><td>consequence</td><td/><td>0..*</td><td><a href="http://hl7.org/fhir/R4/observation.html">Observation</a></td><td/><td><div><p>Consequences must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence]. The target(s) of the consequence's derivedFrom shall also be included in the response.</p>
</div></td></tr><tr><td>OUT</td><td>variant</td><td/><td>0..*</td><td><a href="http://hl7.org/fhir/R4/observation.html">Observation</a></td><td/><td><div><p>Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant].</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-molecular-consequences"/>
  <version value="3.0.0-ballot"/>
  <name value="FindSubjectMolecularConsequences"/>
  <title value="Find Subject Molecular Consequences"/>
  <status value="active"/>
  <kind value="operation"/>
  <date value="2023-12-18T22:45:59+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="Retrieves molecular consequences of a DNA variant."/>
  <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="variants"/>
    <use value="in"/>
    <min value="0"/>
    <max value="*"/>
    <documentation
                   value="List of variants from which consequences are derived. Must be in HGVS or SPDI format."/>
    <type value="string"/>
    <searchType value="string"/>
  </parameter>
  <parameter>
    <name value="ranges"/>
    <use value="in"/>
    <min value="0"/>
    <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="featureConsequences"/>
    <use value="in"/>
    <min value="0"/>
    <max value="*"/>
    <documentation
                   value="List of consequences sought. Must be in token or codesystem|code format. (These will generally be coded with Sequence Ontology codes under SO:0001537)"/>
    <type value="string"/>
    <searchType value="token"/>
  </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>
    <extension
               url="http://hl7.org/fhir/StructureDefinition/operationdefinition-profile">
      <valueUri
                value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"/>
    </extension>
    <name value="consequence"/>
    <use value="out"/>
    <min value="0"/>
    <max value="*"/>
    <documentation
                   value="Consequences must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence]. The target(s) of the consequence's derivedFrom shall also be included in the response."/>
    <type value="Observation"/>
  </parameter>
  <parameter>
    <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="Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant]."/>
    <type value="Observation"/>
  </parameter>
</OperationDefinition>