Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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
| Active as of 2024-04-09 |
<OperationDefinition xmlns="http://hl7.org/fhir">
<id value="find-subject-variants"/>
<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>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#code">code</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>IN</td><td>includePhasing</td><td/><td>0..1</td><td><a href="http://hl7.org/fhir/R4/datatypes.html#boolean">boolean</a></td><td/><td><div><p>If true, then assume includeVariants=true, and return variants and sequence-phase-relationships between returned variants. 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 in 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 in the range. Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] and minimally include valueCodeableConcept; component:genomic-ref-seq; component:ref-allele; component:alt-allele; component:coordinate-system (valued with '0-based interval counting'); component:exact-start-end.</p>
</div></td></tr><tr><td>OUT</td><td>variants.sequencePhaseRelationship</td><td/><td>0..*</td><td><a href="http://hl7.org/fhir/R4/observation.html">Observation</a></td><td/><td><div><p>If includePhasing=true and includeVariants=true then include sequence-phase-relationships between returned variants. Sequence phase relationships must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition-sequence-phase-relationship.html] and minimally include valueCodeableConcept and 2..2 derivedFrom:variant references.</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-variants"/>
<version value="3.0.1-SNAPSHOT"/>
<name value="FindSubjectVariants"/>
<title value="Find Subject Variants"/>
<status value="active"/>
<kind value="operation"/>
<date value="2024-04-09T13:57:55+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 simple variants are present that overlap range(s)."/>
<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="code"/>
</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="includePhasing"/>
<use value="in"/>
<min value="0"/>
<max value="1"/>
<documentation
value="If true, then assume includeVariants=true, and return variants and sequence-phase-relationships between returned variants. 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 in 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 in the range. Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] and minimally include valueCodeableConcept; component:genomic-ref-seq; component:ref-allele; component:alt-allele; component:coordinate-system (valued with '0-based interval counting'); component:exact-start-end."/>
<type value="Observation"/>
</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="sequencePhaseRelationship"/>
<use value="out"/>
<min value="0"/>
<max value="*"/>
<documentation
value="If includePhasing=true and includeVariants=true then include sequence-phase-relationships between returned variants. Sequence phase relationships must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition-sequence-phase-relationship.html] and minimally include valueCodeableConcept and 2..2 derivedFrom:variant references."/>
<type value="Observation"/>
</part>
</parameter>
</OperationDefinition>
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.1-SNAPSHOT based on FHIR 4.0.1. Generated 2024-04-09
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