Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot 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 3.0.1-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

: Find Subject Variants - TTL Representation

Active as of 2024-07-15

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@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

 a fhir:OperationDefinition ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "find-subject-variants"] ; # 
  fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: OperationDefinition find-subject-variants</b></p><a name=\"find-subject-variants\"> </a><a name=\"hcfind-subject-variants\"> </a><a name=\"find-subject-variants-en-US\"> </a><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>\n</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>\n</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>\n</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>\n</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>\n</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>\n</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>\n</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>\n</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>\n</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>\n</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>\n</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>\n</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>\n</div></td></tr></table></div>"
  ] ; # 
  fhir:extension ( [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ] ;
fhir:value [ fhir:v "cg" ]
  ] ) ; # 
  fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-variants"^^xsd:anyURI] ; # 
  fhir:version [ fhir:v "3.0.1-SNAPSHOT"] ; # 
  fhir:name [ fhir:v "FindSubjectVariants"] ; # 
  fhir:title [ fhir:v "Find Subject Variants"] ; # 
  fhir:status [ fhir:v "active"] ; # 
  fhir:kind [ fhir:v "operation"] ; # 
  fhir:date [ fhir:v "2024-07-15T14:36:15+00:00"^^xsd:dateTime] ; # 
  fhir:publisher [ fhir:v "HL7 International / Clinical Genomics"] ; # 
  fhir:contact ( [
fhir:name [ fhir:v "HL7 International / Clinical Genomics" ] ;
    ( fhir:telecom [
fhir:system [ fhir:v "url" ] ;
fhir:value [ fhir:v "http://www.hl7.org/Special/committees/clingenomics" ]     ] [
fhir:system [ fhir:v "email" ] ;
fhir:value [ fhir:v "cg@lists.HL7.org" ]     ] )
  ] ) ; # 
  fhir:description [ fhir:v "Determine if simple variants are present that overlap range(s)."] ; # 
  fhir:jurisdiction ( [
    ( fhir:coding [
fhir:system [ fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm"^^xsd:anyURI ] ;
fhir:code [ fhir:v "001" ] ;
fhir:display [ fhir:v "World" ]     ] )
  ] ) ; # 
  fhir:code [ fhir:v "match"] ; # 
  fhir:system [ fhir:v "false"^^xsd:boolean] ; # 
  fhir:type [ fhir:v "true"^^xsd:boolean] ; # 
  fhir:instance [ fhir:v "false"^^xsd:boolean] ; # 
  fhir:parameter ( [
fhir:name [ fhir:v "subject" ] ;
fhir:use [ fhir:v "in" ] ;
fhir:min [ fhir:v "1"^^xsd:integer ] ;
fhir:max [ fhir:v "1" ] ;
fhir:documentation [ fhir:v "The subject of interest." ] ;
fhir:type [ fhir:v "string" ] ;
fhir:searchType [ fhir:v "reference" ]
  ] [
fhir:name [ fhir:v "ranges" ] ;
fhir:use [ fhir:v "in" ] ;
fhir:min [ fhir:v "1"^^xsd:integer ] ;
fhir:max [ fhir:v "*" ] ;
fhir:documentation [ fhir:v "List of regions to be searched for variants. Must be in zero-based RefSeq:Integer-range format (e.g. 'NC_000007.14:55174721-55174820')." ] ;
fhir:type [ fhir:v "string" ] ;
fhir:searchType [ fhir:v "special" ]
  ] [
fhir:name [ fhir:v "testIdentifiers" ] ;
fhir:use [ fhir:v "in" ] ;
fhir:min [ fhir:v "0"^^xsd:integer ] ;
fhir:max [ fhir:v "*" ] ;
fhir:documentation [ fhir:v "Supply a list of test identifiers. Only results originating from one of these tests will be returned." ] ;
fhir:type [ fhir:v "string" ] ;
fhir:searchType [ fhir:v "token" ]
  ] [
fhir:name [ fhir:v "testDateRange" ] ;
fhir:use [ fhir:v "in" ] ;
fhir:min [ fhir:v "0"^^xsd:integer ] ;
fhir:max [ fhir:v "1" ] ;
fhir:documentation [ fhir:v "Supply a date range. Only results generated during this range will be returned." ] ;
fhir:type [ fhir:v "Period" ]
  ] [
fhir:name [ fhir:v "specimenIdentifiers" ] ;
fhir:use [ fhir:v "in" ] ;
fhir:min [ fhir:v "0"^^xsd:integer ] ;
fhir:max [ fhir:v "*" ] ;
fhir:documentation [ fhir:v "Supply a list of specimen identifiers. Only results derived from one of these specimens will be returned." ] ;
fhir:type [ fhir:v "string" ] ;
fhir:searchType [ fhir:v "token" ]
  ] [
fhir:name [ fhir:v "genomicSourceClass" ] ;
fhir:use [ fhir:v "in" ] ;
fhir:min [ fhir:v "0"^^xsd:integer ] ;
fhir:max [ fhir:v "1" ] ;
fhir:documentation [ fhir:v "Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include variants irrespective of genomic source class." ] ;
fhir:type [ fhir:v "code" ]
  ] [
fhir:name [ fhir:v "includeVariants" ] ;
fhir:use [ fhir:v "in" ] ;
fhir:min [ fhir:v "0"^^xsd:integer ] ;
fhir:max [ fhir:v "1" ] ;
fhir:documentation [ fhir:v "Include variants in response if set to true. Default=false." ] ;
fhir:type [ fhir:v "boolean" ]
  ] [
fhir:name [ fhir:v "includePhasing" ] ;
fhir:use [ fhir:v "in" ] ;
fhir:min [ fhir:v "0"^^xsd:integer ] ;
fhir:max [ fhir:v "1" ] ;
fhir:documentation [ fhir:v "If true, then assume includeVariants=true, and return variants and sequence-phase-relationships between returned variants. Default=false." ] ;
fhir:type [ fhir:v "boolean" ]
  ] [
fhir:name [ fhir:v "variants" ] ;
fhir:use [ fhir:v "out" ] ;
fhir:min [ fhir:v "1"^^xsd:integer ] ;
fhir:max [ fhir:v "*" ] ;
fhir:documentation [ fhir:v "(one for each range in rangeList)" ] ;
    ( fhir:part [
fhir:name [ fhir:v "rangeItem" ] ;
fhir:use [ fhir:v "out" ] ;
fhir:min [ fhir:v "1"^^xsd:integer ] ;
fhir:max [ fhir:v "1" ] ;
fhir:documentation [ fhir:v "range from rangeList" ] ;
fhir:type [ fhir:v "string" ]     ] [
fhir:name [ fhir:v "presence" ] ;
fhir:use [ fhir:v "out" ] ;
fhir:min [ fhir:v "1"^^xsd:integer ] ;
fhir:max [ fhir:v "1" ] ;
fhir:documentation [ fhir:v "True if as least one variant is identified in the range" ] ;
fhir:type [ fhir:v "boolean" ]     ] [
      ( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/operationdefinition-profile"^^xsd:anyURI ] ;
fhir:value [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ]       ] ) ;
fhir:name [ fhir:v "variant" ] ;
fhir:use [ fhir:v "out" ] ;
fhir:min [ fhir:v "0"^^xsd:integer ] ;
fhir:max [ fhir:v "*" ] ;
fhir:documentation [ fhir:v "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." ] ;
fhir:type [ fhir:v "Observation" ]     ] [
      ( fhir:extension [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/operationdefinition-profile"^^xsd:anyURI ] ;
fhir:value [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ]       ] ) ;
fhir:name [ fhir:v "sequencePhaseRelationship" ] ;
fhir:use [ fhir:v "out" ] ;
fhir:min [ fhir:v "0"^^xsd:integer ] ;
fhir:max [ fhir:v "*" ] ;
fhir:documentation [ fhir:v "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." ] ;
fhir:type [ fhir:v "Observation" ]     ] )
  ] ) . #