Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
{
"resourceType" : "OperationDefinition",
"id" : "find-subject-variants",
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><h2>FindSubjectVariants</h2><p>OPERATION: FindSubjectVariants</p><p>The official URL for this operation definition is: </p><pre>http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-variants</pre><p>Parameters</p><table class=\"grid\"><tr><td><b>Use</b></td><td><b>Name</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>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>region</td><td>1..1</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#Range\">Range</a></td><td/><td><div><p>Region of interest is specified as a 0-based integer interval range. Variants that overlap the range are returned.</p>\n</div></td></tr><tr><td>IN</td><td>genomicRefSeq</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#token\">token</a>)</td><td/><td><div><p>Genomic reference sequence is a valid NCBI chromosome-level ('NC_') build 37 or build 38 identifier, or a valid mitochondrion identifier (NC_012920.1, NC_001807.4)</p>\n</div></td></tr><tr><td>OUT</td><td>regionStudied</td><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#canonical\">canonical</a></td><td/><td><div><p>[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied] Must include 1..* component:ranges-examined; 1..1 component:coordinate-system (valued with '0-based interval counting'); 1..1 component:genomic-ref-seq.</p>\n</div></td></tr><tr><td>OUT</td><td>variant</td><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#canonical\">canonical</a></td><td/><td><div><p>[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] Must include valueCodeableConcept; component:genomic-source-class; component:genomic-ref-seq; component:allelic-state; 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>sequencePhaseRelationship</td><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#canonical\">canonical</a></td><td/><td><div><p>[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship] Must include valueCodeableConcept; 2..2 derivedFrom:variant.</p>\n</div></td></tr></table></div>"
},
"url" : "http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-variants",
"version" : "1.1.0",
"name" : "FindSubjectVariants",
"title" : "Find Subject Variants",
"status" : "active",
"kind" : "operation",
"date" : "2021-04-13T19:13:37+00:00",
"publisher" : "HL7 International Clinical Genomics Work Group",
"contact" : [
{
"telecom" : [
{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/clingenomics"
}
]
}
],
"jurisdiction" : [
{
"coding" : [
{
"system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001"
}
]
}
],
"code" : "match",
"system" : false,
"type" : true,
"instance" : false,
"parameter" : [
{
"name" : "subject",
"use" : "in",
"min" : 1,
"max" : "1",
"documentation" : "The subject of interest.",
"type" : "string",
"searchType" : "reference"
},
{
"name" : "region",
"use" : "in",
"min" : 1,
"max" : "1",
"documentation" : "Region of interest is specified as a 0-based integer interval range. Variants that overlap the range are returned.",
"type" : "Range"
},
{
"name" : "genomicRefSeq",
"use" : "in",
"min" : 1,
"max" : "1",
"documentation" : "Genomic reference sequence is a valid NCBI chromosome-level ('NC_') build 37 or build 38 identifier, or a valid mitochondrion identifier (NC_012920.1, NC_001807.4)",
"type" : "string",
"searchType" : "token"
},
{
"name" : "regionStudied",
"use" : "out",
"min" : 0,
"max" : "*",
"documentation" : "[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied] Must include 1..* component:ranges-examined; 1..1 component:coordinate-system (valued with '0-based interval counting'); 1..1 component:genomic-ref-seq.",
"type" : "canonical",
"targetProfile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied"
]
},
{
"name" : "variant",
"use" : "out",
"min" : 0,
"max" : "*",
"documentation" : "[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant] Must include valueCodeableConcept; component:genomic-source-class; component:genomic-ref-seq; component:allelic-state; component:ref-allele; component:alt-allele; component:coordinate-system (valued with '0-based interval counting'); component:exact-start-end.",
"type" : "canonical",
"targetProfile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
{
"name" : "sequencePhaseRelationship",
"use" : "out",
"min" : 0,
"max" : "*",
"documentation" : "[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship] Must include valueCodeableConcept; 2..2 derivedFrom:variant.",
"type" : "canonical",
"targetProfile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship"
]
}
]
}
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
Links: Table of Contents |
QA Report
| Version History |
Search |
|
Propose a change