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 |
{
"resourceType" : "OperationDefinition",
"id" : "find-subject-haplotypes",
"text" : {
"status" : "extensions",
"div" : "<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>\n</div></td></tr><tr><td>IN</td><td>genes</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 genes to be searched. Must be in token or codesystem|code format.</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#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 haplotypes irrespective of genomic source class.</p>\n</div></td></tr><tr><td>OUT</td><td>haplotypes</td><td/><td>1..*</td><td></td><td/><td><div><p>(one for each gene in geneList)</p>\n</div></td></tr><tr><td>OUT</td><td>haplotypes.geneItem</td><td/><td>1..1</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a></td><td/><td><div><p>gene from geneList</p>\n</div></td></tr><tr><td>OUT</td><td>haplotypes.haplotype</td><td/><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/observation.html\">Observation</a></td><td/><td><div><p>Haplotypes must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype].</p>\n</div></td></tr><tr><td>OUT</td><td>haplotypes.genotype</td><td/><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/observation.html\">Observation</a></td><td/><td><div><p>Genotypes must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype].</p>\n</div></td></tr></table></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode" : "cg"
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-haplotypes",
"version" : "3.0.1-SNAPSHOT",
"name" : "FindSubjectHaplotypes",
"title" : "Find Subject Haplotypes",
"status" : "active",
"kind" : "operation",
"date" : "2024-04-09T13:57:55+00:00",
"publisher" : "HL7 International / Clinical Genomics",
"contact" : [
{
"name" : "HL7 International / Clinical Genomics",
"telecom" : [
{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/clingenomics"
},
{
"system" : "email",
"value" : "cg@lists.HL7.org"
}
]
}
],
"description" : "Retrieve haplotypes/genotypes for specified genes.",
"jurisdiction" : [
{
"coding" : [
{
"system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001",
"display" : "World"
}
]
}
],
"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" : "genes",
"use" : "in",
"min" : 1,
"max" : "*",
"documentation" : "List of genes to be searched. Must be in token or codesystem|code format.",
"type" : "string",
"searchType" : "token"
},
{
"name" : "testIdentifiers",
"use" : "in",
"min" : 0,
"max" : "*",
"documentation" : "Supply a list of test identifiers. Only results originating from one of these tests will be returned.",
"type" : "string",
"searchType" : "token"
},
{
"name" : "testDateRange",
"use" : "in",
"min" : 0,
"max" : "1",
"documentation" : "Supply a date range. Only results generated during this range will be returned.",
"type" : "Period"
},
{
"name" : "specimenIdentifiers",
"use" : "in",
"min" : 0,
"max" : "*",
"documentation" : "Supply a list of specimen identifiers. Only results derived from one of these specimens will be returned.",
"type" : "string",
"searchType" : "token"
},
{
"name" : "genomicSourceClass",
"use" : "in",
"min" : 0,
"max" : "1",
"documentation" : "Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include haplotypes irrespective of genomic source class.",
"type" : "string",
"searchType" : "token"
},
{
"name" : "haplotypes",
"use" : "out",
"min" : 1,
"max" : "*",
"documentation" : "(one for each gene in geneList)",
"part" : [
{
"name" : "geneItem",
"use" : "out",
"min" : 1,
"max" : "1",
"documentation" : "gene from geneList",
"type" : "string"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/operationdefinition-profile",
"valueUri" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"
}
],
"name" : "haplotype",
"use" : "out",
"min" : 0,
"max" : "*",
"documentation" : "Haplotypes must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype].",
"type" : "Observation"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/operationdefinition-profile",
"valueUri" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
}
],
"name" : "genotype",
"use" : "out",
"min" : 0,
"max" : "*",
"documentation" : "Genotypes must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype].",
"type" : "Observation"
}
]
}
]
}
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
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change