Genomics Reporting Implementation Guide
2.0.0 - trial-use
Genomics Reporting Implementation Guide
2.0.0 - trial-use
This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions 
@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:Resource.id [ fhir:value "find-subject-variants"];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "extensions" ];
fhir:Narrative.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>"
];
fhir:OperationDefinition.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-variants"];
fhir:OperationDefinition.version [ fhir:value "2.0.0"];
fhir:OperationDefinition.name [ fhir:value "FindSubjectVariants"];
fhir:OperationDefinition.title [ fhir:value "Find Subject Variants"];
fhir:OperationDefinition.status [ fhir:value "active"];
fhir:OperationDefinition.kind [ fhir:value "operation"];
fhir:OperationDefinition.date [ fhir:value "2022-05-09T16:53:07+00:00"^^xsd:dateTime];
fhir:OperationDefinition.publisher [ fhir:value "HL7 Clinical Genomics Working Group"];
fhir:OperationDefinition.contact [
fhir:index 0;
fhir:ContactDetail.name [ fhir:value "HL7 Clinical Genomics Working Group" ];
fhir:ContactDetail.telecom [
fhir:index 0;
fhir:ContactPoint.system [ fhir:value "url" ];
fhir:ContactPoint.value [ fhir:value "http://www.hl7.org/Special/committees/clingenomics" ] ], [
fhir:index 1;
fhir:ContactPoint.system [ fhir:value "email" ];
fhir:ContactPoint.value [ fhir:value "cg@lists.HL7.org" ] ]
];
fhir:OperationDefinition.jurisdiction [
fhir:index 0;
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://unstats.un.org/unsd/methods/m49/m49.htm" ];
fhir:Coding.code [ fhir:value "001" ];
fhir:Coding.display [ fhir:value "World" ] ]
];
fhir:OperationDefinition.code [ fhir:value "match"];
fhir:OperationDefinition.system [ fhir:value "false"^^xsd:boolean];
fhir:OperationDefinition.type [ fhir:value "true"^^xsd:boolean];
fhir:OperationDefinition.instance [ fhir:value "false"^^xsd:boolean];
fhir:OperationDefinition.parameter [
fhir:index 0;
fhir:OperationDefinition.parameter.name [ fhir:value "subject" ];
fhir:OperationDefinition.parameter.use [ fhir:value "in" ];
fhir:OperationDefinition.parameter.min [ fhir:value "1"^^xsd:integer ];
fhir:OperationDefinition.parameter.max [ fhir:value "1" ];
fhir:OperationDefinition.parameter.documentation [ fhir:value "The subject of interest." ];
fhir:OperationDefinition.parameter.type [ fhir:value "string" ];
fhir:OperationDefinition.parameter.searchType [ fhir:value "reference" ]
], [
fhir:index 1;
fhir:OperationDefinition.parameter.name [ fhir:value "region" ];
fhir:OperationDefinition.parameter.use [ fhir:value "in" ];
fhir:OperationDefinition.parameter.min [ fhir:value "1"^^xsd:integer ];
fhir:OperationDefinition.parameter.max [ fhir:value "1" ];
fhir:OperationDefinition.parameter.documentation [ fhir:value "Region of interest is specified as a 0-based integer interval range. Variants that overlap the range are returned." ];
fhir:OperationDefinition.parameter.type [ fhir:value "Range" ]
], [
fhir:index 2;
fhir:OperationDefinition.parameter.name [ fhir:value "genomicRefSeq" ];
fhir:OperationDefinition.parameter.use [ fhir:value "in" ];
fhir:OperationDefinition.parameter.min [ fhir:value "1"^^xsd:integer ];
fhir:OperationDefinition.parameter.max [ fhir:value "1" ];
fhir:OperationDefinition.parameter.documentation [ fhir:value "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)" ];
fhir:OperationDefinition.parameter.type [ fhir:value "string" ];
fhir:OperationDefinition.parameter.searchType [ fhir:value "token" ]
], [
fhir:index 3;
fhir:OperationDefinition.parameter.name [ fhir:value "regionStudied" ];
fhir:OperationDefinition.parameter.use [ fhir:value "out" ];
fhir:OperationDefinition.parameter.min [ fhir:value "0"^^xsd:integer ];
fhir:OperationDefinition.parameter.max [ fhir:value "*" ];
fhir:OperationDefinition.parameter.documentation [ fhir:value "[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." ];
fhir:OperationDefinition.parameter.type [ fhir:value "canonical" ];
fhir:OperationDefinition.parameter.targetProfile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied> ]
], [
fhir:index 4;
fhir:OperationDefinition.parameter.name [ fhir:value "variant" ];
fhir:OperationDefinition.parameter.use [ fhir:value "out" ];
fhir:OperationDefinition.parameter.min [ fhir:value "0"^^xsd:integer ];
fhir:OperationDefinition.parameter.max [ fhir:value "*" ];
fhir:OperationDefinition.parameter.documentation [ fhir:value "[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." ];
fhir:OperationDefinition.parameter.type [ fhir:value "canonical" ];
fhir:OperationDefinition.parameter.targetProfile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ]
], [
fhir:index 5;
fhir:OperationDefinition.parameter.name [ fhir:value "sequencePhaseRelationship" ];
fhir:OperationDefinition.parameter.use [ fhir:value "out" ];
fhir:OperationDefinition.parameter.min [ fhir:value "0"^^xsd:integer ];
fhir:OperationDefinition.parameter.max [ fhir:value "*" ];
fhir:OperationDefinition.parameter.documentation [ fhir:value "[Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship] Must include valueCodeableConcept; 2..2 derivedFrom:variant." ];
fhir:OperationDefinition.parameter.type [ fhir:value "canonical" ];
fhir:OperationDefinition.parameter.targetProfile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship> ]
].
# - ontology header ------------------------------------------------------------
a owl:Ontology;
owl:imports fhir:fhir.ttl.
IG © 2022+ HL7 Clinical Genomics Working Group. Package hl7.fhir.uv.genomics-reporting#2.0.0 based on FHIR 4.0.1. Generated 2022-05-09
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