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. For a full list of available versions, see the Directory of published versions

: ClinVar Evidence Level Example Codes - TTL Representation

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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:CodeSystem;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "clinvar-evidence-level-custom-cs"];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/clinvar-evidence-level-custom-cs defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">4-star<a name=\"clinvar-evidence-level-custom-cs-4-star\"> </a></td><td>4 star</td><td>Supported by practice guideline</td></tr><tr><td style=\"white-space:nowrap\">3-star<a name=\"clinvar-evidence-level-custom-cs-3-star\"> </a></td><td>3 star</td><td>Supported by expert panel review</td></tr><tr><td style=\"white-space:nowrap\">2-star<a name=\"clinvar-evidence-level-custom-cs-2-star\"> </a></td><td>2 star</td><td>Supported by submission by multiple-submitters with documentation of criteria for assertion</td></tr><tr><td style=\"white-space:nowrap\">1-star<a name=\"clinvar-evidence-level-custom-cs-1-star\"> </a></td><td>1 star</td><td>Single submitter providing interpretation and documentation of criteria for assertion</td></tr><tr><td style=\"white-space:nowrap\">no-star<a name=\"clinvar-evidence-level-custom-cs-no-star\"> </a></td><td>no star</td><td>submitted, no evidence</td></tr></table></div>"
  ];
  fhir:CodeSystem.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/clinvar-evidence-level-custom-cs"];
  fhir:CodeSystem.version [ fhir:value "2.0.0"];
  fhir:CodeSystem.name [ fhir:value "ClinVarEvidenceLevelCustomCS"];
  fhir:CodeSystem.title [ fhir:value "ClinVar Evidence Level Example Codes"];
  fhir:CodeSystem.status [ fhir:value "active"];
  fhir:CodeSystem.date [ fhir:value "2022-05-09T16:59:16+00:00"^^xsd:dateTime];
  fhir:CodeSystem.publisher [ fhir:value "HL7 Clinical Genomics Working Group"];
  fhir:CodeSystem.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:CodeSystem.description [ fhir:value "ClinVar contains examples of evidence level concepts that are not conflated with clinical significance. These can be found on  ClinVar https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/ . These examples are informational only, for copyright information contact the relevant source."];
  fhir:CodeSystem.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:CodeSystem.caseSensitive [ fhir:value "true"^^xsd:boolean];
  fhir:CodeSystem.content [ fhir:value "complete"];
  fhir:CodeSystem.count [ fhir:value "5"^^xsd:nonNegativeInteger];
  fhir:CodeSystem.concept [
     fhir:index 0;
     fhir:CodeSystem.concept.code [ fhir:value "4-star" ];
     fhir:CodeSystem.concept.display [ fhir:value "4 star" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Supported by practice guideline" ]
  ], [
     fhir:index 1;
     fhir:CodeSystem.concept.code [ fhir:value "3-star" ];
     fhir:CodeSystem.concept.display [ fhir:value "3 star" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Supported by expert panel review" ]
  ], [
     fhir:index 2;
     fhir:CodeSystem.concept.code [ fhir:value "2-star" ];
     fhir:CodeSystem.concept.display [ fhir:value "2 star" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Supported by submission by multiple-submitters with documentation of criteria for assertion" ]
  ], [
     fhir:index 3;
     fhir:CodeSystem.concept.code [ fhir:value "1-star" ];
     fhir:CodeSystem.concept.display [ fhir:value "1 star" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Single submitter providing interpretation and documentation of criteria for assertion" ]
  ], [
     fhir:index 4;
     fhir:CodeSystem.concept.code [ fhir:value "no-star" ];
     fhir:CodeSystem.concept.display [ fhir:value "no star" ];
     fhir:CodeSystem.concept.definition [ fhir:value "submitted, no evidence" ]
  ].

# - ontology header ------------------------------------------------------------

 a owl:Ontology;
  owl:imports fhir:fhir.ttl.