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

: PharmGKB 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 "pharmgkb-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/pharmgkb-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\">1A<a name=\"pharmgkb-evidence-level-custom-cs-1A\"> </a></td><td>PGKB 1A</td><td>High level of evidence. Supported by a guideline or FDA label with variant specific prescribing guidance. Additionally, supported by at least one publication.</td></tr><tr><td style=\"white-space:nowrap\">1B<a name=\"pharmgkb-evidence-level-custom-cs-1B\"> </a></td><td>PGKB 1B</td><td>High level of evidence. But, NOT supported by a guideline or FDA label with variant specific prescribing guidance. Additionally, supported by at least one publication.</td></tr><tr><td style=\"white-space:nowrap\">2A<a name=\"pharmgkb-evidence-level-custom-cs-2A\"> </a></td><td>PGKB 2A</td><td>Moderate level of evidence. Supported by being a KNOWN pharmacogene on https://www.pharmgkb.org/vips. Also, found in multiple studies but may have a minority of studies that did not support the majority opinion. Supported by at least two indpendent publications.</td></tr><tr><td style=\"white-space:nowrap\">2B<a name=\"pharmgkb-evidence-level-custom-cs-2B\"> </a></td><td>PGKB 2B</td><td>Moderate level of evidence. NOT in the list of very important, KNOWN pharmacogenes. Found in multiple studies but may have a minority of studies that did not support the majority opinion. Supported by at least two indpendent publications.</td></tr><tr><td style=\"white-space:nowrap\">3<a name=\"pharmgkb-evidence-level-custom-cs-3\"> </a></td><td>PGKB 3</td><td>Low-level of evidence. Where either the assocation is based on a single study, failed to be reproduced, or preliminary evidence.</td></tr><tr><td style=\"white-space:nowrap\">4<a name=\"pharmgkb-evidence-level-custom-cs-4\"> </a></td><td>PGKB 4</td><td>The evidence does not support an association between the variant and the drug phenotype. (negative)</td></tr></table></div>"
  ];
  fhir:CodeSystem.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/pharmgkb-evidence-level-custom-cs"];
  fhir:CodeSystem.version [ fhir:value "2.0.0"];
  fhir:CodeSystem.name [ fhir:value "PharmGKBEvidenceLevelCustomCS"];
  fhir:CodeSystem.title [ fhir:value "PharmGKB 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 "PharmGKB contains examples of evidence level concepts that are not conflated with clinical significance. These can be found on PharmGKB https://www.pharmgkb.org/page/clinAnnLevels. 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 "6"^^xsd:nonNegativeInteger];
  fhir:CodeSystem.concept [
     fhir:index 0;
     fhir:CodeSystem.concept.code [ fhir:value "1A" ];
     fhir:CodeSystem.concept.display [ fhir:value "PGKB 1A" ];
     fhir:CodeSystem.concept.definition [ fhir:value "High level of evidence. Supported by a guideline or FDA label with variant specific prescribing guidance. Additionally, supported by at least one publication." ]
  ], [
     fhir:index 1;
     fhir:CodeSystem.concept.code [ fhir:value "1B" ];
     fhir:CodeSystem.concept.display [ fhir:value "PGKB 1B" ];
     fhir:CodeSystem.concept.definition [ fhir:value "High level of evidence. But, NOT supported by a guideline or FDA label with variant specific prescribing guidance. Additionally, supported by at least one publication." ]
  ], [
     fhir:index 2;
     fhir:CodeSystem.concept.code [ fhir:value "2A" ];
     fhir:CodeSystem.concept.display [ fhir:value "PGKB 2A" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Moderate level of evidence. Supported by being a KNOWN pharmacogene on https://www.pharmgkb.org/vips. Also, found in multiple studies but may have a minority of studies that did not support the majority opinion. Supported by at least two indpendent publications." ]
  ], [
     fhir:index 3;
     fhir:CodeSystem.concept.code [ fhir:value "2B" ];
     fhir:CodeSystem.concept.display [ fhir:value "PGKB 2B" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Moderate level of evidence. NOT in the list of very important, KNOWN pharmacogenes. Found in multiple studies but may have a minority of studies that did not support the majority opinion. Supported by at least two indpendent publications." ]
  ], [
     fhir:index 4;
     fhir:CodeSystem.concept.code [ fhir:value "3" ];
     fhir:CodeSystem.concept.display [ fhir:value "PGKB 3" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Low-level of evidence. Where either the assocation is based on a single study, failed to be reproduced, or preliminary evidence." ]
  ], [
     fhir:index 5;
     fhir:CodeSystem.concept.code [ fhir:value "4" ];
     fhir:CodeSystem.concept.display [ fhir:value "PGKB 4" ];
     fhir:CodeSystem.concept.definition [ fhir:value "The evidence does not support an association between the variant and the drug phenotype. (negative)" ]
  ].

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

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