Genomics Reporting Implementation Guide
3.0.0 - release International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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

: PharmGKB Evidence Level Example Codes - TTL Representation

Active as of 2024-11-19

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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:id [ fhir:v "pharmgkb-evidence-level-custom-cs"] ; # 
  fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem pharmgkb-evidence-level-custom-cs</b></p><a name=\"pharmgkb-evidence-level-custom-cs\"> </a><a name=\"hcpharmgkb-evidence-level-custom-cs\"> </a><a name=\"pharmgkb-evidence-level-custom-cs-en-US\"> </a><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/pharmgkb-evidence-level-custom-cs</code> 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:extension ( [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ] ;
fhir:value [ fhir:v "cg" ]
  ] ) ; # 
  fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/pharmgkb-evidence-level-custom-cs"^^xsd:anyURI] ; # 
  fhir:version [ fhir:v "3.0.0"] ; # 
  fhir:name [ fhir:v "PharmGKBEvidenceLevelCustomCS"] ; # 
  fhir:title [ fhir:v "PharmGKB Evidence Level Example Codes"] ; # 
  fhir:status [ fhir:v "active"] ; # 
  fhir:experimental [ fhir:v "true"^^xsd:boolean] ; # 
  fhir:date [ fhir:v "2024-11-19T22:01:39+00:00"^^xsd:dateTime] ; # 
  fhir:publisher [ fhir:v "HL7 International / Clinical Genomics"] ; # 
  fhir:contact ( [
fhir:name [ fhir:v "HL7 International / Clinical Genomics" ] ;
    ( fhir:telecom [
fhir:system [ fhir:v "url" ] ;
fhir:value [ fhir:v "http://www.hl7.org/Special/committees/clingenomics" ]     ] [
fhir:system [ fhir:v "email" ] ;
fhir:value [ fhir:v "cg@lists.HL7.org" ]     ] )
  ] ) ; # 
  fhir:description [ fhir:v "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:jurisdiction ( [
    ( fhir:coding [
fhir:system [ fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm"^^xsd:anyURI ] ;
fhir:code [ fhir:v "001" ] ;
fhir:display [ fhir:v "World" ]     ] )
  ] ) ; # 
  fhir:caseSensitive [ fhir:v "true"^^xsd:boolean] ; # 
  fhir:content [ fhir:v "complete"] ; # 
  fhir:count [ fhir:v "6"^^xsd:nonNegativeInteger] ; # 
  fhir:concept ( [
fhir:code [ fhir:v "1A" ] ;
fhir:display [ fhir:v "PGKB 1A" ] ;
fhir:definition [ fhir:v "High level of evidence. Supported by a guideline or FDA label with variant specific prescribing guidance. Additionally, supported by at least one publication." ]
  ] [
fhir:code [ fhir:v "1B" ] ;
fhir:display [ fhir:v "PGKB 1B" ] ;
fhir:definition [ fhir:v "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:code [ fhir:v "2A" ] ;
fhir:display [ fhir:v "PGKB 2A" ] ;
fhir:definition [ fhir:v "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:code [ fhir:v "2B" ] ;
fhir:display [ fhir:v "PGKB 2B" ] ;
fhir:definition [ fhir:v "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:code [ fhir:v "3" ] ;
fhir:display [ fhir:v "PGKB 3" ] ;
fhir:definition [ fhir:v "Low-level of evidence. Where either the assocation is based on a single study, failed to be reproduced, or preliminary evidence." ]
  ] [
fhir:code [ fhir:v "4" ] ;
fhir:display [ fhir:v "PGKB 4" ] ;
fhir:definition [ fhir:v "The evidence does not support an association between the variant and the drug phenotype. (negative)" ]
  ] ) . #