This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

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: To Be Determined 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:id [ fhir:v "tbd-codes-cs"] ; # 
  fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-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\">associated-therapy<a name=\"tbd-codes-cs-associated-therapy\"> </a></td><td>Associated Therapy</td><td>The non-medication therapy (procedure) associated with this implication.</td></tr><tr><td style=\"white-space:nowrap\">molecular-consequence<a name=\"tbd-codes-cs-molecular-consequence\"> </a></td><td>Molecular Consequence</td><td>The calculated or observed effect of a DNA variant on its downstream transcript and, if applicable, ensuing protein sequence.</td></tr><tr><td style=\"white-space:nowrap\">feature-consequence<a name=\"tbd-codes-cs-feature-consequence\"> </a></td><td>Feature Consequence</td><td>The structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion).</td></tr><tr><td style=\"white-space:nowrap\">diagnostic-implication<a name=\"tbd-codes-cs-diagnostic-implication\"> </a></td><td>Diagnostic Implication</td><td>An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition.</td></tr><tr><td style=\"white-space:nowrap\">therapeutic-implication<a name=\"tbd-codes-cs-therapeutic-implication\"> </a></td><td>Therapeutic Implication</td><td>An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy. Ramifications may include alterations in drug metabolism (or pharmacokinetics) that determine the concentration of the drug, prodrug, and/or break-down products over time; alterations in drug efficacy (or pharmacodynamics) that determine how effective a drug is at a given concentration; alterations that alter the risk of adverse drug events, or other types of implications that indicate altered responsiveness to other types of therapies.</td></tr><tr><td style=\"white-space:nowrap\">functional-effect<a name=\"tbd-codes-cs-functional-effect\"> </a></td><td>Functional Effect</td><td>The effect of a variant on downstream biological products or pathways (from Sequence Ontology).</td></tr><tr><td style=\"white-space:nowrap\">conclusion-string<a name=\"tbd-codes-cs-conclusion-string\"> </a></td><td>Conclusion Text</td><td>Clinical conclusion (interpretation) of the observation.</td></tr><tr><td style=\"white-space:nowrap\">condition-inheritance<a name=\"tbd-codes-cs-condition-inheritance\"> </a></td><td>Condition Inheritance</td><td>The transmission pattern of the condition/phenotype in a pedigree.</td></tr><tr><td style=\"white-space:nowrap\">variant-confidence-status<a name=\"tbd-codes-cs-variant-confidence-status\"> </a></td><td>Variant Confidence Status</td><td>The confidence of a true positive variant call.</td></tr><tr><td style=\"white-space:nowrap\">repeat-motif<a name=\"tbd-codes-cs-repeat-motif\"> </a></td><td>Repeat Expansion Motif</td><td>Nucleotides of a repeat expansion motif.</td></tr><tr><td style=\"white-space:nowrap\">repeat-number<a name=\"tbd-codes-cs-repeat-number\"> </a></td><td>Number of Repeat Expansions</td><td>Number of repeats of a repeat expansion.</td></tr><tr><td style=\"white-space:nowrap\">biomarker-category<a name=\"tbd-codes-cs-biomarker-category\"> </a></td><td>A characterization of a given biomarker observation.</td><td/></tr><tr><td style=\"white-space:nowrap\">protein-ref-seq<a name=\"tbd-codes-cs-protein-ref-seq\"> </a></td><td>An identifier for the protein reference sequence.</td><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/tbd-codes-cs"^^xsd:anyURI] ; # 
  fhir:version [ fhir:v "3.0.0-ballot"] ; # 
  fhir:name [ fhir:v "TbdCodesCS"] ; # 
  fhir:title [ fhir:v "To Be Determined Codes"] ; # 
  fhir:status [ fhir:v "active"] ; # 
  fhir:experimental [ fhir:v "false"^^xsd:boolean] ; # 
  fhir:date [ fhir:v "2023-12-18T22:45:59+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 "These codes are currently 'TBD' codes. The CG WG plans to request formal LOINC codes to replace these codes as these concepts are validated."] ; # 
  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 "13"^^xsd:nonNegativeInteger] ; # 
  fhir:concept ( [
fhir:code [ fhir:v "associated-therapy" ] ;
fhir:display [ fhir:v "Associated Therapy" ] ;
fhir:definition [ fhir:v "The non-medication therapy (procedure) associated with this implication." ]
  ] [
fhir:code [ fhir:v "molecular-consequence" ] ;
fhir:display [ fhir:v "Molecular Consequence" ] ;
fhir:definition [ fhir:v "The calculated or observed effect of a DNA variant on its downstream transcript and, if applicable, ensuing protein sequence." ]
  ] [
fhir:code [ fhir:v "feature-consequence" ] ;
fhir:display [ fhir:v "Feature Consequence" ] ;
fhir:definition [ fhir:v "The structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion)." ]
  ] [
fhir:code [ fhir:v "diagnostic-implication" ] ;
fhir:display [ fhir:v "Diagnostic Implication" ] ;
fhir:definition [ fhir:v "An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition." ]
  ] [
fhir:code [ fhir:v "therapeutic-implication" ] ;
fhir:display [ fhir:v "Therapeutic Implication" ] ;
fhir:definition [ fhir:v "An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy. Ramifications may include alterations in drug metabolism (or pharmacokinetics) that determine the concentration of the drug, prodrug, and/or break-down products over time; alterations in drug efficacy (or pharmacodynamics) that determine how effective a drug is at a given concentration; alterations that alter the risk of adverse drug events, or other types of implications that indicate altered responsiveness to other types of therapies." ]
  ] [
fhir:code [ fhir:v "functional-effect" ] ;
fhir:display [ fhir:v "Functional Effect" ] ;
fhir:definition [ fhir:v "The effect of a variant on downstream biological products or pathways (from Sequence Ontology)." ]
  ] [
fhir:code [ fhir:v "conclusion-string" ] ;
fhir:display [ fhir:v "Conclusion Text" ] ;
fhir:definition [ fhir:v "Clinical conclusion (interpretation) of the observation." ]
  ] [
fhir:code [ fhir:v "condition-inheritance" ] ;
fhir:display [ fhir:v "Condition Inheritance" ] ;
fhir:definition [ fhir:v "The transmission pattern of the condition/phenotype in a pedigree." ]
  ] [
fhir:code [ fhir:v "variant-confidence-status" ] ;
fhir:display [ fhir:v "Variant Confidence Status" ] ;
fhir:definition [ fhir:v "The confidence of a true positive variant call." ]
  ] [
fhir:code [ fhir:v "repeat-motif" ] ;
fhir:display [ fhir:v "Repeat Expansion Motif" ] ;
fhir:definition [ fhir:v "Nucleotides of a repeat expansion motif." ]
  ] [
fhir:code [ fhir:v "repeat-number" ] ;
fhir:display [ fhir:v "Number of Repeat Expansions" ] ;
fhir:definition [ fhir:v "Number of repeats of a repeat expansion." ]
  ] [
fhir:code [ fhir:v "biomarker-category" ] ;
fhir:display [ fhir:v "A characterization of a given biomarker observation." ]
  ] [
fhir:code [ fhir:v "protein-ref-seq" ] ;
fhir:display [ fhir:v "An identifier for the protein reference sequence." ]
  ] ) . #