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

: 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:Resource.id [ fhir:value "tbd-codes-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/tbd-codes-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\">predicted-therapeutic-implication<a name=\"tbd-codes-cs-predicted-therapeutic-implication\"> </a></td><td>Predicted Therapeutic Implication</td><td>A predicted ramification based on the presence of associated molecular finding(s). 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\">prognostic-implication<a name=\"tbd-codes-cs-prognostic-implication\"> </a></td><td>Prognostic Implication</td><td>Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions.</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\">region-coverage<a name=\"tbd-codes-cs-region-coverage\"> </a></td><td>Region Coverage</td><td>Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence.</td></tr><tr><td style=\"white-space:nowrap\">molecular-consequence<a name=\"tbd-codes-cs-molecular-consequence\"> </a></td><td>Molecular Consequence</td><td>Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537. The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence.</td></tr><tr><td style=\"white-space:nowrap\">variant-inheritance<a name=\"tbd-codes-cs-variant-inheritance\"> </a></td><td>Variant Inheritance</td><td>A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762.</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.</td></tr><tr><td style=\"white-space:nowrap\">uncallable-regions<a name=\"tbd-codes-cs-uncallable-regions\"> </a></td><td>Uncallable Regions</td><td>Contiguous regions where a call was not made. Must be inside the range given by 'ranges examined' in the given reference sequence and coordinate system.</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></table></div>"
  ];
  fhir:CodeSystem.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"];
  fhir:CodeSystem.version [ fhir:value "2.0.0"];
  fhir:CodeSystem.name [ fhir:value "TbdCodesCS"];
  fhir:CodeSystem.title [ fhir:value "To Be Determined Codes"];
  fhir:CodeSystem.status [ fhir:value "active"];
  fhir:CodeSystem.date [ fhir:value "2022-05-09T16:53:07+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 "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: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 "13"^^xsd:nonNegativeInteger];
  fhir:CodeSystem.concept [
     fhir:index 0;
     fhir:CodeSystem.concept.code [ fhir:value "predicted-therapeutic-implication" ];
     fhir:CodeSystem.concept.display [ fhir:value "Predicted Therapeutic Implication" ];
     fhir:CodeSystem.concept.definition [ fhir:value "A predicted ramification based on the presence of associated molecular finding(s). 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:index 1;
     fhir:CodeSystem.concept.code [ fhir:value "prognostic-implication" ];
     fhir:CodeSystem.concept.display [ fhir:value "Prognostic Implication" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions." ]
  ], [
     fhir:index 2;
     fhir:CodeSystem.concept.code [ fhir:value "associated-therapy" ];
     fhir:CodeSystem.concept.display [ fhir:value "Associated Therapy" ];
     fhir:CodeSystem.concept.definition [ fhir:value "The non-medication therapy (procedure) associated with this implication." ]
  ], [
     fhir:index 3;
     fhir:CodeSystem.concept.code [ fhir:value "region-coverage" ];
     fhir:CodeSystem.concept.display [ fhir:value "Region Coverage" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence." ]
  ], [
     fhir:index 4;
     fhir:CodeSystem.concept.code [ fhir:value "molecular-consequence" ];
     fhir:CodeSystem.concept.display [ fhir:value "Molecular Consequence" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537. The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence." ]
  ], [
     fhir:index 5;
     fhir:CodeSystem.concept.code [ fhir:value "variant-inheritance" ];
     fhir:CodeSystem.concept.display [ fhir:value "Variant Inheritance" ];
     fhir:CodeSystem.concept.definition [ fhir:value "A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762." ]
  ], [
     fhir:index 6;
     fhir:CodeSystem.concept.code [ fhir:value "diagnostic-implication" ];
     fhir:CodeSystem.concept.display [ fhir:value "Diagnostic Implication" ];
     fhir:CodeSystem.concept.definition [ fhir:value "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:index 7;
     fhir:CodeSystem.concept.code [ fhir:value "therapeutic-implication" ];
     fhir:CodeSystem.concept.display [ fhir:value "Therapeutic Implication" ];
     fhir:CodeSystem.concept.definition [ fhir:value "An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy." ]
  ], [
     fhir:index 8;
     fhir:CodeSystem.concept.code [ fhir:value "uncallable-regions" ];
     fhir:CodeSystem.concept.display [ fhir:value "Uncallable Regions" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Contiguous regions where a call was not made. Must be inside the range given by 'ranges examined' in the given reference sequence and coordinate system." ]
  ], [
     fhir:index 9;
     fhir:CodeSystem.concept.code [ fhir:value "functional-effect" ];
     fhir:CodeSystem.concept.display [ fhir:value "Functional Effect" ];
     fhir:CodeSystem.concept.definition [ fhir:value "The effect of a variant on downstream biological products or pathways (from Sequence Ontology)." ]
  ], [
     fhir:index 10;
     fhir:CodeSystem.concept.code [ fhir:value "conclusion-string" ];
     fhir:CodeSystem.concept.display [ fhir:value "Conclusion Text" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Clinical conclusion (interpretation) of the observation." ]
  ], [
     fhir:index 11;
     fhir:CodeSystem.concept.code [ fhir:value "condition-inheritance" ];
     fhir:CodeSystem.concept.display [ fhir:value "Condition Inheritance" ];
     fhir:CodeSystem.concept.definition [ fhir:value "The transmission pattern of the condition/phenotype in a pedigree." ]
  ], [
     fhir:index 12;
     fhir:CodeSystem.concept.code [ fhir:value "variant-confidence-status" ];
     fhir:CodeSystem.concept.display [ fhir:value "Variant Confidence Status" ];
     fhir:CodeSystem.concept.definition [ fhir:value "The confidence of a true positive variant call." ]
  ].

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

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