Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
@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 "TbdCodes"];
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/TbdCodes 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\">grouper<a name=\"TbdCodes-grouper\"> </a></td><td>grouper</td><td>A means to bundle several observations such as one would find in a genetics test panel.</td></tr><tr><td style=\"white-space:nowrap\">effect-transporter-function<a name=\"TbdCodes-effect-transporter-function\"> </a></td><td>effect-transporter-function</td><td>Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance.</td></tr><tr><td style=\"white-space:nowrap\">effect-medication-efficacy<a name=\"TbdCodes-effect-medication-efficacy\"> </a></td><td>Medication Efficacy</td><td/></tr><tr><td style=\"white-space:nowrap\">effect-medication-metabolism<a name=\"TbdCodes-effect-medication-metabolism\"> </a></td><td>Medication Metabolism</td><td/></tr><tr><td style=\"white-space:nowrap\">effect-medication-transporter<a name=\"TbdCodes-effect-medication-transporter\"> </a></td><td>Medication Transporter Function</td><td/></tr><tr><td style=\"white-space:nowrap\">effect-high-risk-allele<a name=\"TbdCodes-effect-high-risk-allele\"> </a></td><td>High Risk Allele</td><td/></tr><tr><td style=\"white-space:nowrap\">prognostic-implication<a name=\"TbdCodes-prognostic-implication\"> </a></td><td>Prognostic Implication component</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-cancer<a name=\"TbdCodes-associated-cancer\"> </a></td><td>associated-cancer</td><td/></tr><tr><td style=\"white-space:nowrap\">associated-therapy<a name=\"TbdCodes-associated-therapy\"> </a></td><td>Genomically linked therapy</td><td>The non-medication therapy (procedure) associated with this implication.</td></tr><tr><td style=\"white-space:nowrap\">region-coverage<a name=\"TbdCodes-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=\"TbdCodes-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.</td></tr><tr><td style=\"white-space:nowrap\">exact-start-end<a name=\"TbdCodes-exact-start-end\"> </a></td><td>Variant exact start and end</td><td>The genomic coordinates of the exact genomic range in which the variant resides.</td></tr><tr><td style=\"white-space:nowrap\">inner-start-end<a name=\"TbdCodes-inner-start-end\"> </a></td><td>Variant inner start and end</td><td>The genomic coordinates of the inner genomic range in which the variant might reside.</td></tr><tr><td style=\"white-space:nowrap\">outer-start-end<a name=\"TbdCodes-outer-start-end\"> </a></td><td>Variant outer start and end</td><td>The genomic coordinates of the outer genomic range in which the variant might reside.</td></tr><tr><td style=\"white-space:nowrap\">variant-inheritance<a name=\"TbdCodes-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=\"TbdCodes-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=\"TbdCodes-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=\"TbdCodes-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=\"TbdCodes-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=\"TbdCodes-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=\"TbdCodes-condition-inheritance\"> </a></td><td>Condition Inheritance</td><td>The transmission pattern of the condition/phenotype in a pedigree.</td></tr></table></div>"
];
fhir:CodeSystem.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"];
fhir:CodeSystem.version [ fhir:value "1.1.0"];
fhir:CodeSystem.name [ fhir:value "TbdCodes"];
fhir:CodeSystem.title [ fhir:value "ToBeDeterminedCodes ('TbdCodes')"];
fhir:CodeSystem.status [ fhir:value "active"];
fhir:CodeSystem.date [ fhir:value "2021-04-13T19:13:37+00:00"^^xsd:dateTime];
fhir:CodeSystem.publisher [ fhir:value "HL7 International Clinical Genomics Work Group"];
fhir:CodeSystem.contact [
fhir:index 0;
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:CodeSystem.description [ fhir:value "These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes."];
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:CodeSystem.content [ fhir:value "complete"];
fhir:CodeSystem.count [ fhir:value "21"^^xsd:nonNegativeInteger];
fhir:CodeSystem.concept [
fhir:index 0;
fhir:CodeSystem.concept.code [ fhir:value "grouper" ];
fhir:CodeSystem.concept.display [ fhir:value "grouper" ];
fhir:CodeSystem.concept.definition [ fhir:value "A means to bundle several observations such as one would find in a genetics test panel." ]
], [
fhir:index 1;
fhir:CodeSystem.concept.code [ fhir:value "effect-transporter-function" ];
fhir:CodeSystem.concept.display [ fhir:value "effect-transporter-function" ];
fhir:CodeSystem.concept.definition [ fhir:value "Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance." ]
], [
fhir:index 2;
fhir:CodeSystem.concept.code [ fhir:value "effect-medication-efficacy" ];
fhir:CodeSystem.concept.display [ fhir:value "Medication Efficacy" ]
], [
fhir:index 3;
fhir:CodeSystem.concept.code [ fhir:value "effect-medication-metabolism" ];
fhir:CodeSystem.concept.display [ fhir:value "Medication Metabolism" ]
], [
fhir:index 4;
fhir:CodeSystem.concept.code [ fhir:value "effect-medication-transporter" ];
fhir:CodeSystem.concept.display [ fhir:value "Medication Transporter Function" ]
], [
fhir:index 5;
fhir:CodeSystem.concept.code [ fhir:value "effect-high-risk-allele" ];
fhir:CodeSystem.concept.display [ fhir:value "High Risk Allele" ]
], [
fhir:index 6;
fhir:CodeSystem.concept.code [ fhir:value "prognostic-implication" ];
fhir:CodeSystem.concept.display [ fhir:value "Prognostic Implication component" ];
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 7;
fhir:CodeSystem.concept.code [ fhir:value "associated-cancer" ];
fhir:CodeSystem.concept.display [ fhir:value "associated-cancer" ]
], [
fhir:index 8;
fhir:CodeSystem.concept.code [ fhir:value "associated-therapy" ];
fhir:CodeSystem.concept.display [ fhir:value "Genomically linked therapy" ];
fhir:CodeSystem.concept.definition [ fhir:value "The non-medication therapy (procedure) associated with this implication." ]
], [
fhir:index 9;
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 10;
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." ]
], [
fhir:index 11;
fhir:CodeSystem.concept.code [ fhir:value "exact-start-end" ];
fhir:CodeSystem.concept.display [ fhir:value "Variant exact start and end" ];
fhir:CodeSystem.concept.definition [ fhir:value "The genomic coordinates of the exact genomic range in which the variant resides." ]
], [
fhir:index 12;
fhir:CodeSystem.concept.code [ fhir:value "inner-start-end" ];
fhir:CodeSystem.concept.display [ fhir:value "Variant inner start and end" ];
fhir:CodeSystem.concept.definition [ fhir:value "The genomic coordinates of the inner genomic range in which the variant might reside." ]
], [
fhir:index 13;
fhir:CodeSystem.concept.code [ fhir:value "outer-start-end" ];
fhir:CodeSystem.concept.display [ fhir:value "Variant outer start and end" ];
fhir:CodeSystem.concept.definition [ fhir:value "The genomic coordinates of the outer genomic range in which the variant might reside." ]
], [
fhir:index 14;
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 15;
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 16;
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 17;
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 18;
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 19;
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 20;
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." ]
].
# - ontology header ------------------------------------------------------------
a owl:Ontology;
owl:imports fhir:fhir.ttl.
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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