Genomics Reporting Implementation Guide (STU1)

This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 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

TBD Code System - TTL Representation

(back to narrative)

Raw ttl 

@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"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/StructureDefinition/shareablecodesystem";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/StructureDefinition/shareablecodesystem>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><h2>tbd-codes</h2><div><p>These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.</p>\n</div><p>This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes 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=\"tbd-codes-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\">mode-of-inheritance<a name=\"tbd-codes-mode-of-inheritance\"> </a></td><td>mode-of-inheritance</td><td>This is actually LOINC code 79742-3. And the IG will be updated</td></tr><tr><td style=\"white-space:nowrap\">effect-transporter-function<a name=\"tbd-codes-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\">somatic-diagnostic<a name=\"tbd-codes-somatic-diagnostic\"> </a></td><td>somatic-diagnostic</td><td>Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof supports or opposes the diagnosis of a particular cancer. Example values are: Pathognomonic, Supportive, Argues Against, Rules Out.</td></tr><tr><td style=\"white-space:nowrap\">somatic-prognostic<a name=\"tbd-codes-somatic-prognostic\"> </a></td><td>Somatic 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\">somatic-prognostic-medication<a name=\"tbd-codes-somatic-prognostic-medication\"> </a></td><td>somatic-prognostic-medication</td><td>The medication or medication class whose implication on the cancer is being predicted. (Same as somatic-predictive-medication).</td></tr><tr><td style=\"white-space:nowrap\">somatic-prognostic-treatment<a name=\"tbd-codes-somatic-prognostic-treatment\"> </a></td><td>somatic-prognostic-treatment</td><td>The non-medication therapy (procedure) whose implication on the cancer outcome is being predicted. E.g. altered diet, radiation therapy, surgery, etc.</td></tr><tr><td style=\"white-space:nowrap\">somatic-predictive<a name=\"tbd-codes-somatic-predictive\"> </a></td><td>Somatic variant predicted effect on Cancer medication</td><td>Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts an impact on medication efficay or prediction of an adverse event caused by a medication. Example values are: Resistant, Responsive, Not-Responsive, Sensitive, Reduced-Sensitivity, Adverse Response.</td></tr><tr><td style=\"white-space:nowrap\">somatic-predictive-medication<a name=\"tbd-codes-somatic-predictive-medication\"> </a></td><td>somatic-predictive-medication</td><td>The medication or medication class whose implication on the cancer is being predicted.</td></tr><tr><td style=\"white-space:nowrap\">associated-cancer<a name=\"tbd-codes-associated-cancer\"> </a></td><td>associated-cancer</td><td>Associated Cancer</td></tr><tr><td style=\"white-space:nowrap\">region-coverage<a name=\"tbd-codes-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\">functional-annotation<a name=\"tbd-codes-functional-annotation\"> </a></td><td>functional-annotation</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=\"tbd-codes-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=\"tbd-codes-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=\"tbd-codes-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=\"tbd-codes-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></table></div>"
  ];
  fhir:DomainResource.extension [
     fhir:index 0;
     fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg" ];
     fhir:Extension.valueCode [ fhir:value "cg" ]
  ];
  fhir:CodeSystem.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes"];
  fhir:CodeSystem.version [ fhir:value "1.0.0"];
  fhir:CodeSystem.name [ fhir:value "ToBeDeterminedCodes"];
  fhir:CodeSystem.title [ fhir:value "tbd-codes"];
  fhir:CodeSystem.status [ fhir:value "draft"];
  fhir:CodeSystem.experimental [ fhir:value "false"^^xsd:boolean];
  fhir:CodeSystem.date [ fhir:value "2019-08-21T00:00:00-04:00"^^xsd:dateTime];
  fhir:CodeSystem.publisher [ fhir:value "HL7 (Clinical Genomics)"];
  fhir:CodeSystem.contact [
     fhir:index 0;
     fhir:ContactDetail.telecom [
       fhir:index 0;
       fhir:ContactPoint.system [ fhir:value "url" ];
       fhir:ContactPoint.value [ fhir:value "http://hl7.org/fhir" ]     ], [
       fhir:index 1;
       fhir:ContactPoint.system [ fhir:value "email" ];
       fhir:ContactPoint.value [ fhir:value "fhir@lists.hl7.org" ]     ]
  ];
  fhir:CodeSystem.description [ fhir:value "These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes."];
  fhir:CodeSystem.caseSensitive [ fhir:value "true"^^xsd:boolean];
  fhir:CodeSystem.valueSet [
     fhir:value "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/tbd-codes";
     fhir:link <http://hl7.org/fhir/uv/genomics-reporting/ValueSet/tbd-codes>
  ];
  fhir:CodeSystem.content [ fhir:value "complete"];
  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 "mode-of-inheritance" ];
     fhir:CodeSystem.concept.display [ fhir:value "mode-of-inheritance" ];
     fhir:CodeSystem.concept.definition [ fhir:value "This is actually LOINC code 79742-3. And the IG will be updated" ]
  ], [
     fhir:index 2;
     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 3;
     fhir:CodeSystem.concept.code [ fhir:value "somatic-diagnostic" ];
     fhir:CodeSystem.concept.display [ fhir:value "somatic-diagnostic" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof supports or opposes the diagnosis of a particular cancer. Example values are: Pathognomonic, Supportive, Argues Against, Rules Out." ]
  ], [
     fhir:index 4;
     fhir:CodeSystem.concept.code [ fhir:value "somatic-prognostic" ];
     fhir:CodeSystem.concept.display [ fhir:value "Somatic 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 5;
     fhir:CodeSystem.concept.code [ fhir:value "somatic-prognostic-medication" ];
     fhir:CodeSystem.concept.display [ fhir:value "somatic-prognostic-medication" ];
     fhir:CodeSystem.concept.definition [ fhir:value "The medication or medication class whose implication on the cancer is being predicted. (Same as somatic-predictive-medication)." ]
  ], [
     fhir:index 6;
     fhir:CodeSystem.concept.code [ fhir:value "somatic-prognostic-treatment" ];
     fhir:CodeSystem.concept.display [ fhir:value "somatic-prognostic-treatment" ];
     fhir:CodeSystem.concept.definition [ fhir:value "The non-medication therapy (procedure) whose implication on the cancer outcome is being predicted. E.g. altered diet, radiation therapy, surgery, etc." ]
  ], [
     fhir:index 7;
     fhir:CodeSystem.concept.code [ fhir:value "somatic-predictive" ];
     fhir:CodeSystem.concept.display [ fhir:value "Somatic variant predicted effect on Cancer medication" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts an impact on medication efficay or prediction of an adverse event caused by a medication. Example values are: Resistant, Responsive, Not-Responsive, Sensitive, Reduced-Sensitivity, Adverse Response." ]
  ], [
     fhir:index 8;
     fhir:CodeSystem.concept.code [ fhir:value "somatic-predictive-medication" ];
     fhir:CodeSystem.concept.display [ fhir:value "somatic-predictive-medication" ];
     fhir:CodeSystem.concept.definition [ fhir:value "The medication or medication class whose implication on the cancer is being predicted." ]
  ], [
     fhir:index 9;
     fhir:CodeSystem.concept.code [ fhir:value "associated-cancer" ];
     fhir:CodeSystem.concept.display [ fhir:value "associated-cancer" ];
     fhir:CodeSystem.concept.definition [ fhir:value "Associated Cancer" ]
  ], [
     fhir:index 10;
     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 11;
     fhir:CodeSystem.concept.code [ fhir:value "functional-annotation" ];
     fhir:CodeSystem.concept.display [ fhir:value "functional-annotation" ];
     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 12;
     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 13;
     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 14;
     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 15;
     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" ]
  ].

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

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