HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU Ballot 1

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v0.9.1: STU 1 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

Example: mCODEGeneticVariantTestedExample01

@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <http://loinc.org/rdf#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sct: <http://snomed.info/id/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

 a fhir:Observation;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "mCODEGeneticVariantTestedExample01"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantTested";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantTested>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>*** mCODE Example: Genetic Mutation Test Result ***</b></p><p><b>Name</b>: John B. Anyperson </p><p><b>MRN</b>: m123 </p><p><b>Observation date</b>: 04/01/19 </p><p><b>Gene studied [ID]</b>: STK11</p><p><b>Gene variant Description</b>: NM_000455.4(STK11):c.921-1G>C </p><p><b>Gene variant presence</b>: DETECTED</p></div>"
  ];
  fhir:DomainResource.extension [
     fhir:index 0;
     fhir:Element.extension [
       fhir:index 0;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantHGVSName-extension" ];
       fhir:Extension.valueString [ fhir:value "NM_000455.4:c.921-1G>C" ]     ], [
       fhir:index 1;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantIdentifier-extension" ];
       fhir:Extension.valueCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://www.genenames.org/" ];
           fhir:Coding.code [ fhir:value "HGNC:11389" ];
           fhir:Coding.display [ fhir:value "STK11" ]         ]       ]     ], [
       fhir:index 2;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantDescription-extension" ];
       fhir:Extension.valueString [ fhir:value "NM_000455.4:c.921-1G>C" ]     ];
     fhir:Extension.url [ fhir:value "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantTested-extension" ]
  ];
  fhir:Observation.status [ fhir:value "final"];
  fhir:Observation.category [
     fhir:index 0;
     fhir:CodeableConcept.coding [
       fhir:index 0;
       fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ];
       fhir:Coding.code [ fhir:value "laboratory" ];
       fhir:Coding.display [ fhir:value "Laboratory" ]     ]
  ];
  fhir:Observation.code [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:41103-3;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "41103-3" ];
       fhir:Coding.display [ fhir:value "Gene XXX mutations found [Identifier] in Blood or Tissue by Molecular genetics method Nominal" ]     ]
  ];
  fhir:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/mCODEPatientExample01" ];
     fhir:Reference.display [ fhir:value "John B. Anyperson" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2019-04-01"^^xsd:date];
  fhir:Observation.valueCodeableConcept [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a sct:10828004;
       fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
       fhir:Coding.code [ fhir:value "10828004" ];
       fhir:Coding.display [ fhir:value "Positive (qualifier value)" ]     ]
  ];
  fhir:Observation.method [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       fhir:Coding.system [ fhir:value "http://ncit.nci.nih.gov" ];
       fhir:Coding.code [ fhir:value "C101293" ];
       fhir:Coding.display [ fhir:value "Next Generation Sequencing" ]     ]
  ].

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

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