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: mCODEGeneticVariantFoundExample01

@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 xsd: <http://www.w3.org/2001/XMLSchema#> .

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

 a fhir:Observation;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "mCODEGeneticVariantFoundExample01"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantFound";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantFound>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n			<p>\n				<b>*** mCODE Example: Genetic Variant Assessment ***</b>\n			</p>\n			<p>\n				<b>Patient identifier</b>: m123</p>\n			<p><b>Name</b>: John B. Anyperson </p>\n			<p>\n				<b>Test date</b>: April 1, 2019</p>\n			<p>\n				<b>Genomic source class [Type]</b>: Somatic</p>\n			<p>\n				<b>Variant HGVS name</b>: NM_000455.4:c.921-1G>C</p>\n			<p><b>Variant common name</b>: G242E</p>\n			</div>"
  ];
  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:Observation.code [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:69548-6;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "69548-6" ];
       fhir:Coding.display [ fhir:value "Genetic variant assessment" ]     ]
  ];
  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.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" ]     ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48002-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48002-0" ];
         fhir:Coding.display [ fhir:value "Genomic source class [Type]" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA6684-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA6684-0" ];
         fhir:Coding.display [ fhir:value "Somatic" ]       ];
       fhir:CodeableConcept.text [ fhir:value "Somatic" ]     ]
  ], [
     fhir:index 1;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48003-8;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48003-8" ];
         fhir:Coding.display [ fhir:value "DNA sequence variation identifier [Identifier]" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/clinvar/" ];
         fhir:Coding.code [ fhir:value "619728" ];
         fhir:Coding.display [ fhir:value "NM_000455.4(STK11):c.725G>A (p.Gly242Glu)" ]       ];
       fhir:CodeableConcept.text [ fhir:value "NM_000455.4(STK11):c.725G>A (p.Gly242Glu)" ]     ]
  ], [
     fhir:index 2;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:82154-6;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "82154-6" ];
         fhir:Coding.display [ fhir:value "Genomic structural variant name" ]       ]     ];
     fhir:Observation.component.valueString [ fhir:value "NM_000455.4:c.725G>A" ]
  ], [
     fhir:index 3;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:47998-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "47998-0" ];
         fhir:Coding.display [ fhir:value "DNA sequence variation display name [Text] Narrative" ]       ]     ];
     fhir:Observation.component.valueString [ fhir:value "G242E" ]
  ].

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

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