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

Example - HLA genotyping for HLA-A, HLA-B, and HLA-C, using GLStrings - TTL Representation

(back to narrative)

Raw ttl 

@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:DiagnosticReport;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "diagnosticreport-hla-glstring-r4"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <pre>\nHLA-A,-B,-C genotyping report for sample-id=123456789\n\nLOCUS   ALLELE ASSIGNMENT\nHLA-A   HLA-A*03:01:01:01\n        HLA-A*30:01:01\n\nHLA-B   HLA-B*15:01:01:01\n        HLA-B*40:01:02:01/HLA-B*40:01:02:02/HLA-B*40:01:02:04/HLA-B*40:01:02:06\n\nHLA-C   HLA-C*07:04:01:01/HLA-C*07:04:01:03\n        HLA-C*12:03:01:01/HLA-C*12:03:01:06\n\nAllele assignments based on IMGT/HLA 3.31.0\nEffective date: 2018-07-26\n\nLab: aTypingLab Inc\n           </pre>\n        </div>"
  ];
  fhir:DiagnosticReport.basedOn [
     fhir:index 0;
     fhir:Reference.display [ fhir:value "Sequence-based typing of HLA-A for sample-id=123456789" ]
  ], [
     fhir:index 1;
     fhir:Reference.display [ fhir:value "Sequence-based typing of HLA-B for sample-id=123456789" ]
  ], [
     fhir:index 2;
     fhir:Reference.display [ fhir:value "Sequence-based typing of HLA-C for sample-id=123456789" ]
  ];
  fhir:DiagnosticReport.status [ fhir:value "final"];
  fhir:DiagnosticReport.category [
     fhir:index 0;
     fhir:CodeableConcept.coding [
       fhir:index 0;
       fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/v2-0074" ];
       fhir:Coding.code [ fhir:value "GE" ];
       fhir:Coding.display [ fhir:value "Genetics" ]     ]
  ];
  fhir:DiagnosticReport.code [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:81247-9;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "81247-9" ];
       fhir:Coding.display [ fhir:value "Master HL7 genetic variant reporting panel" ]     ], [
       fhir:index 1;
       fhir:Coding.system [ fhir:value "http://genenames.org/geneId" ];
       fhir:Coding.code [ fhir:value "588" ];
       fhir:Coding.display [ fhir:value "Histocompatibility complex (HLA)" ]     ]
  ];
  fhir:DiagnosticReport.effectiveDateTime [ fhir:value "2018-07-26"^^xsd:date];
  fhir:DiagnosticReport.performer [
     fhir:index 0;
     fhir:Reference.display [ fhir:value "aTypingLab, Inc" ]
  ];
  fhir:DiagnosticReport.specimen [
     fhir:index 0;
     fhir:Reference.display [ fhir:value "buccal swab: 123456789" ]
  ];
  fhir:DiagnosticReport.result [
     fhir:index 0;
     fhir:Reference.type [ fhir:value "Observation" ];
     fhir:Reference.display [ fhir:value "HLA-A genotype: HLA-A:01:01:01G+HLA-A*01:02" ]
  ], [
     fhir:index 1;
     fhir:Reference.type [ fhir:value "Observation" ];
     fhir:Reference.display [ fhir:value "HLA-B genotype: HLA-B*15:01:01:01+HLA-B*40:01:02:01/HLA-B*40:01:02:02/HLA-B*40:01:02:04/HLA-B*40:01:02:06" ]
  ], [
     fhir:index 2;
     fhir:Reference.type [ fhir:value "Observation" ];
     fhir:Reference.display [ fhir:value "HLA-C genotype: HLA-C*07:04:01:01/HLA-C*07:04:01:03+HLA-C*12:03:01:01/HLA-C*12:03:01:06" ]
  ].

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

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