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 - subset of CYP2C19 report from 1000 Genomes showing phase - 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 "sequence-phase-relation-CYP2C19"];
  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\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: sequence-phase-relation-CYP2C19</p><p><b>meta</b>: </p><p><b>contained</b>: , , </p><p><b>status</b>: final</p><p><b>code</b>: Genetic analysis report <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81247-9' = 'Master HL7 genetic variant reporting panel)</span></p><p><b>result</b>: </p><ul><li>unknown resource contained</li><li>unknown resource contained</li><li>unknown resource contained</li></ul></div>"
  ];
  fhir:DomainResource.contained [
     a fhir:Observation;
     fhir:index 0;
     fhir:Resource.id [ fhir:value "dv-5c7e9e1ca8252" ];
     fhir:Resource.meta [
       fhir:Meta.profile [
         fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant";
         fhir:index 0;
         fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant>       ]     ];
     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.issued [ fhir:value "2019-03-05T16:04:44+00:00"^^xsd:dateTime ];
     fhir:Observation.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA9633-4;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA9633-4" ];
         fhir:Coding.display [ fhir:value "Present" ]       ]     ];
     fhir:Observation.component [
       fhir:index 0;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:62374-4;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "62374-4" ];
           fhir:Coding.display [ fhir:value "Human reference sequence assembly version" ]         ]       ];
       fhir:Observation.component.valueCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:LA14029-5;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "LA14029-5" ];
           fhir:Coding.display [ fhir:value "GRCh37" ]         ]       ]     ], [
       fhir:index 1;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:48013-7;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "48013-7" ];
           fhir:Coding.display [ fhir:value "Genomic reference sequence ID" ]         ]       ];
       fhir:Observation.component.valueCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore" ];
           fhir:Coding.code [ fhir:value "NC_000010.10" ]         ]       ]     ], [
       fhir:index 2;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:53034-5;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "53034-5" ];
           fhir:Coding.display [ fhir:value "Allelic state" ]         ]       ];
       fhir:Observation.component.valueCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:LA6706-1;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "LA6706-1" ];
           fhir:Coding.display [ fhir:value "heterozygous" ]         ]       ]     ], [
       fhir:index 3;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:69547-8;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "69547-8" ];
           fhir:Coding.display [ fhir:value "Ref nucleotide" ]         ]       ];
       fhir:Observation.component.valueString [ fhir:value "C" ]     ], [
       fhir:index 4;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:69551-0;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "69551-0" ];
           fhir:Coding.display [ fhir:value "Alt allele" ]         ]       ];
       fhir:Observation.component.valueString [ fhir:value "A" ]     ], [
       fhir:index 5;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:92822-6;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "92822-6" ];
           fhir:Coding.display [ fhir:value "Genomic coord system" ]         ]       ];
       fhir:Observation.component.valueCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:LA30102-0;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "LA30102-0" ]         ]       ]     ], [
       fhir:index 6;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes" ];
           fhir:Coding.code [ fhir:value "exact-start-end" ];
           fhir:Coding.display [ fhir:value "Variant exact start and end" ]         ]       ];
       fhir:Observation.component.valueRange [
         fhir:Range.low [
           fhir:Quantity.value [ fhir:value "96527334"^^xsd:decimal ]         ]       ]     ]
  ], [
     a fhir:Observation;
     fhir:index 1;
     fhir:Resource.id [ fhir:value "dv-5c7e9e1ca82e4" ];
     fhir:Resource.meta [
       fhir:Meta.profile [
         fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant";
         fhir:index 0;
         fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant>       ]     ];
     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.issued [ fhir:value "2019-03-05T16:04:44+00:00"^^xsd:dateTime ];
     fhir:Observation.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA9633-4;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA9633-4" ];
         fhir:Coding.display [ fhir:value "Present" ]       ]     ];
     fhir:Observation.component [
       fhir:index 0;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:62374-4;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "62374-4" ];
           fhir:Coding.display [ fhir:value "Human reference sequence assembly version" ]         ]       ];
       fhir:Observation.component.valueCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:LA14029-5;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "LA14029-5" ];
           fhir:Coding.display [ fhir:value "GRCh37" ]         ]       ]     ], [
       fhir:index 1;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:48013-7;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "48013-7" ];
           fhir:Coding.display [ fhir:value "Genomic reference sequence ID" ]         ]       ];
       fhir:Observation.component.valueCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore" ];
           fhir:Coding.code [ fhir:value "NC_000010.10" ]         ]       ]     ], [
       fhir:index 2;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:53034-5;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "53034-5" ];
           fhir:Coding.display [ fhir:value "Allelic state" ]         ]       ];
       fhir:Observation.component.valueCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:LA6706-1;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "LA6706-1" ];
           fhir:Coding.display [ fhir:value "heterozygous" ]         ]       ]     ], [
       fhir:index 3;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:69547-8;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "69547-8" ];
           fhir:Coding.display [ fhir:value "Ref nucleotide" ]         ]       ];
       fhir:Observation.component.valueString [ fhir:value "C" ]     ], [
       fhir:index 4;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:69551-0;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "69551-0" ];
           fhir:Coding.display [ fhir:value "Alt allele" ]         ]       ];
       fhir:Observation.component.valueString [ fhir:value "G" ]     ], [
       fhir:index 5;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:92822-6;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "92822-6" ];
           fhir:Coding.display [ fhir:value "Genomic coord system" ]         ]       ];
       fhir:Observation.component.valueCodeableConcept [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a loinc:LA30102-0;
           fhir:Coding.system [ fhir:value "http://loinc.org" ];
           fhir:Coding.code [ fhir:value "LA30102-0" ]         ]       ]     ], [
       fhir:index 6;
       fhir:Observation.component.code [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes" ];
           fhir:Coding.code [ fhir:value "exact-start-end" ];
           fhir:Coding.display [ fhir:value "Variant exact start and end" ]         ]       ];
       fhir:Observation.component.valueRange [
         fhir:Range.low [
           fhir:Quantity.value [ fhir:value "96527722"^^xsd:decimal ]         ]       ]     ]
  ], [
     a fhir:Observation;
     fhir:index 2;
     fhir:Resource.id [ fhir:value "sid-5c7e9e1ca8a29" ];
     fhir:Resource.meta [
       fhir:Meta.profile [
         fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship";
         fhir:index 0;
         fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship>       ]     ];
     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:82120-7;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "82120-7" ];
         fhir:Coding.display [ fhir:value "Allelic phase" ]       ]     ];
     fhir:Observation.issued [ fhir:value "2019-03-05T16:04:44+00:00"^^xsd:dateTime ];
     fhir:Observation.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/seq-phase-relationship" ];
         fhir:Coding.code [ fhir:value "Cis" ];
         fhir:Coding.display [ fhir:value "Cis" ]       ]     ];
     fhir:Observation.derivedFrom [
       fhir:index 0;
       fhir:Reference.reference [ fhir:value "#dv-5c7e9e1ca8252" ]     ], [
       fhir:index 1;
       fhir:Reference.reference [ fhir:value "#dv-5c7e9e1ca82e4" ]     ]
  ];
  fhir:DiagnosticReport.status [ fhir:value "final"];
  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:CodeableConcept.text [ fhir:value "Genetic analysis report" ]
  ];
  fhir:DiagnosticReport.result [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "#dv-5c7e9e1ca8252" ]
  ], [
     fhir:index 1;
     fhir:Reference.reference [ fhir:value "#dv-5c7e9e1ca82e4" ]
  ], [
     fhir:index 2;
     fhir:Reference.reference [ fhir:value "#sid-5c7e9e1ca8a29" ]
  ].

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

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