Genomics Reporting Implementation Guide
1.1.0 - Ballot

This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 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 - Inherited Disease Pathogenicity - TTL Representation

Raw ttl | Download


@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 "obs-idh-ex"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "extensions" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>Related Artifact</b>: </p><p><b style=\"color: maroon\">Exception generating Narrative: type org.hl7.fhir.r5.model.RelatedArtifact not handled - should not be here</b></p></div>"
  ];
  fhir:DomainResource.extension [
     fhir:index 0;
     fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/CGRelatedArtifact" ];
     fhir:Extension.valueRelatedArtifact [
       fhir:RelatedArtifact.type [ fhir:value "citation" ];
       fhir:RelatedArtifact.url [ fhir:value "https://www.ncbi.nlm.nih.gov/clinvar/variation/53685/#clinical-assertions" ]     ]
  ];
  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;
       fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes" ];
       fhir:Coding.code [ fhir:value "diagnostic-implication" ];
       fhir:Coding.display [ fhir:value "Diagnostic Implication" ]     ]
  ];
  fhir:Observation.derivedFrom [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/SNVexample" ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:53037-8;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "53037-8" ];
         fhir:Coding.display [ fhir:value "Genetic variation clinical significance [Imp]" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA6668-3;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA6668-3" ];
         fhir:Coding.display [ fhir:value "Pathogenic" ]       ]     ]
  ], [
     fhir:index 1;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81259-4;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81259-4" ];
         fhir:Coding.display [ fhir:value "Associated phenotype" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/medgen" ];
         fhir:Coding.code [ fhir:value "C0010674" ];
         fhir:Coding.display [ fhir:value "Cystic fibrosis" ]       ], [
         fhir:index 1;
         fhir:Coding.system [ fhir:value "http://www.orpha.net" ];
         fhir:Coding.code [ fhir:value "ORPHA:586" ]       ], [
         fhir:index 2;
         fhir:Coding.system [ fhir:value "http://www.omim.org" ];
         fhir:Coding.code [ fhir:value "219700" ]       ];
       fhir:CodeableConcept.text [ fhir:value "Cystic fibrosis" ]     ]
  ], [
     fhir:index 2;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes" ];
         fhir:Coding.code [ fhir:value "condition-inheritance" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/ConditionInheritanceMode" ];
         fhir:Coding.code [ fhir:value "HP:0000007" ];
         fhir:Coding.display [ fhir:value "Autosomal recessive inheritance" ]       ]     ]
  ].

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

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