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 - Inherited Disease Pathogenicity - 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: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/inherited-disease-pathogenicity";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity>     ]
  ];
  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>: obs-idh-ex</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow\">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '53037-8' = 'Genetic variation clinical significance [Imp]', given as 'Genetic variation clinical significance [Imp]'})</span></p><p><b>value</b>: Pathogenic <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA6668-3' = 'Pathogenic', given as 'Pathogenic'})</span></p><p><b>derivedFrom</b>: <a href=\"obs-idh-ex.html\">Generated Summary: id: SNVexample; <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></p><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81259-4' = 'Associated phenotype', given as 'Associated phenotype'})</span></p><p><b>value</b>: Cystic fibrosis <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/medgen code 'C0010674' = 'C0010674', given as 'Cystic fibrosis'}; {http://www.orpha.net code 'ORPHA:586' = 'ORPHA:586; {http://www.omim.org code '219700' = '219700)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81259-4' = 'Associated phenotype', given as 'Associated phenotype'})</span></p><p><b>value</b>: Congenital bilateral absence of the vas deferens <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/medgen code 'C0403814' = 'C0403814; {http://www.orpha.net code 'ORPHA:48' = 'ORPHA:48; {http://www.omim.org code '277180' = '277180; {http://www.omim.org code '300985' = '300985)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: mode-of-inheritance <span style=\"background: LightGoldenRodYellow\">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'mode-of-inheritance' = 'mode-of-inheritance', given as 'mode-of-inheritance'})</span></p><p><b>value</b>: Autosomal recessive <span style=\"background: LightGoldenRodYellow\">(Details : {http://ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns code 'Autosomal recessive' = 'Autosomal recessive', given as 'Autosomal recessive'})</span></p></blockquote></div>"
  ];
  fhir:DomainResource.extension [
     fhir:index 0;
     fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RelatedArtifact" ];
     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;
       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.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: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: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 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 "C0403814" ]       ], [
         fhir:index 1;
         fhir:Coding.system [ fhir:value "http://www.orpha.net" ];
         fhir:Coding.code [ fhir:value "ORPHA:48" ]       ], [
         fhir:index 2;
         fhir:Coding.system [ fhir:value "http://www.omim.org" ];
         fhir:Coding.code [ fhir:value "277180" ]       ], [
         fhir:index 3;
         fhir:Coding.system [ fhir:value "http://www.omim.org" ];
         fhir:Coding.code [ fhir:value "300985" ]       ];
       fhir:CodeableConcept.text [ fhir:value "Congenital bilateral absence of the vas deferens" ]     ]
  ], [
     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/tbd-codes" ];
         fhir:Coding.code [ fhir:value "mode-of-inheritance" ];
         fhir:Coding.display [ fhir:value "mode-of-inheritance" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns" ];
         fhir:Coding.code [ fhir:value "Autosomal recessive" ];
         fhir:Coding.display [ fhir:value "Autosomal recessive" ]       ]     ]
  ].

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

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