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 - NGS - 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 "SNVexample"];
  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: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>: SNVexample</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 variant assessment <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>method</b>: Sequencing <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA26398-0' = 'Sequencing', given as 'Sequencing'})</span></p><p><b>specimen</b>: </p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48018-6' = 'Gene studied [ID]', given as 'Gene studied ID'})</span></p><p><b>value</b>: AR <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.genenames.org/geneId code 'HGNC:644' = 'HGNC:644', given as 'AR'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Cytogenetic (chromosome) location <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48001-2' = 'Cytogenetic (chromosome) location', given as 'Cytogenetic (chromosome) location'})</span></p><p><b>value</b>: chrX <span style=\"background: LightGoldenRodYellow\">(Details )</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Human reference sequence assembly version <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '62374-4' = 'Human reference sequence assembly version', given as 'Human reference sequence assembly version'})</span></p><p><b>value</b>: GRCh37 <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA14029-5' = 'GRCh37', given as 'GRCh37'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48002-0' = 'Genomic source class [Type]', given as 'Genomic source class'})</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA6684-0' = 'Somatic', given as 'Somatic'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48005-3' = 'Amino acid change (pHGVS)', given as 'Amino acid change (pHGVS)'})</span></p><p><b>value</b>: p.(Ala412Val) <span style=\"background: LightGoldenRodYellow\">(Details : {http://varnomen.hgvs.org code 'p.(Ala412Val)' = 'p.(Ala412Val)', given as 'p.(Ala412Val)'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change type <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48006-1' = 'Amino acid change [Type]', given as 'Amino acid change type'})</span></p><p><b>value</b>: Missense <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA6698-0' = 'Missense', given as 'Missense'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '51958-7' = 'Transcript reference sequence [ID]', given as 'Transcript reference sequence [ID]'})</span></p><p><b>value</b>: NM_000044.3 <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/refseq code 'NM_000044.3' = 'NM_000044.3', given as 'NM_000044.3'})</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample variant allelic frequency [NFr] <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81258-6' = 'Sample variant allelic frequency [NFr]', given as 'Sample variant allelic frequency [NFr]'})</span></p><p><b>value</b>: 0.44 decimal</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '82121-5' = 'Allelic read depth', given as 'Allelic read depth'})</span></p><p><b>value</b>: 120 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code {reads}/{base} = '{reads}/{base}')</span></p></blockquote></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.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.method [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:LA26398-0;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "LA26398-0" ];
       fhir:Coding.display [ fhir:value "Sequencing" ]     ]
  ];
  fhir:Observation.specimen [
     fhir:Reference.identifier [
       fhir:Identifier.system [ fhir:value "http://slk-kliniken.de/fhir/namingSystem/tissueID" ];
       fhir:Identifier.value [ fhir:value "16-123456-23" ]     ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48018-6;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48018-6" ];
         fhir:Coding.display [ fhir:value "Gene studied ID" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.genenames.org/geneId" ];
         fhir:Coding.code [ fhir:value "HGNC:644" ];
         fhir:Coding.display [ fhir:value "AR" ]       ]     ]
  ], [
     fhir:index 1;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48001-2;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48001-2" ];
         fhir:Coding.display [ fhir:value "Cytogenetic (chromosome) location" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.text [ fhir:value "chrX" ]     ]
  ], [
     fhir:index 2;
     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 3;
     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" ]       ]     ];
     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:index 4;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48005-3;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48005-3" ];
         fhir:Coding.display [ fhir:value "Amino acid change (pHGVS)" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
         fhir:Coding.code [ fhir:value "p.(Ala412Val)" ];
         fhir:Coding.display [ fhir:value "p.(Ala412Val)" ]       ]     ]
  ], [
     fhir:index 5;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48006-1;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48006-1" ];
         fhir:Coding.display [ fhir:value "Amino acid change type" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA6698-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA6698-0" ];
         fhir:Coding.display [ fhir:value "Missense" ]       ]     ]
  ], [
     fhir:index 6;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:51958-7;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "51958-7" ];
         fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
         fhir:Coding.code [ fhir:value "NM_000044.3" ];
         fhir:Coding.display [ fhir:value "NM_000044.3" ]       ]     ]
  ], [
     fhir:index 7;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81258-6;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81258-6" ];
         fhir:Coding.display [ fhir:value "Sample variant allelic frequency [NFr]" ]       ]     ];
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "0.44"^^xsd:decimal ];
       fhir:Quantity.unit [ fhir:value "decimal" ];
       fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ]     ]
  ], [
     fhir:index 8;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:82121-5;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "82121-5" ];
         fhir:Coding.display [ fhir:value "Allelic read depth" ]       ]     ];
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "120"^^xsd:decimal ];
       fhir:Quantity.unit [ fhir:value "reads per base pair" ];
       fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
       fhir:Quantity.code [ fhir:value "{reads}/{base}" ]     ]
  ].

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

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