Genomics Reporting Implementation Guide
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Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: SNVexample - TTL Representation

Page standards status: Informative

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@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 -------------------------------------------------------------------

<http://hl7.org/fhir/Observation/SNVexample> 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 class=\"res-header-id\"><b>Generated Narrative: Observation SNVexample</b></p><a name=\"SNVexample\"> </a><a name=\"hcSNVexample\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></p><p><b>specimen</b>: Identifier: <code>http://slk-kliniken.de/fhir/namingSystem/tissueID</code>/16-123456-23</p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:644}\">AR</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48001-2}\">Cytogenetic (chromosome) location</span></p><p><b>value</b>: <span title=\"Codes:\">chrX</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 62374-4}\">Human reference sequence assembly version</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA14029-5}\">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_000044.6:c.7G>A}\">NM_000044.6:c.7G&gt;A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48005-3}\">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NP_000035.2:p.Val3Met}\">NP_000035.2:p.Val3Met</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000044.3}\">NM_000044.6</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81258-6}\">Sample VAF</span></p><p><b>value</b>: 0.44 decimal</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82121-5}\">Allelic read depth</span></p><p><b>value</b>: 120 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM  code1 = '1')</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:index 1 ;
     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: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.subject [
     fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ;
     fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
  ] ;
  fhir:Observation.effectiveDateTime [ fhir:value "2023-06-01"^^xsd:date] ;
  fhir:Observation.performer [
     fhir:index 0 ;
     fhir:link <http://hl7.org/fhir/Organization/ExampleLab> ;
     fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
  ] ;
  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" ] ;
         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:48004-6 ;
         fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
         fhir:Coding.code [ fhir:value "48004-6" ] ;
         fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ]
       ]
     ] ;
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ] ;
         fhir:Coding.code [ fhir:value "NM_000044.6:c.7G>A" ]
       ]
     ]
  ], [
     fhir:index 5 ;
     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 "NP_000035.2:p.Val3Met" ] ;
         fhir:Coding.display [ fhir:value "NP_000035.2:p.Val3Met" ]
       ]
     ]
  ], [
     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_000044.6" ]
       ]
     ]
  ], [
     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 VAF" ]
       ]
     ] ;
     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 "1" ]
     ]
  ] .

<http://hl7.org/fhir/Patient/ExamplePatient> a fhir:Patient .

<http://hl7.org/fhir/Organization/ExampleLab> a fhir:Organization .

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

<http://hl7.org/fhir/Observation/SNVexample.ttl> a owl:Ontology ;
  owl:imports fhir:fhir.ttl ;
  owl:versionIRI <http://build.fhir.org/Observation/SNVexample.ttl> .