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

: STAG2-insertion-var - 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/STAG2-insertion-var> a fhir:Observation ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:Resource.id [ fhir:value "STAG2-insertion-var"] ;
  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 STAG2-insertion-var</b></p><a name=\"STAG2-insertion-var\"> </a><a name=\"hcSTAG2-insertion-var\"> </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-somaticPatient.html\">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>effective</b>: 2023-02-01</p><p><b>performer</b>: <a href=\"Practitioner-pathologistPractitioner.html\">Practitioner Test Dolin </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><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_006594.3:p.S1178*}\">NP_006594.3:p.S1178*</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_006603.5}\">NM_006603.5</span></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>: 88 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48019-4}\">DNA change type</span></p><p><b>value</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0000667}\">insertion</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_006603.5:c.3530_3531insGTGACTATTAATAT}\">NM_006603.5:c.3530_3531insGTGACTATTAATAT</span></p></blockquote><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:11355}\">STAG2</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Genomic alt allele [ID]</span></p><p><b>value</b>: GTGACTA</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48000-4}\">Chromosome [Identifier] in Blood or Tissue by Molecular genetics method</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA21276-3}\">Chromosome X</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 123227930-123227930</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000023.10}\">NC_000023.10</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81290-9}\">Genomic DNA change (gHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NC_000023.10:g.123227930_123227931insGTGACTATTAATAT}\">NC_000023.10:g.123227930_123227931insGTGACTATTAATAT</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class [Type]</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 81258-6}\">Sample variant allelic frequency [NFr]</span></p><p><b>value</b>: 0.08 decimal</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:Observation.subject [
     fhir:link <http://hl7.org/fhir/Patient/somaticPatient> ;
     fhir:Reference.reference [ fhir:value "Patient/somaticPatient" ]
  ] ;
  fhir:Observation.effectiveDateTime [ fhir:value "2023-02-01"^^xsd:date] ;
  fhir:Observation.performer [
     fhir:index 0 ;
     fhir:link <http://hl7.org/fhir/Practitioner/pathologistPractitioner> ;
     fhir:Reference.reference [ fhir:value "Practitioner/pathologistPractitioner" ]
  ] ;
  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.component [
     fhir:index 0 ;
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ] ;
         fhir:Coding.code [ fhir:value "NP_006594.3:p.S1178*" ]
       ]
     ]
  ], [
     fhir:index 1 ;
     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: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_006603.5" ]
       ]
     ]
  ], [
     fhir:index 2 ;
     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:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "88"^^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" ]
     ]
  ], [
     fhir:index 3 ;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         a loinc:48019-4 ;
         fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
         fhir:Coding.code [ fhir:value "48019-4" ]
       ]
     ] ;
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         fhir:Coding.system [ fhir:value "http://www.sequenceontology.org" ] ;
         fhir:Coding.code [ fhir:value "SO:0000667" ] ;
         fhir:Coding.display [ fhir:value "insertion" ]
       ]
     ]
  ], [
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ] ;
         fhir:Coding.code [ fhir:value "NM_006603.5:c.3530_3531insGTGACTATTAATAT" ]
       ]
     ]
  ], [
     fhir:index 5 ;
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         fhir:Coding.system [ fhir:value "http://www.genenames.org" ] ;
         fhir:Coding.code [ fhir:value "HGNC:11355" ] ;
         fhir:Coding.display [ fhir:value "STAG2" ]
       ]
     ]
  ], [
     fhir:index 6 ;
     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:Observation.component.valueString [ fhir:value "GTGACTA" ]
  ], [
     fhir:index 7 ;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         a loinc:48000-4 ;
         fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
         fhir:Coding.code [ fhir:value "48000-4" ]
       ]
     ] ;
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         a loinc:LA21276-3 ;
         fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
         fhir:Coding.code [ fhir:value "LA21276-3" ] ;
         fhir:Coding.display [ fhir:value "Chromosome X" ]
       ]
     ]
  ], [
     fhir:index 8 ;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         a loinc:81254-5 ;
         fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
         fhir:Coding.code [ fhir:value "81254-5" ]
       ]
     ] ;
     fhir:Observation.component.valueRange [
       fhir:Range.low [
         fhir:Quantity.value [ fhir:value "123227930"^^xsd:decimal ]
       ] ;
       fhir:Range.high [
         fhir:Quantity.value [ fhir:value "123227930"^^xsd:decimal ]
       ]
     ]
  ], [
     fhir:index 9 ;
     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: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 "NC_000023.10" ]
       ]
     ]
  ], [
     fhir:index 10 ;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         a loinc:81290-9 ;
         fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
         fhir:Coding.code [ fhir:value "81290-9" ]
       ]
     ] ;
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ] ;
         fhir:Coding.code [ fhir:value "NC_000023.10:g.123227930_123227931insGTGACTATTAATAT" ]
       ]
     ]
  ], [
     fhir:index 11 ;
     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: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 12 ;
     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:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "0.08"^^xsd:decimal ] ;
       fhir:Quantity.unit [ fhir:value "decimal" ] ;
       fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ]
     ]
  ] .

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

<http://hl7.org/fhir/Practitioner/pathologistPractitioner> a fhir:Practitioner .

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

<http://hl7.org/fhir/Observation/STAG2-insertion-var.ttl> a owl:Ontology ;
  owl:imports fhir:fhir.ttl ;
  owl:versionIRI <http://build.fhir.org/Observation/STAG2-insertion-var.ttl> .