@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <https://loinc.org/rdf/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

<http://hl7.org/fhir/uv/genomics-reporting/Observation/STAG2-insertion-var> a fhir:Observation ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "STAG2-insertion-var"] ; # 
  fhir:meta [
     fhir:profile ( [
       fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ;
       fhir:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant>
     ] )
  ] ; # 
  fhir:text [
     fhir:status [ fhir:v "generated" ] ;
     fhir:div [ fhir:v "<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>"^^rdf:XMLLiteral ]
  ] ; # 
  fhir:status [ fhir:v "final"] ; # 
  fhir:category ( [
     fhir:coding ( [
       fhir:system [
         fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ;
         fhir:l <http://terminology.hl7.org/CodeSystem/observation-category>
       ] ;
       fhir:code [ fhir:v "laboratory" ]
     ] )
  ] [
     fhir:coding ( [
       fhir:system [
         fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ;
         fhir:l <http://terminology.hl7.org/CodeSystem/v2-0074>
       ] ;
       fhir:code [ fhir:v "GE" ]
     ] )
  ] ) ; # 
  fhir:code [
     fhir:coding ( [
       a loinc:69548-6 ;
       fhir:system [
         fhir:v "http://loinc.org"^^xsd:anyURI ;
         fhir:l <http://loinc.org>
       ] ;
       fhir:code [ fhir:v "69548-6" ]
     ] )
  ] ; # 
  fhir:subject [
     fhir:l <http://hl7.org/fhir/uv/genomics-reporting/Patient/somaticPatient> ;
     fhir:reference [ fhir:v "Patient/somaticPatient" ]
  ] ; # 
  fhir:effective [
     a fhir:DateTime ;
     fhir:v "2023-02-01"^^xsd:date
  ] ; # 
  fhir:performer ( [
     fhir:l <http://hl7.org/fhir/uv/genomics-reporting/Practitioner/pathologistPractitioner> ;
     fhir:reference [ fhir:v "Practitioner/pathologistPractitioner" ]
  ] ) ; # 
  fhir:value [
     a fhir:CodeableConcept ;
     fhir:coding ( [
       a loinc:LA9633-4 ;
       fhir:system [
         fhir:v "http://loinc.org"^^xsd:anyURI ;
         fhir:l <http://loinc.org>
       ] ;
       fhir:code [ fhir:v "LA9633-4" ] ;
       fhir:display [ fhir:v "Present" ]
     ] )
  ] ; # 
  fhir:method [
     fhir:coding ( [
       a loinc:LA26398-0 ;
       fhir:system [
         fhir:v "http://loinc.org"^^xsd:anyURI ;
         fhir:l <http://loinc.org>
       ] ;
       fhir:code [ fhir:v "LA26398-0" ] ;
       fhir:display [ fhir:v "Sequencing" ]
     ] )
  ] ; # 
  fhir:component ( [
     fhir:code [
       fhir:coding ( [
         a loinc:48005-3 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "48005-3" ]
       ] )
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         fhir:system [
           fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ;
           fhir:l <http://varnomen.hgvs.org>
         ] ;
         fhir:code [ fhir:v "NP_006594.3:p.S1178*" ]
       ] )
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:51958-7 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "51958-7" ]
       ] )
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ;
           fhir:l <http://www.ncbi.nlm.nih.gov/refseq>
         ] ;
         fhir:code [ fhir:v "NM_006603.5" ]
       ] )
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:82121-5 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "82121-5" ]
       ] )
     ] ;
     fhir:value [
       a fhir:Quantity ;
       fhir:value [ fhir:v "88"^^xsd:decimal ] ;
       fhir:unit [ fhir:v "reads per base pair" ] ;
       fhir:system [
         fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ;
         fhir:l <http://unitsofmeasure.org>
       ] ;
       fhir:code [ fhir:v "1" ]
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:48019-4 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "48019-4" ]
       ] )
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
           fhir:l <http://www.sequenceontology.org>
         ] ;
         fhir:code [ fhir:v "SO:0000667" ] ;
         fhir:display [ fhir:v "insertion" ]
       ] )
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:48004-6 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "48004-6" ]
       ] )
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         fhir:system [
           fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ;
           fhir:l <http://varnomen.hgvs.org>
         ] ;
         fhir:code [ fhir:v "NM_006603.5:c.3530_3531insGTGACTATTAATAT" ]
       ] )
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:48018-6 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "48018-6" ]
       ] )
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.genenames.org"^^xsd:anyURI ;
           fhir:l <http://www.genenames.org>
         ] ;
         fhir:code [ fhir:v "HGNC:11355" ] ;
         fhir:display [ fhir:v "STAG2" ]
       ] )
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:69551-0 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "69551-0" ]
       ] )
     ] ;
     fhir:value [
       a fhir:String ;
       fhir:v "GTGACTA"
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:48000-4 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "48000-4" ]
       ] )
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         a loinc:LA21276-3 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "LA21276-3" ] ;
         fhir:display [ fhir:v "Chromosome X" ]
       ] )
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:81254-5 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "81254-5" ]
       ] )
     ] ;
     fhir:value [
       a fhir:Range ;
       fhir:low [
         fhir:value [ fhir:v "123227930"^^xsd:decimal ]
       ] ;
       fhir:high [
         fhir:value [ fhir:v "123227930"^^xsd:decimal ]
       ]
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:48013-7 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "48013-7" ]
       ] )
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ;
           fhir:l <http://www.ncbi.nlm.nih.gov/refseq>
         ] ;
         fhir:code [ fhir:v "NC_000023.10" ]
       ] )
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:81290-9 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "81290-9" ]
       ] )
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         fhir:system [
           fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ;
           fhir:l <http://varnomen.hgvs.org>
         ] ;
         fhir:code [ fhir:v "NC_000023.10:g.123227930_123227931insGTGACTATTAATAT" ]
       ] )
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:48002-0 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "48002-0" ]
       ] )
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         a loinc:LA6684-0 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "LA6684-0" ] ;
         fhir:display [ fhir:v "Somatic" ]
       ] )
     ]
  ] [
     fhir:code [
       fhir:coding ( [
         a loinc:81258-6 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         fhir:code [ fhir:v "81258-6" ]
       ] )
     ] ;
     fhir:value [
       a fhir:Quantity ;
       fhir:value [ fhir:v 0.08 ] ;
       fhir:unit [ fhir:v "decimal" ] ;
       fhir:system [
         fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ;
         fhir:l <http://unitsofmeasure.org>
       ]
     ]
  ] ) . # 

<http://hl7.org/fhir/uv/genomics-reporting/Patient/somaticPatient> a fhir:Uv .

<http://hl7.org/fhir/uv/genomics-reporting/Practitioner/pathologistPractitioner> a fhir:Uv .

# -------------------------------------------------------------------------------------