Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

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

## : Pgx-var-1013 - TTL Representation

Page standards status: Informative

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

     a fhir:Observation ;
      fhir:nodeRole fhir:treeRoot ;
      fhir:id [ fhir:v "Pgx-var-1013"] ; #
      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 Pgx-var-1013</b></p><a name=\"Pgx-var-1013\"> </a><a name=\"hcPgx-var-1013\"> </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-CGPatientExample01.html\">Adam B. Everyman  Male, DoB: 1951-01-20 ( Medical Record Number: m123 (use: usual, ))</a></p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href=\"Organization-ExampleOrg.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><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_000010.10}\">b37 Chr10</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 92822-6}\">Genomic coordinate system [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA30102-0}\">1-based character counting</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>: 96535173-96535173</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Genomic ref allele [ID]</span></p><p><b>value</b>: T</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>: T</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 LA6683-2}\">Germline</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6705-3}\">homozygous</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:2621}\">CYP2C19</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:0002073}\">wild type</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>: &gt;20</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs variant-confidence-status}\">Variant Confidence Status</span></p><p><b>value</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs high}\">High</span></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 fhir:Patient/CGPatientExample01 ;
    fhir:reference [ fhir:v "Patient/CGPatientExample01" ]
      ] ; #
      fhir:effective [
    a fhir:DateTime ;
    fhir:v "2019-04-01"^^xsd:date
      ] ; #
      fhir:performer ( [
    fhir:l fhir:Organization/ExampleOrg ;
    fhir:reference [ fhir:v "Organization/ExampleOrg" ]
      ] ) ; #
      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: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_000010.10" ] ;
    fhir:display [ fhir:v "b37 Chr10" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:92822-6 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "92822-6" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    a loinc:LA30102-0 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "LA30102-0" ] ;
    fhir:display [ fhir:v "1-based character counting" ]       ] )     ]
      ] [
    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 "96535173"^^xsd:decimal ]       ] ;
    fhir:high [
    fhir:value [ fhir:v "96535173"^^xsd:decimal ]       ]     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:69547-8 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "69547-8" ]       ] )     ] ;
    fhir:value [
    a fhir:String ;
    fhir:v "T"     ]
      ] [
    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 "T"     ]
      ] [
    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:LA6683-2 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "LA6683-2" ] ;
    fhir:display [ fhir:v "Germline" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:53034-5 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "53034-5" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    a loinc:LA6705-3 ;
    fhir:system [
    fhir:v "http://loinc.org"^^xsd:anyURI ;
    fhir:l <http://loinc.org>         ] ;
    fhir:code [ fhir:v "LA6705-3" ] ;
    fhir:display [ fhir:v "homozygous" ]       ] )     ]
      ] [
    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:2621" ] ;
    fhir:display [ fhir:v "CYP2C19" ]       ] )     ]
      ] [
    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:0002073" ] ;
    fhir:display [ fhir:v "wild type" ]       ] )     ]
      ] [
    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 "20"^^xsd:decimal ] ;
    fhir:comparator [ fhir:v ">" ]     ]
      ] [
    fhir:code [
          ( fhir:coding [
    fhir:system [
    fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ;
    fhir:l <http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs>         ] ;
    fhir:code [ fhir:v "variant-confidence-status" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [
    fhir:v "http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs"^^xsd:anyURI ;
    fhir:l <http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs>         ] ;
    fhir:code [ fhir:v "high" ]       ] )     ]
      ] ) . #