FHIR Osiris Implementation Guide
1.1.0 - trial-implementation

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## : fhir-osiris-annotation-1 - TTL Representation

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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 "fhir-osiris-annotation-1"] ; #
      fhir:meta [
        ( fhir:profile [
    fhir:v "https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/variant-annotation"^^xsd:anyURI ;
    fhir:link <https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/variant-annotation>     ] )
      ] ; #
      fhir:text [
    fhir:status [ fhir:v "generated" ] ;
    fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation fhir-osiris-annotation-1</b></p><a name=\"fhir-osiris-annotation-1\"> </a><a name=\"hcfhir-osiris-annotation-1\"> </a><a name=\"fhir-osiris-annotation-1-en-US\"> </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\">Profil: <a href=\"StructureDefinition-variant-annotation.html\">Variant Annotation</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></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-L304.html\">Patient Anonyme Male, Date de Naissance :1967-11-08</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>hasMember</b>: </p><ul><li><a href=\"MolecularSequence-fhir-osiris-genome-entity-1.html\">MolecularSequence : extension = C0439673; coordinateSystem = 0</a></li><li><a href=\"MolecularSequence-fhir-osiris-annotation-reference-1.html\">MolecularSequence : coordinateSystem = 0</a></li></ul><p><b>derivedFrom</b>: <a href=\"Observation-fhir-osiris-example-snp-1.html\">Observation Genetic variant assessment</a></p><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:{https://github.com/siric-osiris/OSIRIS O15-4}\">O15-4</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:{https://www.genenames.org/ PI3K}\">PI3K</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org LP91038-7}\">Prediction software</span></p><p><b>value</b>: <span title=\"Codes:{https://github.com/siric-osiris/OSIRIS SIFT}\">SIFT</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org LP70194-3}\">Prediction of the variation effect over the protein</span></p><p><b>value</b>: 0.35</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 93044-6}\">Confidence score</span></p><p><b>value</b>: Deleterious</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:\">exon 2</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 p.E542K}\">p.E542K</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48006-1}\">Amino acid change [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6698-0}\">Missense</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://terminology.hl7.org/CodeSystem/umls C0439673}\">C0439673</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 c.1624G&gt;A}\">c.1624G&gt;A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org LP232001-0}\">Incidence on the transcript</span></p><p><b>value</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/umls C0439673}\">C0439673</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:code [ fhir:v "laboratory" ]     ] )
      ] ) ; #
      fhir:code [
        ( fhir:coding [
    a loinc:69548-6 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "69548-6" ]     ] )
      ] ; #
      fhir:subject [
    fhir:reference [ fhir:v "Patient/L304" ]
      ] ; #
      fhir:value [
    a fhir:CodeableConcept ;
        ( fhir:coding [
    a loinc:LA9633-4 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "LA9633-4" ]     ] )
      ] ; #
      fhir:hasMember ( [
    fhir:reference [ fhir:v "MolecularSequence/fhir-osiris-genome-entity-1" ]
      ] [
    fhir:reference [ fhir:v "MolecularSequence/fhir-osiris-annotation-reference-1" ]
      ] ) ; #
      fhir:derivedFrom ( [
    fhir:reference [ fhir:v "Observation/fhir-osiris-example-snp-1" ]
      ] ) ; #
      fhir:component ( [
    fhir:code [
          ( fhir:coding [
    a loinc:48019-4 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "48019-4" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [ fhir:v "https://github.com/siric-osiris/OSIRIS"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "O15-4" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48018-6 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "48018-6" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [ fhir:v "https://www.genenames.org/"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "PI3K" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:LP91038-7 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "LP91038-7" ]       ] ) ;
    fhir:text [ fhir:v "Prediction software" ]     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [ fhir:v "https://github.com/siric-osiris/OSIRIS"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "SIFT" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:LP70194-3 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "LP70194-3" ]       ] ) ;
    fhir:text [ fhir:v "Prediction of the variation effect over the protein" ]     ] ;
    fhir:value [
    a fhir:Quantity ;
    fhir:value [ fhir:v 0.35 ]     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:93044-6 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "93044-6" ]       ] ) ;
    fhir:text [ fhir:v "Confidence score" ]     ] ;
    fhir:value [
    a fhir:string ;
    fhir:v "Deleterious"     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48001-2 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "48001-2" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
    fhir:text [ fhir:v "exon 2" ]     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48005-3 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "48005-3" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "p.E542K" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48006-1 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "48006-1" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    a loinc:LA6698-0 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "LA6698-0" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:81290-9 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "81290-9" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/umls"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "C0439673" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:48004-6 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "48004-6" ]       ] )     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "c.1624G>A" ]       ] )     ]
      ] [
    fhir:code [
          ( fhir:coding [
    a loinc:LP232001-0 ;
    fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "LP232001-0" ]       ] ) ;
    fhir:text [ fhir:v "Incidence on the transcript" ]     ] ;
    fhir:value [
    a fhir:CodeableConcept ;
          ( fhir:coding [
    fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/umls"^^xsd:anyURI ] ;
    fhir:code [ fhir:v "C0439673" ]       ] )     ]
      ] ) . #