FHIR Osiris Implementation Guide
1.1.0 - trial-implementation

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

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    {
      "resourceType" : "Observation",
      "id" : "fhir-osiris-annotation-1",
      "meta" : {
        "profile" : [
          🔗 "https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/variant-annotation"
        ]
      },
      "text" : {
        "status" : "generated",
        "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>"
      },
      "status" : "final",
      "category" : [
        {
          "coding" : [
            {
              "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
              "code" : "laboratory"
            }
          ]
        }
      ],
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "69548-6"
          }
        ]
      },
      "subject" : {
        🔗 "reference" : "Patient/L304"
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA9633-4"
          }
        ]
      },
      "hasMember" : [
        {
          🔗 "reference" : "MolecularSequence/fhir-osiris-genome-entity-1"
        },
        {
          🔗 "reference" : "MolecularSequence/fhir-osiris-annotation-reference-1"
        }
      ],
      "derivedFrom" : [
        {
          🔗 "reference" : "Observation/fhir-osiris-example-snp-1"
        }
      ],
      "component" : [
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48019-4"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "https://github.com/siric-osiris/OSIRIS",
                "code" : "O15-4"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48018-6"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "https://www.genenames.org/",
                "code" : "PI3K"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LP91038-7"
              }
            ],
            "text" : "Prediction software"
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "https://github.com/siric-osiris/OSIRIS",
                "code" : "SIFT"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LP70194-3"
              }
            ],
            "text" : "Prediction of the variation effect over the protein"
          },
          "valueQuantity" : {
            "value" : 0.35
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "93044-6"
              }
            ],
            "text" : "Confidence score"
          },
          "valueString" : "Deleterious"
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48001-2"
              }
            ]
          },
          "valueCodeableConcept" : {
            "text" : "exon 2"
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48005-3"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://varnomen.hgvs.org",
                "code" : "p.E542K"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48006-1"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LA6698-0"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "81290-9"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/umls",
                "code" : "C0439673"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48004-6"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://varnomen.hgvs.org",
                "code" : "c.1624G>A"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LP232001-0"
              }
            ],
            "text" : "Incidence on the transcript"
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://terminology.hl7.org/CodeSystem/umls",
                "code" : "C0439673"
              }
            ]
          }
        }
      ]
    }