{
  "description": "Data elements for recording molecular markers in the CCE",
  "_filename": "StructureDefinition-cce-core-Observation-GeneticVariant.json",
  "package_name": "cce.fhir.full",
  "date": null,
  "derivation": "constraint",
  "publisher": null,
  "fhirVersion": "4.0.1",
  "name": "GeneticVariant",
  "abstract": false,
  "type": "Observation",
  "experimental": null,
  "resourceType": "StructureDefinition",
  "title": null,
  "package_version": "0.2.0",
  "status": "draft",
  "id": "32157b7e-4280-4faa-a9cc-481642a20e66",
  "kind": "resource",
  "url": "https://www.cancercoreeurope.eu/fhir/StructureDefinition/cce-core-Observation-GeneticVariant",
  "version": "0.0.1",
  "differential": {
    "element": [ {
      "id": "Observation.status",
      "path": "Observation.status",
      "mustSupport": true
    }, {
      "id": "Observation.category.coding.system",
      "min": 1,
      "path": "Observation.category.coding.system",
      "fixedUri": "http://hl7.org/fhir/observation-category"
    }, {
      "id": "Observation.category.coding.code",
      "min": 1,
      "path": "Observation.category.coding.code",
      "fixedCode": "laboratory"
    }, {
      "id": "Observation.code",
      "path": "Observation.code",
      "short": "Name of the molecular marker",
      "definition": "Name of the molecular marker",
      "mustSupport": true
    }, {
      "id": "Observation.code.coding.system",
      "min": 1,
      "path": "Observation.code.coding.system",
      "fixedUri": "http://loinc.org",
      "mustSupport": true
    }, {
      "id": "Observation.code.coding.code",
      "min": 1,
      "path": "Observation.code.coding.code",
      "fixedCode": "69548-6",
      "mustSupport": true
    }, {
      "id": "Observation.subject",
      "min": 1,
      "path": "Observation.subject",
      "type": [ {
        "code": "Reference",
        "targetProfile": [ "https://www.cancercoreeurope.eu/fhir/StructureDefinition/cce-core-Patient-Patient", "https://www.cancercoreeurope.eu/fhir/StructureDefinition/cce-core-Patient-Pseudonym" ]
      } ],
      "mustSupport": true
    }, {
      "id": "Observation.focus",
      "path": "Observation.focus",
      "type": [ {
        "code": "Reference",
        "targetProfile": [ "http://hl7.org/fhir/StructureDefinition/Resource", "https://www.cancercoreeurope.eu/fhir/StructureDefinition/cce-core-Condition-Primarydiagnosis" ]
      } ],
      "mustSupport": true
    }, {
      "id": "Observation.encounter",
      "path": "Observation.encounter",
      "type": [ {
        "code": "Reference",
        "targetProfile": [ "https://www.cancercoreeurope.eu/fhir/StructureDefinition/cce-core-Encounter-Fall" ]
      } ]
    }, {
      "id": "Observation.effective[x]",
      "path": "Observation.effective[x]",
      "type": [ {
        "code": "dateTime"
      } ],
      "short": "Date of Data collection",
      "mapping": [ {
        "map": "urn:dktk:dataelement:1:3",
        "comment": "urn:dktk:dataelement:1:3",
        "identity": "ISO-11179"
      } ],
      "definition": "Date of data collection of the molecular marker",
      "mustSupport": true
    }, {
      "id": "Observation.value[x]",
      "min": 1,
      "path": "Observation.value[x]",
      "type": [ {
        "code": "CodeableConcept"
      } ],
      "short": "Status of the molecular marker",
      "binding": {
        "strength": "extensible",
        "valueSet": "https://www.cancercoreeurope.eu/fhir/core/ValueSet/GeneticVariantVS",
        "description": "Genetic Variant expression"
      },
      "definition": "Condition or status of the molecular marker",
      "mustSupport": true
    }, {
      "id": "Observation.value[x].coding.system",
      "path": "Observation.value[x].coding.system",
      "mustSupport": true
    }, {
      "id": "Observation.value[x].coding.code",
      "min": 1,
      "path": "Observation.value[x].coding.code",
      "short": "Status of the molecular marker",
      "mapping": [ {
        "map": "urn:dktk:dataelement:3:2",
        "comment": "urn:dktk:dataelement:3:2",
        "identity": "ISO-11179"
      } ],
      "definition": "Condition or status of the molecular marker",
      "mustSupport": true
    }, {
      "id": "Observation.value[x].text",
      "path": "Observation.value[x].text",
      "mapping": [ {
        "map": "urn:dktk:dataelement:4:3",
        "comment": "urn:dktk:dataelement:4:3",
        "identity": "ISO-11179"
      } ],
      "mustSupport": true
    }, {
      "id": "Observation.specimen",
      "path": "Observation.specimen",
      "type": [ {
        "code": "Reference",
        "targetProfile": [ "https://fhir.bbmri.de/StructureDefinition/Specimen" ]
      } ]
    }, {
      "id": "Observation.specimen.reference",
      "min": 1,
      "path": "Observation.specimen.reference"
    }, {
      "id": "Observation.component",
      "path": "Observation.component",
      "slicing": {
        "rules": "open",
        "description": "Slice based on the component.code pattern",
        "discriminator": [ {
          "path": "code",
          "type": "pattern"
        } ]
      }
    }, {
      "id": "Observation.component:GeneNomenclature",
      "max": "1",
      "path": "Observation.component",
      "short": "Gene Name",
      "sliceName": "GeneNomenclature",
      "definition": "Name of the molecular marker according to HGNC or own name if required",
      "mustSupport": true
    }, {
      "id": "Observation.component:GeneNomenclature.code",
      "path": "Observation.component.code",
      "mustSupport": true,
      "patternCodeableConcept": {
        "coding": [ {
          "code": "48018-6",
          "system": "http://loinc.org"
        } ]
      }
    }, {
      "id": "Observation.component:GeneNomenclature.value[x]",
      "min": 1,
      "path": "Observation.component.value[x]",
      "type": [ {
        "code": "CodeableConcept"
      } ],
      "binding": {
        "strength": "extensible",
        "valueSet": "https://www.cancercoreeurope.eu/fhir/core/ValueSet/GeneNomenclatureVS",
        "description": "HGNC"
      },
      "mapping": [ {
        "map": "urn:dktk:dataelement:2:2",
        "comment": "urn:dktk:dataelement:2:2",
        "identity": "ISO-11179"
      } ],
      "mustSupport": true
    }, {
      "id": "Observation.component:Amino-acid-change",
      "path": "Observation.component",
      "sliceName": "Amino-acid-change",
      "mustSupport": true
    }, {
      "id": "Observation.component:Amino-acid-change.code",
      "path": "Observation.component.code",
      "patternCodeableConcept": {
        "coding": [ {
          "code": "48005-3",
          "system": "http://loinc.org"
        } ]
      }
    }, {
      "id": "Observation.component:Amino-acid-change.value[x]",
      "min": 1,
      "path": "Observation.component.value[x]",
      "type": [ {
        "code": "string"
      } ]
    }, {
      "id": "Observation.component:DNA-change",
      "max": "1",
      "path": "Observation.component",
      "sliceName": "DNA-change",
      "mustSupport": true
    }, {
      "id": "Observation.component:DNA-change.code",
      "path": "Observation.component.code",
      "patternCodeableConcept": {
        "coding": [ {
          "code": "81290-9",
          "system": "http://loinc.org"
        } ]
      }
    }, {
      "id": "Observation.component:DNA-change.value[x]",
      "min": 1,
      "path": "Observation.component.value[x]",
      "type": [ {
        "code": "string"
      } ]
    }, {
      "id": "Observation.component:RefSeq-NCBI",
      "max": "1",
      "path": "Observation.component",
      "sliceName": "RefSeq-NCBI",
      "mustSupport": true
    }, {
      "id": "Observation.component:RefSeq-NCBI.code",
      "path": "Observation.component.code",
      "patternCodeableConcept": {
        "coding": [ {
          "code": "81248-7",
          "system": "http://loinc.org"
        } ]
      }
    }, {
      "id": "Observation.component:RefSeq-NCBI.value[x]",
      "min": 1,
      "path": "Observation.component.value[x]",
      "type": [ {
        "code": "string"
      } ]
    }, {
      "id": "Observation.component:Ensembl-ID",
      "max": "1",
      "path": "Observation.component",
      "sliceName": "Ensembl-ID",
      "mustSupport": true
    }, {
      "id": "Observation.component:Ensembl-ID.code",
      "path": "Observation.component.code",
      "patternCodeableConcept": {
        "coding": [ {
          "code": "81249-5",
          "system": "http://loinc.org"
        } ]
      }
    }, {
      "id": "Observation.component:Ensembl-ID.value[x]",
      "min": 1,
      "path": "Observation.component.value[x]",
      "type": [ {
        "code": "string"
      } ]
    } ]
  },
  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Observation"
}