{
  "resourceType": "StructureDefinition",
  "id": "observation-genetics",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">to do</div>"
  },
  "extension": [
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
      "valueInteger": 5
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
      "valueCode": "oo"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
      "valueCode": "trial-use"
    }
  ],
  "url": "http://hl7.org/fhir/StructureDefinition/observation-genetics",
  "version": "4.0.0",
  "name": "Observation-genetics",
  "status": "draft",
  "experimental": false,
  "date": "2016-03-14",
  "publisher": "Health Level Seven International (Clinical Genomics)",
  "contact": [
    {
      "telecom": [
        {
          "system": "url",
          "value": "http://www.hl7.org/Special/committees/clingenomics"
        }
      ]
    }
  ],
  "description": "Describes how the observation resource is used to report structured genetic test results",
  "fhirVersion": "4.0.0",
  "mapping": [
    {
      "identity": "workflow",
      "uri": "http://hl7.org/fhir/workflow",
      "name": "Workflow Pattern"
    },
    {
      "identity": "sct-concept",
      "uri": "http://snomed.info/conceptdomain",
      "name": "SNOMED CT Concept Domain Binding"
    },
    {
      "identity": "v2",
      "uri": "http://hl7.org/v2",
      "name": "HL7 v2 Mapping"
    },
    {
      "identity": "rim",
      "uri": "http://hl7.org/v3",
      "name": "RIM Mapping"
    },
    {
      "identity": "w5",
      "uri": "http://hl7.org/fhir/fivews",
      "name": "FiveWs Pattern Mapping"
    },
    {
      "identity": "sct-attr",
      "uri": "http://snomed.org/attributebinding",
      "name": "SNOMED CT Attribute Binding"
    }
  ],
  "kind": "resource",
  "abstract": false,
  "type": "Observation",
  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Observation",
  "derivation": "constraint",
  "differential": {
    "element": [
      {
        "id": "Observation",
        "path": "Observation",
        "min": 0,
        "max": "*"
      },
      {
        "id": "Observation.extension:Gene",
        "path": "Observation.extension",
        "sliceName": "Gene",
        "short": "HGNC gene symbol",
        "definition": "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions ([SO:0000704](http://www.sequenceontology.org/browser/current_svn/term/SO:0000704)). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ([HGNC](http://www.genenames.org)). LOINC Code: ([48018-6](http://loinc.org/48018-6)).",
        "min": 0,
        "max": "1",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://hl7.org/fhir/StructureDefinition/observation-geneticsGene"
            ]
          }
        ]
      },
      {
        "id": "Observation.extension:DNARegionName",
        "path": "Observation.extension",
        "sliceName": "DNARegionName",
        "short": "DNA region name",
        "definition": "A human readable name for the region of interest. Typically Exon #, Intron # or other. NOTE: This is not standardized and is mainly for convenience and display purposes.  LOINC Code: ([47999-8](http://loinc.org/47999-8)).",
        "min": 0,
        "max": "1",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://hl7.org/fhir/StructureDefinition/observation-geneticsDNARegionName"
            ]
          }
        ]
      },
      {
        "id": "Observation.extension:CopyNumberEvent",
        "path": "Observation.extension",
        "sliceName": "CopyNumberEvent",
        "short": "Copy number variation",
        "definition": "A variation that increases or decreases the copy number of a given region ([SO:0001019](http://www.sequenceontology.org/browser/current_svn/term/SO:0001019)). Values: amplification/deletion/LOH.",
        "min": 0,
        "max": "1",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://hl7.org/fhir/StructureDefinition/observation-geneticsCopyNumberEvent"
            ]
          }
        ]
      },
      {
        "id": "Observation.extension:GenomicSourceClass",
        "path": "Observation.extension",
        "sliceName": "GenomicSourceClass",
        "short": "Genomic source class",
        "definition": "Source of sample used to determine the sequence in sequencing lab -- germline, somatic, prenatal. LOINC Code: ([48002-0](http://loinc.org/48002-0)).",
        "min": 0,
        "max": "1",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://hl7.org/fhir/StructureDefinition/observation-geneticsGenomicSourceClass"
            ]
          }
        ]
      },
      {
        "id": "Observation.extension:Interpretation",
        "path": "Observation.extension",
        "sliceName": "Interpretation",
        "short": "Clinical interpretations for variant",
        "definition": "Clinical Interpretations for variant. It's a reference to an Observation resource.",
        "min": 0,
        "max": "1",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://hl7.org/fhir/StructureDefinition/observation-geneticsInterpretation"
            ]
          }
        ]
      },
      {
        "id": "Observation.extension:Variant",
        "path": "Observation.extension",
        "sliceName": "Variant",
        "short": "Variant",
        "definition": "Variant information.",
        "min": 0,
        "max": "1",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"
            ]
          }
        ]
      },
      {
        "id": "Observation.extension:AminoAcidChange",
        "path": "Observation.extension",
        "sliceName": "AminoAcidChange",
        "short": "AminoAcidChange",
        "definition": "AminoAcidChange information.",
        "comment": "Loss of heterozygosity (LOH) is a functional variant whereby the sequence alteration causes a loss of function of one allele of a gene ([SO:0001786](http://www.sequenceontology.org/browser/current_svn/term/SO:0001786)).",
        "min": 0,
        "max": "1",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"
            ]
          }
        ]
      },
      {
        "id": "Observation.extension:Allele",
        "path": "Observation.extension",
        "sliceName": "Allele",
        "short": "Allele",
        "definition": "Allele information.",
        "min": 0,
        "max": "1",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele"
            ]
          }
        ]
      },
      {
        "id": "Observation.extension:Ancestry",
        "path": "Observation.extension",
        "sliceName": "Ancestry",
        "short": "Ancestry",
        "definition": "Ancestry information.",
        "min": 0,
        "max": "1",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://hl7.org/fhir/StructureDefinition/observation-geneticsAncestry"
            ]
          }
        ]
      },
      {
        "id": "Observation.extension:PhaseSet",
        "path": "Observation.extension",
        "sliceName": "PhaseSet",
        "short": "Phase set",
        "definition": "Phase set information.",
        "min": 0,
        "max": "*",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://hl7.org/fhir/StructureDefinition/observation-geneticsPhaseSet"
            ]
          }
        ]
      }
    ]
  }
}