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Extension-observation-geneticsvariant.json

Orders and Observations Work GroupMaturity Level: N/ABallot Status: Informative

Raw JSON (каноническая форма + also see JSON Format Specification)

Variant

{
  "resourceType" : "StructureDefinition",
  "id" : "observation-geneticsVariant",
  "extension" : [{
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
    "valueCode" : "oo"
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
    "valueInteger" : 1
  }],
  "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant",
  "version" : "3.6.0",
  "name" : "Variant",
  "status" : "draft",
  "date" : "2016-03-14",
  "publisher" : "Health Level Seven International (Clinical Genomics)",
  "contact" : [{
    "telecom" : [{
      "system" : "url",
      "value" : "http://www.hl7.org/Special/committees/clingenomics"
    }]
  }],
  "description" : "Variant information.",
  "fhirVersion" : "3.6.0",
  "mapping" : [{
    "identity" : "v2",
    "uri" : "http://hl7.org/v2",
    "name" : "HL7 v2 Mapping"
  },
  {
    "identity" : "rim",
    "uri" : "http://hl7.org/v3",
    "name" : "RIM Mapping"
  }],
  "kind" : "complex-type",
  "abstract" : false,
  "context" : [{
    "type" : "element",
    "expression" : "Observation"
  }],
  "type" : "Extension",
  "baseDefinition" : "http://hl7.org/fhir/StructureDefinition/Extension",
  "derivation" : "constraint",
  "snapshot" : {
    "element" : [{
      "id" : "Extension",
      "extension" : [{
        "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
        "valueCode" : "normative"
      }],
      "path" : "Extension",
      "short" : "Variant",
      "definition" : "Variant information.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Extension",
        "min" : 0,
        "max" : "*"
      },
      "condition" : ["ele-1"],
      "constraint" : [{
        "key" : "ele-1",
        "severity" : "error",
        "human" : "All FHIR elements must have a @value or children",
        "expression" : "hasValue() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "Element"
      },
      {
        "key" : "ext-1",
        "severity" : "error",
        "human" : "Must have either extensions or value[x], not both",
        "expression" : "extension.exists() != value.exists()",
        "xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
        "source" : "Extension"
      }],
      "isModifier" : false
    },
    {
      "id" : "Extension.id",
      "path" : "Extension.id",
      "representation" : ["xmlAttr"],
      "short" : "xml:id (or equivalent in JSON)",
      "definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Element.id",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "Extension.extension",
      "path" : "Extension.extension",
      "slicing" : {
        "discriminator" : [{
          "type" : "value",
          "path" : "url"
        }],
        "description" : "Extensions are always sliced by (at least) url",
        "rules" : "open"
      },
      "short" : "Additional content defined by implementations",
      "definition" : "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance  applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
      "comment" : "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions.  The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
      "alias" : ["extensions",
      "user content"],
      "min" : 0,
      "max" : "*",
      "base" : {
        "path" : "Element.extension",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Extension"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "Extension.extension:Name",
      "path" : "Extension.extension",
      "sliceName" : "Name",
      "short" : "HGVS nomenclature for observed DNA sequence variant",
      "definition" : "Human Genome Variation Society (HGVS) nomenclature for a single or set of DNA Sequence Variation(s) identified in testing.  The use of the nomenclature is also used to describe non-variations (aka. wild types). LOINC Code: ([48004-6](http://loinc.org/48004-6)).",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Element.extension",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Extension"
      }],
      "isModifier" : false,
      "isSummary" : false
    },
    {
      "id" : "Extension.extension:Name.id",
      "path" : "Extension.extension.id",
      "representation" : ["xmlAttr"],
      "short" : "xml:id (or equivalent in JSON)",
      "definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Element.id",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "Extension.extension:Name.extension",
      "path" : "Extension.extension.extension",
      "slicing" : {
        "discriminator" : [{
          "type" : "value",
          "path" : "url"
        }],
        "description" : "Extensions are always sliced by (at least) url",
        "rules" : "open"
      },
      "short" : "Extension",
      "definition" : "An Extension",
      "min" : 0,
      "max" : "0",
      "base" : {
        "path" : "Element.extension",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Extension"
      }],
      "isModifier" : false,
      "isSummary" : false
    },
    {
      "id" : "Extension.extension:Name.url",
      "path" : "Extension.extension.url",
      "representation" : ["xmlAttr"],
      "short" : "identifies the meaning of the extension",
      "definition" : "Source of the definition for the extension code - a logical name or a URL.",
      "comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
      "min" : 1,
      "max" : "1",
      "base" : {
        "path" : "Extension.url",
        "min" : 1,
        "max" : "1"
      },
      "type" : [{
        "code" : "uri"
      }],
      "fixedUri" : "Name",
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.extension:Name.valueCodeableConcept",
      "path" : "Extension.extension.valueCodeableConcept",
      "short" : "Value of extension",
      "definition" : "Value of extension - may be a resource or one of a constrained set of the data types (see Extensibility in the spec for list).",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Extension.value[x]",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "ClinVar-variant-database"
        }],
        "strength" : "preferred",
        "description" : "NCBI central repository of potentially clinically relevant variants.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/clinvar"
      },
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.extension:Id",
      "path" : "Extension.extension",
      "sliceName" : "Id",
      "short" : "DNA sequence variant ID",
      "definition" : "Identifier for DNA sequence variant.  If a germline variant, ClinVar or dbSNP identifier should be used.  If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC) LOINC Code: ([48003-8](http://loinc.org/48003-8)).",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Element.extension",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Extension"
      }],
      "isModifier" : false,
      "isSummary" : false
    },
    {
      "id" : "Extension.extension:Id.id",
      "path" : "Extension.extension.id",
      "representation" : ["xmlAttr"],
      "short" : "xml:id (or equivalent in JSON)",
      "definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Element.id",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "Extension.extension:Id.extension",
      "path" : "Extension.extension.extension",
      "slicing" : {
        "discriminator" : [{
          "type" : "value",
          "path" : "url"
        }],
        "description" : "Extensions are always sliced by (at least) url",
        "rules" : "open"
      },
      "short" : "Extension",
      "definition" : "An Extension",
      "min" : 0,
      "max" : "0",
      "base" : {
        "path" : "Element.extension",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Extension"
      }],
      "isModifier" : false,
      "isSummary" : false
    },
    {
      "id" : "Extension.extension:Id.url",
      "path" : "Extension.extension.url",
      "representation" : ["xmlAttr"],
      "short" : "identifies the meaning of the extension",
      "definition" : "Source of the definition for the extension code - a logical name or a URL.",
      "comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
      "min" : 1,
      "max" : "1",
      "base" : {
        "path" : "Extension.url",
        "min" : 1,
        "max" : "1"
      },
      "type" : [{
        "code" : "uri"
      }],
      "fixedUri" : "Id",
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.extension:Id.valueCodeableConcept",
      "path" : "Extension.extension.valueCodeableConcept",
      "short" : "Value of extension",
      "definition" : "Value of extension - may be a resource or one of a constrained set of the data types (see Extensibility in the spec for list).",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Extension.value[x]",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.extension:Type",
      "path" : "Extension.extension",
      "sliceName" : "Type",
      "short" : "DNA sequence variant type",
      "definition" : "Codified type for associated DNA sequence variant. DNA sequence variants use the HGVS notation, which implies the DNA sequence variant type. LOINC Code: ([48019-4](http://loinc.org/48019-4)).",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Element.extension",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Extension"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "v2",
        "map" : "N/A"
      },
      {
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.extension:Type.id",
      "path" : "Extension.extension.id",
      "representation" : ["xmlAttr"],
      "short" : "xml:id (or equivalent in JSON)",
      "definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Element.id",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "string"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "n/a"
      }]
    },
    {
      "id" : "Extension.extension:Type.extension",
      "path" : "Extension.extension.extension",
      "slicing" : {
        "discriminator" : [{
          "type" : "value",
          "path" : "url"
        }],
        "description" : "Extensions are always sliced by (at least) url",
        "rules" : "open"
      },
      "short" : "Extension",
      "definition" : "An Extension",
      "min" : 0,
      "max" : "0",
      "base" : {
        "path" : "Element.extension",
        "min" : 0,
        "max" : "*"
      },
      "type" : [{
        "code" : "Extension"
      }],
      "isModifier" : false,
      "isSummary" : false
    },
    {
      "id" : "Extension.extension:Type.url",
      "path" : "Extension.extension.url",
      "representation" : ["xmlAttr"],
      "short" : "identifies the meaning of the extension",
      "definition" : "Source of the definition for the extension code - a logical name or a URL.",
      "comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
      "min" : 1,
      "max" : "1",
      "base" : {
        "path" : "Extension.url",
        "min" : 1,
        "max" : "1"
      },
      "type" : [{
        "code" : "uri"
      }],
      "fixedUri" : "Type",
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.extension:Type.valueCodeableConcept",
      "path" : "Extension.extension.valueCodeableConcept",
      "short" : "Value of extension",
      "definition" : "Value of extension - may be a resource or one of a constrained set of the data types (see Extensibility in the spec for list).",
      "min" : 0,
      "max" : "1",
      "base" : {
        "path" : "Extension.value[x]",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.url",
      "path" : "Extension.url",
      "representation" : ["xmlAttr"],
      "short" : "identifies the meaning of the extension",
      "definition" : "Source of the definition for the extension code - a logical name or a URL.",
      "comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
      "min" : 1,
      "max" : "1",
      "base" : {
        "path" : "Extension.url",
        "min" : 1,
        "max" : "1"
      },
      "type" : [{
        "code" : "uri"
      }],
      "fixedUri" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant",
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.value[x]",
      "path" : "Extension.value[x]",
      "short" : "Value of extension",
      "definition" : "Value of extension - may be a resource or one of a constrained set of the data types (see Extensibility in the spec for list).",
      "min" : 0,
      "max" : "0",
      "base" : {
        "path" : "Extension.value[x]",
        "min" : 0,
        "max" : "1"
      },
      "type" : [{
        "code" : "base64Binary"
      },
      {
        "code" : "boolean"
      },
      {
        "code" : "canonical"
      },
      {
        "code" : "code"
      },
      {
        "code" : "date"
      },
      {
        "code" : "dateTime"
      },
      {
        "code" : "decimal"
      },
      {
        "code" : "id"
      },
      {
        "code" : "instant"
      },
      {
        "code" : "integer"
      },
      {
        "code" : "markdown"
      },
      {
        "code" : "oid"
      },
      {
        "code" : "positiveInt"
      },
      {
        "code" : "string"
      },
      {
        "code" : "time"
      },
      {
        "code" : "unsignedInt"
      },
      {
        "code" : "uri"
      },
      {
        "code" : "url"
      },
      {
        "code" : "uuid"
      },
      {
        "code" : "Address"
      },
      {
        "code" : "Age"
      },
      {
        "code" : "Annotation"
      },
      {
        "code" : "Attachment"
      },
      {
        "code" : "CodeableConcept"
      },
      {
        "code" : "Coding"
      },
      {
        "code" : "ContactPoint"
      },
      {
        "code" : "Count"
      },
      {
        "code" : "Distance"
      },
      {
        "code" : "Duration"
      },
      {
        "code" : "HumanName"
      },
      {
        "code" : "Identifier"
      },
      {
        "code" : "Money"
      },
      {
        "code" : "Period"
      },
      {
        "code" : "Quantity"
      },
      {
        "code" : "Range"
      },
      {
        "code" : "Ratio"
      },
      {
        "code" : "Reference"
      },
      {
        "code" : "SampledData"
      },
      {
        "code" : "Signature"
      },
      {
        "code" : "Timing"
      },
      {
        "code" : "ContactDetail"
      },
      {
        "code" : "Contributor"
      },
      {
        "code" : "DataRequirement"
      },
      {
        "code" : "Expression"
      },
      {
        "code" : "ParameterDefinition"
      },
      {
        "code" : "RelatedArtifact"
      },
      {
        "code" : "TriggerDefinition"
      },
      {
        "code" : "UsageContext"
      },
      {
        "code" : "Dosage"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
        "map" : "N/A"
      }]
    }]
  },
  "differential" : {
    "element" : [{
      "id" : "Extension",
      "path" : "Extension",
      "short" : "Variant",
      "definition" : "Variant information.",
      "min" : 0,
      "max" : "1"
    },
    {
      "id" : "Extension.extension:Name",
      "path" : "Extension.extension",
      "sliceName" : "Name",
      "short" : "HGVS nomenclature for observed DNA sequence variant",
      "definition" : "Human Genome Variation Society (HGVS) nomenclature for a single or set of DNA Sequence Variation(s) identified in testing.  The use of the nomenclature is also used to describe non-variations (aka. wild types). LOINC Code: ([48004-6](http://loinc.org/48004-6)).",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "Extension"
      }]
    },
    {
      "id" : "Extension.extension:Name.extension",
      "path" : "Extension.extension.extension",
      "max" : "0"
    },
    {
      "id" : "Extension.extension:Name.url",
      "path" : "Extension.extension.url",
      "type" : [{
        "code" : "uri"
      }],
      "fixedUri" : "Name"
    },
    {
      "id" : "Extension.extension:Name.valueCodeableConcept",
      "path" : "Extension.extension.valueCodeableConcept",
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "ClinVar-variant-database"
        }],
        "strength" : "preferred",
        "description" : "NCBI central repository of potentially clinically relevant variants.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/clinvar"
      }
    },
    {
      "id" : "Extension.extension:Id",
      "path" : "Extension.extension",
      "sliceName" : "Id",
      "short" : "DNA sequence variant ID",
      "definition" : "Identifier for DNA sequence variant.  If a germline variant, ClinVar or dbSNP identifier should be used.  If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC) LOINC Code: ([48003-8](http://loinc.org/48003-8)).",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "Extension"
      }]
    },
    {
      "id" : "Extension.extension:Id.extension",
      "path" : "Extension.extension.extension",
      "max" : "0"
    },
    {
      "id" : "Extension.extension:Id.url",
      "path" : "Extension.extension.url",
      "type" : [{
        "code" : "uri"
      }],
      "fixedUri" : "Id"
    },
    {
      "id" : "Extension.extension:Id.valueCodeableConcept",
      "path" : "Extension.extension.valueCodeableConcept",
      "type" : [{
        "code" : "CodeableConcept"
      }]
    },
    {
      "id" : "Extension.extension:Type",
      "path" : "Extension.extension",
      "sliceName" : "Type",
      "short" : "DNA sequence variant type",
      "definition" : "Codified type for associated DNA sequence variant. DNA sequence variants use the HGVS notation, which implies the DNA sequence variant type. LOINC Code: ([48019-4](http://loinc.org/48019-4)).",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "Extension"
      }],
      "mapping" : [{
        "identity" : "v2",
        "map" : "N/A"
      },
      {
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.extension:Type.extension",
      "path" : "Extension.extension.extension",
      "max" : "0"
    },
    {
      "id" : "Extension.extension:Type.url",
      "path" : "Extension.extension.url",
      "type" : [{
        "code" : "uri"
      }],
      "fixedUri" : "Type"
    },
    {
      "id" : "Extension.extension:Type.valueCodeableConcept",
      "path" : "Extension.extension.valueCodeableConcept",
      "type" : [{
        "code" : "CodeableConcept"
      }]
    },
    {
      "id" : "Extension.url",
      "path" : "Extension.url",
      "type" : [{
        "code" : "uri"
      }],
      "fixedUri" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"
    },
    {
      "id" : "Extension.value[x]",
      "path" : "Extension.value[x]",
      "min" : 0,
      "max" : "0"
    }]
  }
}

Примечание к использованию: мы очень стараемся приводить корректные и полезные примеры, но нормативно они не являются частью спецификации.