{
"description": "Variant information.",
"_filename": "StructureDefinition-observation-geneticsVariant.json",
"package_name": "hl7.fhir.uv.extensions.r3",
"date": "2016-03-14",
"derivation": "constraint",
"publisher": "HL7 International / Orders and Observations",
"fhirVersion": "3.0.2",
"jurisdiction": [ {
"coding": [ {
"code": "001",
"system": "http://unstats.un.org/unsd/methods/m49/m49.htm"
} ]
} ],
"name": "Variant",
"mapping": [ {
"uri": "http://hl7.org/v2",
"name": "HL7 v2 Mapping",
"identity": "v2"
}, {
"uri": "http://hl7.org/v3",
"name": "RIM Mapping",
"identity": "rim"
} ],
"abstract": false,
"type": "Extension",
"experimental": null,
"resourceType": "StructureDefinition",
"title": "Variant",
"package_version": "5.3.0-ballot-tc1",
"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/structuredefinition-standards-status",
"valueCode": "deprecated",
"_valueCode": {
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status-reason",
"valueMarkdown": "This extension has been replaced by the profiles and extensions defined in the [Genomics Reporting Guide](https://hl7.org/fhir/uv/genomics-reporting/)"
} ]
}
}, {
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-type-characteristics",
"valueCode": "can-bind"
} ],
"snapshot": {
"element": [ {
"constraint": [ {
"key": "ele-1",
"human": "All FHIR elements must have a @value or children",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element",
"severity": "error",
"expression": "hasValue() | (children().count() > id.count())"
}, {
"key": "ext-1",
"human": "Must have either extensions or value[x], not both",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension",
"severity": "error",
"expression": "extension.exists() != value.exists()"
} ],
"path": "Extension",
"min": 0,
"definition": "Variant information.",
"short": "Variant",
"max": "1",
"id": "Extension",
"condition": [ "ele-1" ],
"base": {
"max": "*",
"min": 0,
"path": "Extension"
}
}, {
"path": "Extension.id",
"min": 0,
"definition": "unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "xml:id (or equivalent in JSON)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "string"
} ],
"representation": [ "xmlAttr" ],
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"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
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"min": 0,
"definition": "May be used to represent additional information that is not part of the basic definition of the element. In order 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 is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
"short": "Additional Content defined by implementations",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
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"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"alias": [ "extensions", "user content" ],
"max": "*",
"id": "Extension.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.",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"path": "Extension.extension",
"min": 0,
"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)).",
"short": "HGVS nomenclature for observed DNA sequence variant",
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"code": "Extension"
} ],
"sliceName": "Name",
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"min": 0,
"definition": "unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
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"identity": "rim"
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"type": [ {
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"path": "Element.id"
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}, {
"path": "Extension.extension.extension",
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"definition": "An Extension",
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"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
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},
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"code": "Extension"
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"max": "0",
"id": "Extension.extension:Name.extension",
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"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"path": "Extension.extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"short": "identifies the meaning of the extension",
"fixedUri": "Name",
"mapping": [ {
"map": "N/A",
"identity": "rim"
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"type": [ {
"code": "uri"
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"max": "1",
"id": "Extension.extension:Name.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
}
}, {
"path": "Extension.extension.value[x]",
"min": 1,
"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).",
"short": "Value of extension",
"mapping": [ {
"map": "N/A",
"identity": "rim"
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"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "example",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "ClinVar-variant-database"
} ],
"description": "NCBI central repository of potentially clinically relevant variants."
},
"max": "1",
"id": "Extension.extension:Name.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
}
}, {
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"min": 0,
"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)).",
"short": "DNA sequence variant ID",
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"code": "Extension"
} ],
"sliceName": "Id",
"max": "1",
"id": "Extension.extension:Id",
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"max": "*",
"min": 0,
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}
}, {
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"definition": "unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "xml:id (or equivalent in JSON)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
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"representation": [ "xmlAttr" ],
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"id": "Extension.extension:Id.id",
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"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
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"min": 0,
"definition": "An Extension",
"short": "Extension",
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"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
"path": "url",
"type": "value"
} ]
},
"type": [ {
"code": "Extension"
} ],
"max": "0",
"id": "Extension.extension:Id.extension",
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"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"path": "Extension.extension.url",
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"definition": "Source of the definition for the extension code - a logical name or a URL.",
"short": "identifies the meaning of the extension",
"fixedUri": "Id",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "uri"
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:Id.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
}
}, {
"path": "Extension.extension.value[x]",
"min": 1,
"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).",
"short": "Value of extension",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"max": "1",
"id": "Extension.extension:Id.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
}
}, {
"path": "Extension.extension",
"min": 0,
"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)).",
"short": "DNA sequence variant type",
"mapping": [ {
"map": "N/A",
"identity": "v2"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension"
} ],
"sliceName": "Type",
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"id": "Extension.extension:Type",
"base": {
"max": "*",
"min": 0,
"path": "Element.extension"
}
}, {
"path": "Extension.extension.id",
"min": 0,
"definition": "unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
"short": "xml:id (or equivalent in JSON)",
"mapping": [ {
"map": "n/a",
"identity": "rim"
} ],
"type": [ {
"code": "string"
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"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:Type.id",
"base": {
"max": "1",
"min": 0,
"path": "Element.id"
}
}, {
"path": "Extension.extension.extension",
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"definition": "An Extension",
"short": "Extension",
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"rules": "open",
"description": "Extensions are always sliced by (at least) url",
"discriminator": [ {
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"type": "value"
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},
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"code": "Extension"
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"max": "0",
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"path": "Element.extension"
}
}, {
"path": "Extension.extension.url",
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"definition": "Source of the definition for the extension code - a logical name or a URL.",
"short": "identifies the meaning of the extension",
"fixedUri": "Type",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "uri"
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.extension:Type.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
}
}, {
"path": "Extension.extension.value[x]",
"min": 1,
"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).",
"short": "Value of extension",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "CodeableConcept"
} ],
"max": "1",
"id": "Extension.extension:Type.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
}
}, {
"path": "Extension.url",
"min": 1,
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"short": "identifies the meaning of the extension",
"fixedUri": "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "uri"
} ],
"representation": [ "xmlAttr" ],
"max": "1",
"id": "Extension.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.",
"base": {
"max": "1",
"min": 1,
"path": "Extension.url"
}
}, {
"path": "Extension.value[x]",
"min": 0,
"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).",
"short": "Value of extension",
"mapping": [ {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "base64Binary"
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"code": "boolean"
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"code": "date"
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"code": "dateTime"
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"code": "decimal"
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"code": "id"
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"code": "instant"
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"code": "markdown"
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"code": "string"
}, {
"code": "time"
}, {
"code": "unsignedInt"
}, {
"code": "uri"
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"code": "Address"
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"code": "Age"
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"code": "Annotation"
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"code": "Attachment"
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}, {
"code": "Coding"
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"code": "ContactPoint"
}, {
"code": "Count"
}, {
"code": "Distance"
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"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": "Meta"
} ],
"max": "0",
"id": "Extension.value[x]",
"base": {
"max": "1",
"min": 0,
"path": "Extension.value[x]"
}
} ]
},
"status": "retired",
"id": "74604348-9841-48a7-a2b7-5b471302035a",
"kind": "complex-type",
"url": "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant",
"context": [ "Observation" ],
"version": "5.3.0-ballot-tc1",
"differential": {
"element": [ {
"id": "Extension",
"max": "1",
"min": 0,
"path": "Extension",
"short": "Variant",
"definition": "Variant information."
}, {
"id": "Extension.extension:Name",
"max": "1",
"min": 0,
"path": "Extension.extension",
"type": [ {
"code": "Extension"
} ],
"short": "HGVS nomenclature for observed DNA sequence variant",
"sliceName": "Name",
"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))."
}, {
"id": "Extension.extension:Name.extension",
"max": "0",
"path": "Extension.extension.extension"
}, {
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"path": "Extension.extension.url",
"type": [ {
"code": "uri"
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"fixedUri": "Name"
}, {
"id": "Extension.extension:Name.value[x]",
"min": 1,
"path": "Extension.extension.value[x]",
"type": [ {
"code": "CodeableConcept"
} ],
"binding": {
"strength": "example",
"extension": [ {
"url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
"valueString": "ClinVar-variant-database"
} ],
"description": "NCBI central repository of potentially clinically relevant variants."
}
}, {
"id": "Extension.extension:Id",
"max": "1",
"min": 0,
"path": "Extension.extension",
"type": [ {
"code": "Extension"
} ],
"short": "DNA sequence variant ID",
"sliceName": "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))."
}, {
"id": "Extension.extension:Id.extension",
"max": "0",
"path": "Extension.extension.extension"
}, {
"id": "Extension.extension:Id.url",
"path": "Extension.extension.url",
"type": [ {
"code": "uri"
} ],
"fixedUri": "Id"
}, {
"id": "Extension.extension:Id.value[x]",
"min": 1,
"path": "Extension.extension.value[x]",
"type": [ {
"code": "CodeableConcept"
} ]
}, {
"path": "Extension.extension",
"min": 0,
"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)).",
"short": "DNA sequence variant type",
"mapping": [ {
"map": "N/A",
"identity": "v2"
}, {
"map": "N/A",
"identity": "rim"
} ],
"type": [ {
"code": "Extension"
} ],
"sliceName": "Type",
"max": "1",
"id": "Extension.extension:Type"
}, {
"id": "Extension.extension:Type.extension",
"max": "0",
"path": "Extension.extension.extension"
}, {
"id": "Extension.extension:Type.url",
"path": "Extension.extension.url",
"type": [ {
"code": "uri"
} ],
"fixedUri": "Type"
}, {
"id": "Extension.extension:Type.value[x]",
"min": 1,
"path": "Extension.extension.value[x]",
"type": [ {
"code": "CodeableConcept"
} ]
}, {
"id": "Extension.url",
"path": "Extension.url",
"fixedUri": "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"
}, {
"id": "Extension.value[x]",
"max": "0",
"min": 0,
"path": "Extension.value[x]"
} ]
},
"contact": [ {
"telecom": [ {
"value": "http://www.hl7.org/Special/committees/orders",
"system": "url"
} ]
} ],
"contextType": "resource",
"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension"
}