R4 Ballot #1 (Mixed Normative/Trial use)
DiagnosticsThis page is part of the FHIR Specification (v3.3.0: R4 Ballot 2). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions 
. Page versions: R4B R4
| Orders and Observations Work Group | Maturity Level: N/A | Ballot Status: Informative |
Allele
{
"resourceType": "StructureDefinition",
"id": "observation-geneticsAllele",
"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-geneticsAllele",
"name": "Allele",
"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": "Allele information.",
"fhirVersion": "3.3.0",
"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",
"path": "Extension",
"short": "Allele",
"definition": "Allele 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() | (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": "Name of allele",
"definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). This element is the common name for the allele. LOINC Code: ([48008-7](http://loinc.org/48008-7)).",
"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: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": "EBI-AlleleName"
}
],
"strength": "preferred",
"description": "EMBL-EBI database of AlleleName",
"valueSetUri": "http://www.ebi.ac.uk/"
},
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:state",
"path": "Extension.extension",
"sliceName": "State",
"short": "The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous",
"definition": "The level of occurrence of a single DNA Sequence Variant within a set of chromosomes. Heterozygous indicates the DNA sequence variant is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variant is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variant exists in the only single copy of a gene in a non-homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variant is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variant is present in all of the copies of mitochondrial DNA. LOINC Code: ([53034-5](http://loinc.org/53034-5)).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:state.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:state.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:state.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": "State",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:state.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:frequency",
"path": "Extension.extension",
"sliceName": "Frequency",
"short": "Allele frequency",
"definition": "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. LOINC Code: ([81258-6](http://loinc.org/81258-6)).",
"min": 0,
"max": "1",
"base": {
"path": "Element.extension",
"min": 0,
"max": "*"
},
"type": [
{
"code": "Extension"
}
],
"isModifier": false,
"isSummary": false
},
{
"id": "Extension.extension:frequency.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:frequency.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:frequency.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": "Frequency",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"id": "Extension.extension:frequency.valueDecimal",
"path": "Extension.extension.valueDecimal",
"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": "decimal"
}
],
"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-geneticsAllele",
"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": "ParameterDefinition"
},
{
"code": "DataRequirement"
},
{
"code": "RelatedArtifact"
},
{
"code": "ContactDetail"
},
{
"code": "Contributor"
},
{
"code": "TriggerDefinition"
},
{
"code": "UsageContext"
},
{
"code": "Dosage"
}
],
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]
}
]
},
"differential": {
"element": [
{
"id": "Extension",
"path": "Extension",
"short": "Allele",
"definition": "Allele information.",
"min": 0,
"max": "1"
},
{
"id": "Extension.extension:name",
"path": "Extension.extension",
"sliceName": "Name",
"short": "Name of allele",
"definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). This element is the common name for the allele. LOINC Code: ([48008-7](http://loinc.org/48008-7)).",
"min": 0,
"max": "1",
"type": [
{
"code": "Extension"
}
],
"mapping": [
{
"identity": "v2",
"map": "N/A"
},
{
"identity": "rim",
"map": "N/A"
}
]
},
{
"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": "EBI-AlleleName"
}
],
"strength": "preferred",
"description": "EMBL-EBI database of AlleleName",
"valueSetUri": "http://www.ebi.ac.uk/"
}
},
{
"id": "Extension.extension:state",
"path": "Extension.extension",
"sliceName": "State",
"short": "The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous",
"definition": "The level of occurrence of a single DNA Sequence Variant within a set of chromosomes. Heterozygous indicates the DNA sequence variant is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variant is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variant exists in the only single copy of a gene in a non-homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variant is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variant is present in all of the copies of mitochondrial DNA. LOINC Code: ([53034-5](http://loinc.org/53034-5)).",
"min": 0,
"max": "1",
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Extension.extension:state.extension",
"path": "Extension.extension.extension",
"max": "0"
},
{
"id": "Extension.extension:state.url",
"path": "Extension.extension.url",
"type": [
{
"code": "uri"
}
],
"fixedUri": "State"
},
{
"id": "Extension.extension:state.valueCodeableConcept",
"path": "Extension.extension.valueCodeableConcept",
"type": [
{
"code": "CodeableConcept"
}
]
},
{
"id": "Extension.extension:frequency",
"path": "Extension.extension",
"sliceName": "Frequency",
"short": "Allele frequency",
"definition": "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. LOINC Code: ([81258-6](http://loinc.org/81258-6)).",
"min": 0,
"max": "1",
"type": [
{
"code": "Extension"
}
]
},
{
"id": "Extension.extension:frequency.extension",
"path": "Extension.extension.extension",
"max": "0"
},
{
"id": "Extension.extension:frequency.url",
"path": "Extension.extension.url",
"type": [
{
"code": "uri"
}
],
"fixedUri": "Frequency"
},
{
"id": "Extension.extension:frequency.valueDecimal",
"path": "Extension.extension.valueDecimal",
"type": [
{
"code": "decimal"
}
]
},
{
"id": "Extension.url",
"path": "Extension.url",
"type": [
{
"code": "uri"
}
],
"fixedUri": "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele"
},
{
"id": "Extension.value[x]",
"path": "Extension.value[x]",
"min": 0,
"max": "0"
}
]
}
}
Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.
®© HL7.org 2011+. FHIR Mixed Nomative/Trial Use Ballot (v3.3.0-13671) generated on Tue, Apr 3, 2018 12:12+1000. QA Page
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