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Extension: Allele

URL for this extension:

http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele

Status: draft. Extension maintained by: Health Level Seven International (Clinical Genomics)

Allele information.

Context of Use: Use on Element ID Observation

Extension Content

• Summary
• Full Structure
• XML
• JSON
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Summary

Name	Flags	Card.	Type	Description & Constraints
Allele		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele Allele: Allele information. Use on Element ID Observation
Name		0..1	CodeableConcept	An allele is one of a set of coexisting sequence variants of a gene (SO:0001023). This element is the common name for the allele. LOINC Code: (48008-7).
State		0..1	CodeableConcept	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).
Frequency		0..1	decimal	A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. LOINC Code: (81258-6).
Documentation for this format

Full Structure

Name	Flags	Card.	Type	Description & Constraints
extension		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele Allele: Allele information. Use on Element ID Observation
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
extension:Name		0..1	Extension	Name of allele
id		0..1	string	Unique id for inter-element referencing
extension		0..0
url		1..1	uri	"Name"
value[x]		1..1	CodeableConcept	Value of extension Binding: HLA (preferred): The nomenclature from European Bioinformatics Institute to name the genetic Allele
extension:State		0..1	Extension	The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
id		0..1	string	Unique id for inter-element referencing
extension		0..0
url		1..1	uri	"State"
value[x]		1..1	CodeableConcept	Value of extension
extension:Frequency		0..1	Extension	Allele frequency
id		0..1	string	Unique id for inter-element referencing
extension		0..0
url		1..1	uri	"Frequency"
value[x]		1..1	decimal	Value of extension
url		1..1	uri	"http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele"
value[x]		0..0
valueBase64Binary			base64Binary
valueBoolean			boolean
valueCanonical			canonical(Any)
valueCode			code
valueDate			date
valueDateTime			dateTime
valueDecimal			decimal
valueId			id
valueInstant			instant
valueInteger			integer
valueMarkdown			markdown
valueOid			oid
valuePositiveInt			positiveInt
valueString			string
valueTime			time
valueUnsignedInt			unsignedInt
valueUri			uri
valueUrl			url
valueUuid			uuid
valueAddress			Address
valueAge			Age
valueAnnotation			Annotation
valueAttachment			Attachment
valueCodeableConcept			CodeableConcept
valueCoding			Coding
valueContactPoint			ContactPoint
valueCount			Count
valueDistance			Distance
valueDuration			Duration
valueHumanName			HumanName
valueIdentifier			Identifier
valueMoney			Money
valuePeriod			Period
valueQuantity			Quantity
valueRange			Range
valueRatio			Ratio
valueReference			Reference(Any)
valueSampledData			SampledData
valueSignature			Signature
valueTiming			Timing
valueContactDetail			ContactDetail
valueContributor			Contributor
valueDataRequirement			DataRequirement
valueExpression			Expression
valueParameterDefinition			ParameterDefinition
valueRelatedArtifact			RelatedArtifact
valueTriggerDefinition			TriggerDefinition
valueUsageContext			UsageContext
valueDosage			Dosage
valueMeta			Meta
Documentation for this format

XML Template

<!-- Allele -->

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele" >
 <-- extension sliced by value:url  in the specified orderOpen-->
 <extension url="Name">  0..1 Extension  <!--  0..1 Name of allele -->
  <valueCodeableConcept><!--  1..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="State">  0..1 Extension  <!--  0..1 The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous -->
  <valueCodeableConcept><!--  1..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Frequency">  0..1 Extension  <!--  0..1 Allele frequency -->
  <valueDecimal value="[decimal]"/><!--  1..1 Value of extension -->
 </extension>
</extension>

JSON Template

{ // Allele
    "extension" : [ //  sliced by value:url  in the specified order, Open 
      { // Name of allele // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension
      },
      { // The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "State", // R! 
        "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension
      },
      { // Allele frequency // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Frequency", // R! 
        "valueDecimal" : <decimal> // C? R! Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele", // R! 
// value[x]: Value of extension. One of these 50:
  }

Summary

Name	Flags	Card.	Type	Description & Constraints
Allele		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele Allele: Allele information. Use on Element ID Observation
Name		0..1	CodeableConcept	An allele is one of a set of coexisting sequence variants of a gene (SO:0001023). This element is the common name for the allele. LOINC Code: (48008-7).
State		0..1	CodeableConcept	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).
Frequency		0..1	decimal	A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. LOINC Code: (81258-6).
Documentation for this format

Full Structure

Name	Flags	Card.	Type	Description & Constraints
extension		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele Allele: Allele information. Use on Element ID Observation
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
extension:Name		0..1	Extension	Name of allele
id		0..1	string	Unique id for inter-element referencing
extension		0..0
url		1..1	uri	"Name"
value[x]		1..1	CodeableConcept	Value of extension Binding: HLA (preferred): The nomenclature from European Bioinformatics Institute to name the genetic Allele
extension:State		0..1	Extension	The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
id		0..1	string	Unique id for inter-element referencing
extension		0..0
url		1..1	uri	"State"
value[x]		1..1	CodeableConcept	Value of extension
extension:Frequency		0..1	Extension	Allele frequency
id		0..1	string	Unique id for inter-element referencing
extension		0..0
url		1..1	uri	"Frequency"
value[x]		1..1	decimal	Value of extension
url		1..1	uri	"http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele"
value[x]		0..0
valueBase64Binary			base64Binary
valueBoolean			boolean
valueCanonical			canonical(Any)
valueCode			code
valueDate			date
valueDateTime			dateTime
valueDecimal			decimal
valueId			id
valueInstant			instant
valueInteger			integer
valueMarkdown			markdown
valueOid			oid
valuePositiveInt			positiveInt
valueString			string
valueTime			time
valueUnsignedInt			unsignedInt
valueUri			uri
valueUrl			url
valueUuid			uuid
valueAddress			Address
valueAge			Age
valueAnnotation			Annotation
valueAttachment			Attachment
valueCodeableConcept			CodeableConcept
valueCoding			Coding
valueContactPoint			ContactPoint
valueCount			Count
valueDistance			Distance
valueDuration			Duration
valueHumanName			HumanName
valueIdentifier			Identifier
valueMoney			Money
valuePeriod			Period
valueQuantity			Quantity
valueRange			Range
valueRatio			Ratio
valueReference			Reference(Any)
valueSampledData			SampledData
valueSignature			Signature
valueTiming			Timing
valueContactDetail			ContactDetail
valueContributor			Contributor
valueDataRequirement			DataRequirement
valueExpression			Expression
valueParameterDefinition			ParameterDefinition
valueRelatedArtifact			RelatedArtifact
valueTriggerDefinition			TriggerDefinition
valueUsageContext			UsageContext
valueDosage			Dosage
valueMeta			Meta
Documentation for this format

XML Template

<!-- Allele -->

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele" >
 <-- extension sliced by value:url  in the specified orderOpen-->
 <extension url="Name">  0..1 Extension  <!--  0..1 Name of allele -->
  <valueCodeableConcept><!--  1..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="State">  0..1 Extension  <!--  0..1 The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous -->
  <valueCodeableConcept><!--  1..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Frequency">  0..1 Extension  <!--  0..1 Allele frequency -->
  <valueDecimal value="[decimal]"/><!--  1..1 Value of extension -->
 </extension>
</extension>

JSON Template

{ // Allele
    "extension" : [ //  sliced by value:url  in the specified order, Open 
      { // Name of allele // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension
      },
      { // The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "State", // R! 
        "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension
      },
      { // Allele frequency // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Frequency", // R! 
        "valueDecimal" : <decimal> // C? R! Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele", // R! 
// value[x]: Value of extension. One of these 50:
  }

Constraints

• ele-1: All FHIR elements must have a @value or children unless an empty Parameters resource (xpath: @value|f:*|h:div|self::f:Parameters)
• ext-1: Must have either extensions or value[x], not both (xpath: exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')]))
• ele-1: On Extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.value[x]: All FHIR elements must have a @value or children (xpath on Extension.extension.value[x]: @value|f:*|h:div)
• ele-1: On Extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.value[x]: All FHIR elements must have a @value or children (xpath on Extension.extension.value[x]: @value|f:*|h:div)
• ele-1: On Extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.value[x]: All FHIR elements must have a @value or children (xpath on Extension.extension.value[x]: @value|f:*|h:div)
• ele-1: On Extension.value[x]: All FHIR elements must have a @value or children (xpath on Extension.value[x]: @value|f:*|h:div)