Release 4 4B

This page is part of the FHIR Specification (v4.0.1: R4 (v4.3.0: R4B - Mixed Normative and STU ) in it's permanent home (it will always be available at this URL). ). 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 R4B R4

Extension: Allele

Orders and Observations Work Group   Maturity Level : 1 Informative Use Context : Any

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

Name Flags Card. Type Description & Constraints doco
. . Allele 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele
Allele: Allele information.


Use on Element ID Observation
. . . Name 0..1 CodeableConcept The material on this page will be removed in a future release. This content is deprecated and SHOULD NOT be used. Implementers are instead directed to the ( Genomics Reporting Implementation Guide ) for guidance. 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 ).


doco Documentation for this format

Full Structure

I I I I
Name Flags Card. Type Description & Constraints doco
. . extension 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele
Allele: Allele information.


Use on Element ID Observation
. . . Slices for extension I 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
. . . extension:Name I 0..1 Extension Name of allele
. . . extension . id I 0..0 0..1 id Unique id for inter-element referencing
.... extension 0..0
. . . . url 1..1 uri "Name"
. . . . value[x] 1..1 CodeableConcept Value of extension
Binding: H l a 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 id Unique id for inter-element referencing
. . . . extension I 0..0
. . . . url 1..1 uri "State"
. . . . value[x] I 1..1 CodeableConcept Value of extension
. . . extension . id I 0..0 0..1 id 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
. . . . valueBase64Binary valueBoolean base64Binary boolean
. . . valueBoolean . valueCanonical boolean canonical (Any)
. . . valueCanonical . valueCode canonical code ()
. . . . valueCode valueDate code date
. . . . valueDate valueDateTime date dateTime
. . . . valueDateTime valueDecimal dateTime decimal
. . . . valueDecimal valueId decimal id
. . . . valueId valueInstant id instant
. . . . valueInstant valueInteger instant integer
. . . . valueInteger valueMarkdown integer markdown
. . . . valueMarkdown valueOid markdown oid
. . . . valueOid valuePositiveInt oid positiveInt
. . . . valuePositiveInt valueString positiveInt string
. . . . valueString valueTime string time
. . . . valueTime valueUnsignedInt time unsignedInt
. . . . valueUnsignedInt valueUri unsignedInt uri
. . . . valueUri valueUrl uri url
. . . . valueUrl valueUuid url uuid
. . . valueUuid . valueAddress uuid Address
. . . . valueAddress valueAge Address Age
. . . . valueAge valueAnnotation Age Annotation
. . . . valueAnnotation valueAttachment Annotation Attachment
. . . . valueAttachment valueCodeableConcept Attachment CodeableConcept
. . . . valueCodeableConcept valueCodeableReference CodeableConcept CodeableReference
. . . . 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 . valueRatioRange Reference RatioRange ()
. . . valueSampledData . valueReference SampledData Reference (Any)
. . . . valueSignature valueSampledData Signature SampledData
. . . . valueTiming valueSignature Timing Signature
. . . . valueContactDetail valueTiming ContactDetail Timing
. . . . valueContributor valueContactDetail Contributor ContactDetail
. . . . valueDataRequirement valueContributor DataRequirement Contributor
. . . . valueExpression valueDataRequirement Expression DataRequirement
. . . . valueParameterDefinition valueExpression ParameterDefinition Expression
. . . . valueRelatedArtifact valueParameterDefinition RelatedArtifact ParameterDefinition
. . . . valueTriggerDefinition valueRelatedArtifact TriggerDefinition RelatedArtifact
. . . . valueUsageContext valueTriggerDefinition UsageContext TriggerDefinition
. . . . valueDosage valueUsageContext Dosage UsageContext
. . . . valueMeta valueDosage Meta Dosage

doco Documentation for this format

XML Template 

<!-- Allele -->doco

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele" >
 <-- extension sliced by value:url  in the specified orderOpen-->
 <
  <</valueCodeableConcept>

 <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 51:
  }

Summary

Name Flags Card. Type Description & Constraints doco
. . Allele 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele
Allele: Allele information.


Use on Element ID Observation
. . . Name 0..1 CodeableConcept The material on this page will be removed in a future release. This content is deprecated and SHOULD NOT be used. Implementers are instead directed to the ( Genomics Reporting Implementation Guide ) for guidance. 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 ).


doco Documentation for this format

Full Structure

I I I I
Name Flags Card. Type Description & Constraints doco
. . extension 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele
Allele: Allele information.


Use on Element ID Observation
. . . Slices for extension I 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
. . . extension:Name I 0..1 Extension Name of allele
. . . extension . id I 0..0 0..1 id Unique id for inter-element referencing
.... extension 0..0
. . . . url 1..1 uri "Name"
. . . . value[x] 1..1 CodeableConcept Value of extension
Binding: H l a 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 id Unique id for inter-element referencing
. . . . extension I 0..0
. . . . url 1..1 uri "State"
. . . . value[x] I 1..1 CodeableConcept Value of extension
. . . extension . id I 0..0 0..1 id 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
. . . . valueBase64Binary valueBoolean base64Binary boolean
. . . valueBoolean . valueCanonical boolean canonical (Any)
. . . valueCanonical . valueCode canonical code ()
. . . . valueCode valueDate code date
. . . . valueDate valueDateTime date dateTime
. . . . valueDateTime valueDecimal dateTime decimal
. . . . valueDecimal valueId decimal id
. . . . valueId valueInstant id instant
. . . . valueInstant valueInteger instant integer
. . . . valueInteger valueMarkdown integer markdown
. . . . valueMarkdown valueOid markdown oid
. . . . valueOid valuePositiveInt oid positiveInt
. . . . valuePositiveInt valueString positiveInt string
. . . . valueString valueTime string time
. . . . valueTime valueUnsignedInt time unsignedInt
. . . . valueUnsignedInt valueUri unsignedInt uri
. . . . valueUri valueUrl uri url
. . . . valueUrl valueUuid url uuid
. . . valueUuid . valueAddress uuid Address
. . . . valueAddress valueAge Address Age
. . . . valueAge valueAnnotation Age Annotation
. . . . valueAnnotation valueAttachment Annotation Attachment
. . . . valueAttachment valueCodeableConcept Attachment CodeableConcept
. . . . valueCodeableConcept valueCodeableReference CodeableConcept CodeableReference
. . . . 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 . valueRatioRange Reference RatioRange ()
. . . valueSampledData . valueReference SampledData Reference (Any)
. . . . valueSignature valueSampledData Signature SampledData
. . . . valueTiming valueSignature Timing Signature
. . . . valueContactDetail valueTiming ContactDetail Timing
. . . . valueContributor valueContactDetail Contributor ContactDetail
. . . . valueDataRequirement valueContributor DataRequirement Contributor
. . . . valueExpression valueDataRequirement Expression DataRequirement
. . . . valueParameterDefinition valueExpression ParameterDefinition Expression
. . . . valueRelatedArtifact valueParameterDefinition RelatedArtifact ParameterDefinition
. . . . valueTriggerDefinition valueRelatedArtifact TriggerDefinition RelatedArtifact
. . . . valueUsageContext valueTriggerDefinition UsageContext TriggerDefinition
. . . . valueDosage valueUsageContext Dosage UsageContext
. . . . valueMeta valueDosage Meta Dosage

doco Documentation for this format

XML Template 

<!-- Allele -->doco

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele" >
 <-- extension sliced by value:url  in the specified orderOpen-->
 <
  <</valueCodeableConcept>

 <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 51:
  }

 

Constraints

  • ele-1 : All FHIR elements must have a @value or children unless an empty Parameters resource (xpath: @value|f:*|h:div @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 )