R4 Ballot #1 (Mixed Normative/Trial use)

This 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

Extension: Allele

Orders and Observations Work Group Maturity Level: 1InformativeUse 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

usage info: insert a list of places where this extension is used

Extension Content

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele
Allele: Allele information.


Use on Element ID Observation
... Name0..1CodeableConceptAn 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).

... State0..1CodeableConceptThe 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).

... Frequency0..1decimalA 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

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele
Allele: Allele information.


Use on Element ID Observation
... extension 0..1ExtensionName of allele
.... url 1..1uri"Name"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
Binding: EMBL-EBI database of AlleleName (preferred)
... extension 0..1ExtensionThe level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
.... url 1..1uri"State"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
... extension 0..1ExtensionAllele frequency
.... url 1..1uri"Frequency"
.... valueDecimal 0..1decimalValue of extension
... url 1..1uri"http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele"
... value[x] 0..0

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-->
 <extension url="Name"> 0..1 Extension  <!-- 0..1 Name of allele -->
  <valueCodeableConcept><!-- 0..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><!-- 0..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Frequency"> 0..1 Extension  <!-- 0..1 Allele frequency -->
  <valueDecimal value="[decimal]"/><!-- 0..1 Value of extension -->
 </extension>
</extension>

JSON Template

{ // Allele
    "extension" : [ //  sliced by value:url  in the specified order, Open 
      { // Name of allele //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      },
      { // The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "State", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      },
      { // Allele frequency //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Frequency", // R! 
        "valueDecimal" : <decimal> //Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele", // R! 
// value[x]: Value of extension. One of these 48:
  }

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele
Allele: Allele information.


Use on Element ID Observation
... Name0..1CodeableConceptAn 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).

... State0..1CodeableConceptThe 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).

... Frequency0..1decimalA 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

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele
Allele: Allele information.


Use on Element ID Observation
... extension 0..1ExtensionName of allele
.... url 1..1uri"Name"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
Binding: EMBL-EBI database of AlleleName (preferred)
... extension 0..1ExtensionThe level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
.... url 1..1uri"State"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
... extension 0..1ExtensionAllele frequency
.... url 1..1uri"Frequency"
.... valueDecimal 0..1decimalValue of extension
... url 1..1uri"http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele"
... value[x] 0..0

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-->
 <extension url="Name"> 0..1 Extension  <!-- 0..1 Name of allele -->
  <valueCodeableConcept><!-- 0..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><!-- 0..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Frequency"> 0..1 Extension  <!-- 0..1 Allele frequency -->
  <valueDecimal value="[decimal]"/><!-- 0..1 Value of extension -->
 </extension>
</extension>

JSON Template

{ // Allele
    "extension" : [ //  sliced by value:url  in the specified order, Open 
      { // Name of allele //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      },
      { // The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "State", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      },
      { // Allele frequency //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Frequency", // R! 
        "valueDecimal" : <decimal> //Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele", // R! 
// value[x]: Value of extension. One of these 48:
  }

 

Constraints

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