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 R3

Extension: Gene

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

URL for this extension: 


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

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

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. A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions ( SO:0000704 ). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ( HGNC ). LOINC Code: ( 48018-6 ).

Comment :

Other systems or genes not defined in HGNC (e.g., BCR-ABL fusion gene) can be added by using a local extension.

Context of Use: Use on Element ID Observation

Extension Content

Summary

Name Flags Card. Type Description & Constraints doco
. . Gene 0..1 CodeableConcept URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
Gene: 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. A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions ( SO:0000704 ). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ( HGNC ). LOINC Code: ( 48018-6 ).


Binding: H g n c HGNC ( preferred ) ): Gene Identifiers Reference


Use on Element ID Observation

doco Documentation for this format

Full Structure

Name Flags Card. Type Description & Constraints doco
. . extension 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
Gene: 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. A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions ( SO:0000704 ). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ( HGNC ). LOINC Code: ( 48018-6 ).


Use on Element ID Observation
. . . extension I 0..0
. . . url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsGene"
. . . value[x] I 1..1 CodeableConcept Value of extension
Binding: H g n c HGNC ( preferred ) ): Gene Identifiers Reference


doco Documentation for this format

XML Template 

<!-- Gene -->doco

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsGene" >
  <!-- from Element: extension -->
 <</valueCodeableConcept>

 <valueCodeableConcept><!-- ?? 1..1 CodeableConcept Value of extension --></valueCodeableConcept>

</extension>

JSON Template 

{ // Gene
  // from Element: extension
    "extension" : [ //  sliced by value:url  in the specified order, Open ]
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsGene", // R! 
    "

    "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension

  }

Summary

Name Flags Card. Type Description & Constraints doco
. . Gene 0..1 CodeableConcept URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
Gene: 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. A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions ( SO:0000704 ). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ( HGNC ). LOINC Code: ( 48018-6 ).


Binding: H g n c HGNC ( preferred ) ): Gene Identifiers Reference


Use on Element ID Observation

doco Documentation for this format

Full Structure

Name Flags Card. Type Description & Constraints doco
. . extension 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
Gene: 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. A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions ( SO:0000704 ). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ( HGNC ). LOINC Code: ( 48018-6 ).


Use on Element ID Observation
. . . extension I 0..0
. . . url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsGene"
. . . value[x] I 1..1 CodeableConcept Value of extension
Binding: H g n c HGNC ( preferred ) ): Gene Identifiers Reference


doco Documentation for this format

XML Template 

<!-- Gene -->doco

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsGene" >
  <!-- from Element: extension -->
 <</valueCodeableConcept>

 <valueCodeableConcept><!-- ?? 1..1 CodeableConcept Value of extension --></valueCodeableConcept>

</extension>

JSON Template 

{ // Gene
  // from Element: extension
    "extension" : [ //  sliced by value:url  in the specified order, Open ]
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsGene", // R! 
    "

    "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension

  }

 

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.value[x]: All FHIR elements must have a @value or children (xpath on Extension.value[x]: @value|f:*|h:div )