FHIR Release 3 (STU) R4 Ballot #2 (Mixed Normative/Trial use)

This page is part of the FHIR Specification (v3.0.2: STU 3). (v3.5.0: 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 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)

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: Element ID Observation

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

Extension Content

Summary

Name Flags Card. Type Description & Constraints doco
. . extension Gene 0..1 CodeableConcept URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
Gene: 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](http://www.sequenceontology.org/browser/current_svn/term/SO:0000704)). ( SO:0000704 ). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ([HGNC](http://www.genenames.org)). ( HGNC ). LOINC Code: ([48018-6](http://loinc.org/48018-6)). ( 48018-6 ).


Binding: ???? H g n c ( preferred )
Use on element: 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: 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](http://www.sequenceontology.org/browser/current_svn/term/SO:0000704)). ( SO:0000704 ). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ([HGNC](http://www.genenames.org)). ( HGNC ). LOINC Code: ([48018-6](http://loinc.org/48018-6)). ( 48018-6 ).


Use on element: Element ID Observation
. . . extension 0..0
. . . url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsGene" "http://hl7.org/fhir/StructureDefinition/observation-geneticsGene"
. . . valueCodeableConcept 0..1 CodeableConcept Value of extension
Binding: ???? H g n c ( preferred )

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><!-- 0..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 } //Value of extension

  }

Summary

Name Flags Card. Type Description & Constraints doco
. . extension Gene 0..1 CodeableConcept URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
Gene: 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](http://www.sequenceontology.org/browser/current_svn/term/SO:0000704)). ( SO:0000704 ). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ([HGNC](http://www.genenames.org)). ( HGNC ). LOINC Code: ([48018-6](http://loinc.org/48018-6)). ( 48018-6 ).


Binding: ???? H g n c ( preferred )
Use on element: 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: 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](http://www.sequenceontology.org/browser/current_svn/term/SO:0000704)). ( SO:0000704 ). This element is the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name ([HGNC](http://www.genenames.org)). ( HGNC ). LOINC Code: ([48018-6](http://loinc.org/48018-6)). ( 48018-6 ).


Use on element: Element ID Observation
. . . extension 0..0
. . . url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsGene" "http://hl7.org/fhir/StructureDefinition/observation-geneticsGene"
. . . valueCodeableConcept 0..1 CodeableConcept Value of extension
Binding: ???? H g n c ( preferred )

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><!-- 0..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 } //Value of extension

  }

 

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')]) )