Release 5 Preview #1

This page is part of the FHIR Specification (v4.2.0: R5 Preview #1). 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 ID Observation

Summary

Name	Flags	Card.	Type	Description & Constraints
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). 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 (preferred) Use on Element ID Observation
Documentation for this format

Full Structure

Name	Flags	Card.	Type	Description & Constraints
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). 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 (preferred)
Documentation for this format

XML Template

<!-- Gene -->

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsGene" >
  <!-- from Element: extension -->
 <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
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). 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 (preferred) Use on Element ID Observation
Documentation for this format

Full Structure

Name	Flags	Card.	Type	Description & Constraints
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). 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 (preferred)
Documentation for this format

XML Template

<!-- Gene -->

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