FHIR Genomics Implementation Guide

Notice

Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.

Extension: Alternate Reference

Usage

A generic extension used to replicate the changes within R5 to support adding a reference to image or data source(DocumentReference).

Note:

Reference to DocumentReference resources pointing to the Genomic Data Files used as the basis for the report. Usage of this field over extension:supporting-info is pending further investigation.

Context of Use

DiagnosticReport

Tree View

AlternateReference (Extension)	C		Extension	Element id Extension Short description Alternative reference (target type is wrong) Definition Used when the target of the reference has a type that is not allowed by the definition of the element. In general, this should only arise when wrangling between versions using cross-version extensions. Comments Given that a reference SHALL have a display or reference, using this extension implies that there's a display present. Data type Extension Conditions The cardinality or value of this element may be affected by these constraints: ele-1 Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
id		0..1	string	There are no (further) constraints on this element Element id Extension.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	C	0..0	Extension	There are no (further) constraints on this element Element id Extension.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Slicing Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Conditions The cardinality or value of this element may be affected by these constraints: ele-1 Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
url		1..1	uriFixed Value	Element id Extension.url Short description identifies the meaning of the extension Definition Source of the definition for the extension code - a logical name or a URL. Comments The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension. Data type uri Fixed value http://hl7.org/fhir/StructureDefinition/alternate-reference Mappings rim: N/A
value[x]		1..1		There are no (further) constraints on this element Element id Extension.value[x] Short description Value of extension Definition Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). Conditions The cardinality or value of this element may be affected by these constraints: ele-1 Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
valueReference			Reference(Resource)	Data type Reference(Resource)

Detailed Descriptions

Extension		C
Short	Alternative reference (target type is wrong)
Definition	Used when the target of the reference has a type that is not allowed by the definition of the element. In general, this should only arise when wrangling between versions using cross-version extensions.
Cardinality	0..1
Comments	Given that a reference SHALL have a display or reference, using this extension implies that there's a display present.
Conditions	The cardinality or value of this element may be affected by these constraints: ele-1
Constraints	ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()`
Mappings	rim: n/a rim: N/A
Extension.id
Short	Unique id for inter-element referencing
Definition	Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Cardinality	0..1
Type	string
Mappings	rim: n/a
Extension.extension		C
Short	Additional content defined by implementations
Definition	May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
Cardinality	0..0
Type	Extension
Alias	extensions, user content
Comments	There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
Slicing	Unordered, Open, by url(Value) Extensions are always sliced by (at least) url
Conditions	The cardinality or value of this element may be affected by these constraints: ele-1
Constraints	ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()`
Mappings	rim: n/a rim: N/A
Extension.url
Short	identifies the meaning of the extension
Definition	Source of the definition for the extension code - a logical name or a URL.
Cardinality	1..1
Type	uri
Comments	The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
Fixed Value	http://hl7.org/fhir/StructureDefinition/alternate-reference
Mappings	rim: N/A
Extension.value[x]
Short	Value of extension
Definition	Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).
Cardinality	1..1
Type	Reference(Resource)
Conditions	The cardinality or value of this element may be affected by these constraints: ele-1
Constraints	ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())`
Mappings	rim: n/a rim: N/A

Table View

Extension		0..1
Extension.id	string	0..1
Extension.extension	Extension	0..0
Extension.url	uri	1..1
Extension.value[x]	Reference(Resource)	1..1

XML View

</extension>

</extension>

</extension>

</extension>

</identifier>

</telecom>

</contact>

</coding>

</jurisdiction>

<identity value="rim" />
<uri value="http://hl7.org/v3" />
<name value="RIM Mapping" />

</mapping>

</context>

</extension>

<path value="Extension" />
<short value="Alternative reference (target type is wrong)" />
<definition value="Used when the target of the reference has a type that is not allowed by the definition of the element. In general, this should only arise when wrangling between versions using cross-version extensions." />
<comment value="Given that a reference SHALL have a display or reference, using this extension implies that there's a display present." />
<min value="0" />
<max value="1" />
<base>
<path value="Extension" />
<min value="0" />
<max value="*" />
</base>
<condition value="ele-1" />
<constraint>
<key value="ele-1" />
<severity value="error" />
<human value="All FHIR elements must have a @value or children" />
<expression value="hasValue() or (children().count() > id.count())" />
<xpath value="@value|f:*|h:div" />
<source value="http://hl7.org/fhir/StructureDefinition/Element" />
</constraint>
<constraint>
<key value="ext-1" />
<severity value="error" />
<human value="Must have either extensions or value[x], not both" />
<expression value="extension.exists() != value.exists()" />
<xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" />
<source value="http://hl7.org/fhir/StructureDefinition/Extension" />
</constraint>
<isModifier value="false" />

</element>

<path value="Extension.id" />
<representation value="xmlAttr" />
<short value="Unique id for inter-element referencing" />
<definition value="Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces." />
<min value="0" />
<max value="1" />
<base>
<path value="Element.id" />
<min value="0" />
<max value="1" />
</base>
<type>
<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type">
<valueUrl value="string" />
</extension>
<code value="http://hl7.org/fhirpath/System.String" />
</type>
<isModifier value="false" />
<isSummary value="false" />
<mapping>
<identity value="rim" />
<map value="n/a" />
</mapping>

</element>

</discriminator>

</slicing>

<base>

<path value="Element.extension" />
<min value="0" />
<max value="*" />

</base>

<type>

</type>

<key value="ele-1" />
<severity value="error" />
<human value="All FHIR elements must have a @value or children" />
<expression value="hasValue() or (children().count() > id.count())" />
<xpath value="@value|f:*|h:div" />
<source value="http://hl7.org/fhir/StructureDefinition/Element" />

</constraint>

<key value="ext-1" />
<severity value="error" />
<human value="Must have either extensions or value[x], not both" />
<expression value="extension.exists() != value.exists()" />
<xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])" />
<source value="http://hl7.org/fhir/StructureDefinition/Extension" />

</constraint>

</element>

<path value="Extension.url" />
<representation value="xmlAttr" />
<short value="identifies the meaning of the extension" />
<definition value="Source of the definition for the extension code - a logical name or a URL." />
<comment value="The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension." />
<min value="1" />
<max value="1" />
<base>
<path value="Extension.url" />
<min value="1" />
<max value="1" />
</base>
<type>
<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type">
<valueUrl value="uri" />
</extension>
<code value="http://hl7.org/fhirpath/System.String" />
</type>
<fixedUri value="http://hl7.org/fhir/StructureDefinition/alternate-reference" />
<isModifier value="false" />
<isSummary value="false" />
<mapping>
<identity value="rim" />
<map value="N/A" />
</mapping>

</element>

<base>

<path value="Extension.value[x]" />
<min value="0" />
<max value="1" />

</base>

<type>

</type>

<key value="ele-1" />
<severity value="error" />
<human value="All FHIR elements must have a @value or children" />
<expression value="hasValue() or (children().count() > id.count())" />
<xpath value="@value|f:*|h:div" />
<source value="http://hl7.org/fhir/StructureDefinition/Element" />

</constraint>

</mapping>

</element>

</snapshot>

<path value="Extension" />
<short value="Alternative reference (target type is wrong)" />
<definition value="Used when the target of the reference has a type that is not allowed by the definition of the element. In general, this should only arise when wrangling between versions using cross-version extensions." />
<comment value="Given that a reference SHALL have a display or reference, using this extension implies that there's a display present." />
<min value="0" />
<max value="1" />

</element>

</element>

</element>

<type>

</type>

</element>

</differential>

</StructureDefinition>

JSON View

{

"resourceType": "StructureDefinition",

"id": "alternate-reference",

"extension": [

{

"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",

"valueCode": "fhir"

{

"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",

"valueInteger": 2

{

"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",

"valueCode": "trial-use"

{

"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-type-characteristics",

"valueCode": "can-bind"

}

"url": "http://hl7.org/fhir/StructureDefinition/alternate-reference",

"identifier": [

{

"system": "urn:ietf:rfc:3986",

"value": "urn:oid:2.16.840.1.113883.4.642.5.1662"

}

"version": "5.3.0-ballot-tc1",

"name": "AlternateReference",

"title": "Alternate Reference",

"status": "active",

"experimental": false,

"date": "2014-04-27",

"publisher": "HL7 International / FHIR Infrastructure",

"contact": [

{

"telecom": [

{

"system": "url",

"value": "http://www.hl7.org/Special/committees/fiwg"

}

]

}

"description": "Used when the target of the reference has a type that is not allowed by the definition of the element. In general, this should only arise when wrangling between versions using cross-version extensions.",

"jurisdiction": [

{

"coding": [

{

"system": "http://unstats.un.org/unsd/methods/m49/m49.htm",

"code": "001"

}

]

}

"fhirVersion": "4.0.1",

"mapping": [

{

"identity": "rim",
"uri": "http://hl7.org/v3",
"name": "RIM Mapping"

}

"kind": "complex-type",

"abstract": false,

"context": [

{

"type": "element",

"expression": "Reference"

}

"type": "Extension",

"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension",

"derivation": "constraint",

"snapshot": {

"extension": [

{

"url": "http://hl7.org/fhir/tools/StructureDefinition/snapshot-base-version",

"valueString": "4.0.1"

}

"element": [

{

"id": "Extension",
"path": "Extension",
"short": "Alternative reference (target type is wrong)",
"definition": "Used when the target of the reference has a type that is not allowed by the definition of the element. In general, this should only arise when wrangling between versions using cross-version extensions.",
"comment": "Given that a reference SHALL have a display or reference, using this extension implies that there's a display present.",
"min": 0,
"max": "1",
"base": {
"path": "Extension",
"min": 0,
"max": "*"
},
"condition": [
"ele-1"
],
"constraint": [
{
"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"
},
{
"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension"
}
],
"isModifier": false

{

"id": "Extension.id",

"path": "Extension.id",

"representation": [

"xmlAttr"

"short": "Unique id for inter-element referencing",

"definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",

"min": 0,

"max": "1",

"base": {

"path": "Element.id",
"min": 0,
"max": "1"

"type": [

{

"extension": [

{

"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",

"valueUrl": "string"

}

"code": "http://hl7.org/fhirpath/System.String"

}

"isModifier": false,

"isSummary": false,

"mapping": [

{

"identity": "rim",

"map": "n/a"

}

]

{

"id": "Extension.extension",

"path": "Extension.extension",

"slicing": {

"discriminator": [

{

"type": "value",

"path": "url"

}

"description": "Extensions are always sliced by (at least) url",

"rules": "open"

"short": "Extension",

"definition": "An Extension",

"min": 0,

"max": "0",

"base": {

"path": "Element.extension",
"min": 0,
"max": "*"

"type": [

{

"code": "Extension"

}

"constraint": [

{

"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"

{

"key": "ext-1",
"severity": "error",
"human": "Must have either extensions or value[x], not both",
"expression": "extension.exists() != value.exists()",
"xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
"source": "http://hl7.org/fhir/StructureDefinition/Extension"

}

"isModifier": false,

"isSummary": false

{

"id": "Extension.url",
"path": "Extension.url",
"representation": [
"xmlAttr"
],
"short": "identifies the meaning of the extension",
"definition": "Source of the definition for the extension code - a logical name or a URL.",
"comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
"min": 1,
"max": "1",
"base": {
"path": "Extension.url",
"min": 1,
"max": "1"
},
"type": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
"valueUrl": "uri"
}
],
"code": "http://hl7.org/fhirpath/System.String"
}
],
"fixedUri": "http://hl7.org/fhir/StructureDefinition/alternate-reference",
"isModifier": false,
"isSummary": false,
"mapping": [
{
"identity": "rim",
"map": "N/A"
}
]

{

"id": "Extension.value[x]",

"path": "Extension.value[x]",

"short": "Value of extension",

"definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list).",

"min": 1,

"max": "1",

"base": {

"path": "Extension.value[x]",
"min": 0,
"max": "1"

"type": [

{

"code": "Reference",

"targetProfile": [

"http://hl7.org/fhir/StructureDefinition/Resource"

]

}

"constraint": [

{

"key": "ele-1",
"severity": "error",
"human": "All FHIR elements must have a @value or children",
"expression": "hasValue() or (children().count() > id.count())",
"xpath": "@value|f:*|h:div",
"source": "http://hl7.org/fhir/StructureDefinition/Element"

}

"isModifier": false,

"isSummary": false,

"mapping": [

{

"identity": "rim",

"map": "N/A"

}

]

}

]

"differential": {

"element": [

{

"id": "Extension",
"path": "Extension",
"short": "Alternative reference (target type is wrong)",
"definition": "Used when the target of the reference has a type that is not allowed by the definition of the element. In general, this should only arise when wrangling between versions using cross-version extensions.",
"comment": "Given that a reference SHALL have a display or reference, using this extension implies that there's a display present.",
"min": 0,
"max": "1"

{

"id": "Extension.extension",
"path": "Extension.extension",
"max": "0"

{

"id": "Extension.url",
"path": "Extension.url",
"fixedUri": "http://hl7.org/fhir/StructureDefinition/alternate-reference"

{

"id": "Extension.value[x]",
"path": "Extension.value[x]",
"min": 1,
"type": [
{
"code": "Reference",
"targetProfile": [
"http://hl7.org/fhir/StructureDefinition/Resource"
]
}
]

}

]

}

Example-Extension-GenomicTest-ParticipantCount

Notice

Extension: Alternate Reference

Usage

Note:

Tree View

Detailed Descriptions

Table View

XML View

JSON View

Propose a change to