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Extension: Variant

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

URL for this extension:


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

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

Variant information.

Context of Use: Use on 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 Variant 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.


Use on Element ID Observation
. . . Name 0..1 CodeableConcept Human Genome Variation Society (HGVS) nomenclature for a single or set of DNA Sequence Variation(s) identified in testing. The use of the nomenclature is also used to describe non-variations (aka. wild types). LOINC Code: ( 48004-6 ).

. . . Id 0..1 CodeableConcept Identifier for DNA sequence variant. If a germline variant, ClinVar or dbSNP identifier should be used. If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC) LOINC Code: ( 48003-8 ).

. . . Type 0..1 CodeableConcept Codified type for associated DNA sequence variant. DNA sequence variants use the HGVS notation, which implies the DNA sequence variant type. LOINC Code: ( 48019-4 ).


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-geneticsVariant
Variant: Variant information.


Use on Element ID Observation
. . . extension I 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
. . extension . extension:Name I 0..1 Extension HGVS nomenclature for observed DNA sequence variant
. . . . extension I 0..0
. . . . url 1..1 uri url "Name"
. . . valueCodeableConcept . value[x] I 0 .. 1 (Slice Definition) Value of extension
Slice: Unordered, Closed by type:$this
..... value[x]:valueCodeableConcept I 0..1 CodeableConcept Value of extension
Binding: ClinVar Clin var ( preferred )
. . extension . extension:Id I 0..1 Extension DNA sequence variant ID
. . . url . extension I 0..0
. . . . url 1..1 uri url "Id"
. . . valueCodeableConcept . value[x] I 0..1 0 .. 1 (Slice Definition) Value of extension
Slice: Unordered, Closed by type:$this
..... value[x]:valueCodeableConcept I 0..1 CodeableConcept Value of extension
. . extension . extension:Type I 0..1 Extension DNA sequence variant type
. . . . extension I 0..0
. . . . url 1..1 uri url "Type"
. . . valueCodeableConcept . value[x] I 0 .. 1 (Slice Definition) Value of extension
Slice: Unordered, Closed by type:$this
..... value[x]:valueCodeableConcept I 0..1 CodeableConcept Value of extension
. . . url 1..1 uri url "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"
. . . value[x] I 0 .. 0
. . . . valueBase64Binary base64Binary
.... valueBoolean boolean
.... valueCanonical canonical ()
.... valueCode code
.... valueDate date
.... valueDateTime dateTime
.... valueDecimal decimal
.... valueId id
.... valueInstant instant
.... valueInteger integer
.... valueMarkdown markdown
.... valueOid oid
.... 0)"> valuePositiveInt style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> href=datatypes.html#positiveInt> positiveInt style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy>
.... valueString string
.... valueTime time
.... = 0)"> valueUnsignedInt style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> href=datatypes.html#unsignedInt> unsignedInt style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy>
.... valueUri uri
.... valueUrl url
.... valueUuid uuid
.... valueAddress Address
.... valueAge Age
.... valueAnnotation Annotation
.... valueAttachment Attachment
.... valueCodeableConcept CodeableConcept
.... valueCoding Coding
.... valueContactPoint ContactPoint
.... valueCount Count
.... valueDistance Distance
.... valueDuration Duration
.... valueHumanName HumanName
.... valueIdentifier Identifier
.... valueMoney Money
.... valuePeriod Period
.... valueQuantity Quantity
.... valueRange Range
.... valueRatio Ratio
.... valueReference Reference ()
.... valueSampledData SampledData
.... valueSignature Signature
.... valueTiming Timing
.... valueContactDetail ContactDetail
.... valueContributor Contributor
.... valueDataRequirement DataRequirement
.... valueExpression Expression
.... valueParameterDefinition ParameterDefinition
.... valueRelatedArtifact RelatedArtifact
.... valueTriggerDefinition TriggerDefinition
.... valueUsageContext UsageContext
.... valueDosage Dosage
.... valueMeta Meta

doco Documentation for this format

XML Template

<!-- Variant -->doco
<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant" >
 <-- extension sliced by value:url  in the specified orderOpen-->
 <
  <</valueCodeableConcept>

 <extension url="Name"> ?? 0..1 Extension  <!-- ?? 0..1 HGVS nomenclature for observed DNA sequence variant -->
  <-- valueCodeableConcept sliced by type:$this  in the specified orderClosed-->
  <valueCodeableConcept><!-- ?? 0..1 CodeableConcept Value of extension --></valueCodeableConcept>

 </extension>
 <
  <

 <extension url="Id"> ?? 0..1 Extension  <!-- ?? 0..1 DNA sequence variant ID -->
  <-- valueCodeableConcept sliced by type:$this  in the specified orderClosed-->
  <valueCodeableConcept><!-- ?? 0..1 CodeableConcept 

      Value of extension --></valueCodeableConcept>
 </extension>
 <
  <

 <extension url="Type"> ?? 0..1 Extension  <!-- ?? 0..1 DNA sequence variant type -->
  <-- valueCodeableConcept sliced by type:$this  in the specified orderClosed-->
  <valueCodeableConcept><!-- ?? 0..1 CodeableConcept 

      Value of extension --></valueCodeableConcept>
 </extension>
</extension>

JSON Template

{ // Variant
    "extension" : [ //  sliced by value:url  in the specified order, Open 
      { // 

      { // HGVS nomenclature for observed DNA sequence variant // C?

        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "

        "valueCodeableConcept" : [ //  sliced by type:$this  in the specified order, Closed ]
        "valueCodeableConcept" : { CodeableConcept } // C?Value of extension

      },
      { // 

      { // DNA sequence variant ID // C?

        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Id", // R! 
        "

        "valueCodeableConcept" : [ //  sliced by type:$this  in the specified order, Closed ]
        "valueCodeableConcept" : { CodeableConcept } // C?Value of extension

      },
      { // 

      { // DNA sequence variant type // C?

        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Type", // R! 
        "

        "valueCodeableConcept" : [ //  sliced by type:$this  in the specified order, Closed ]
        "valueCodeableConcept" : { CodeableConcept } // C?Value of extension

      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant", // R! 
// value[x]: Value of extension. One of these 50:
  }

Summary

Name Flags Card. Type Description & Constraints doco
. . extension Variant 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.


Use on Element ID Observation
. . . Name 0..1 CodeableConcept Human Genome Variation Society (HGVS) nomenclature for a single or set of DNA Sequence Variation(s) identified in testing. The use of the nomenclature is also used to describe non-variations (aka. wild types). LOINC Code: ( 48004-6 ).

. . . Id 0..1 CodeableConcept Identifier for DNA sequence variant. If a germline variant, ClinVar or dbSNP identifier should be used. If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC) LOINC Code: ( 48003-8 ).

. . . Type 0..1 CodeableConcept Codified type for associated DNA sequence variant. DNA sequence variants use the HGVS notation, which implies the DNA sequence variant type. LOINC Code: ( 48019-4 ).


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-geneticsVariant
Variant: Variant information.


Use on Element ID Observation
. . . extension I 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
. . extension . extension:Name I 0..1 Extension HGVS nomenclature for observed DNA sequence variant
. . . . extension I 0..0
. . . . url 1..1 uri url "Name"
. . . valueCodeableConcept . value[x] I 0 .. 1 (Slice Definition) Value of extension
Slice: Unordered, Closed by type:$this
..... value[x]:valueCodeableConcept I 0..1 CodeableConcept Value of extension
Binding: ClinVar Clin var ( preferred )
. . extension . extension:Id I 0..1 Extension DNA sequence variant ID
. . . url . extension I 1..1 0..0 uri
. . . . url 1..1 url "Id"
. . . valueCodeableConcept . value[x] I 0..1 0 .. 1 (Slice Definition) Value of extension
Slice: Unordered, Closed by type:$this
..... value[x]:valueCodeableConcept I 0..1 CodeableConcept Value of extension
. . extension . extension:Type I 0..1 Extension DNA sequence variant type
. . . . extension I 0..0
. . . . url 1..1 uri url "Type"
. . . valueCodeableConcept . value[x] I 0 .. 1 (Slice Definition) Value of extension
Slice: Unordered, Closed by type:$this
..... value[x]:valueCodeableConcept I 0..1 CodeableConcept Value of extension
. . . url 1..1 uri url "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"
. . . value[x] I 0 .. 0
. . . . valueBase64Binary base64Binary
.... valueBoolean boolean
.... valueCanonical canonical ()
.... valueCode code
.... valueDate date
.... valueDateTime dateTime
.... valueDecimal decimal
.... valueId id
.... valueInstant instant
.... valueInteger integer
.... valueMarkdown markdown
.... valueOid oid
.... 0)"> valuePositiveInt style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> href=datatypes.html#positiveInt> positiveInt style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy>
.... valueString string
.... valueTime time
.... = 0)"> valueUnsignedInt style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy> href=datatypes.html#unsignedInt> unsignedInt style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class=hierarchy>
.... valueUri uri
.... valueUrl url
.... valueUuid uuid
.... valueAddress Address
.... valueAge Age
.... valueAnnotation Annotation
.... valueAttachment Attachment
.... valueCodeableConcept CodeableConcept
.... valueCoding Coding
.... valueContactPoint ContactPoint
.... valueCount Count
.... valueDistance Distance
.... valueDuration Duration
.... valueHumanName HumanName
.... valueIdentifier Identifier
.... valueMoney Money
.... valuePeriod Period
.... valueQuantity Quantity
.... valueRange Range
.... valueRatio Ratio
.... valueReference Reference ()
.... valueSampledData SampledData
.... valueSignature Signature
.... valueTiming Timing
.... valueContactDetail ContactDetail
.... valueContributor Contributor
.... valueDataRequirement DataRequirement
.... valueExpression Expression
.... valueParameterDefinition ParameterDefinition
.... valueRelatedArtifact RelatedArtifact
.... valueTriggerDefinition TriggerDefinition
.... valueUsageContext UsageContext
.... valueDosage Dosage
.... valueMeta Meta

doco Documentation for this format

XML Template

<!-- Variant -->doco
<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant" >
 <-- extension sliced by value:url  in the specified orderOpen-->
 <
  <</valueCodeableConcept>

 <extension url="Name"> ?? 0..1 Extension  <!-- ?? 0..1 HGVS nomenclature for observed DNA sequence variant -->
  <-- valueCodeableConcept sliced by type:$this  in the specified orderClosed-->
  <valueCodeableConcept><!-- ?? 0..1 CodeableConcept Value of extension --></valueCodeableConcept>

 </extension>
 <
  <

 <extension url="Id"> ?? 0..1 Extension  <!-- ?? 0..1 DNA sequence variant ID -->
  <-- valueCodeableConcept sliced by type:$this  in the specified orderClosed-->
  <valueCodeableConcept><!-- ?? 0..1 CodeableConcept 

      Value of extension --></valueCodeableConcept>
 </extension>
 <
  <

 <extension url="Type"> ?? 0..1 Extension  <!-- ?? 0..1 DNA sequence variant type -->
  <-- valueCodeableConcept sliced by type:$this  in the specified orderClosed-->
  <valueCodeableConcept><!-- ?? 0..1 CodeableConcept 

      Value of extension --></valueCodeableConcept>
 </extension>
</extension>

JSON Template

{ // Variant
    "extension" : [ //  sliced by value:url  in the specified order, Open 
      { // 

      { // HGVS nomenclature for observed DNA sequence variant // C?

        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "

        "valueCodeableConcept" : [ //  sliced by type:$this  in the specified order, Closed ]
        "valueCodeableConcept" : { CodeableConcept } // C?Value of extension

      },
      { // 

      { // DNA sequence variant ID // C?

        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Id", // R! 
        "

        "valueCodeableConcept" : [ //  sliced by type:$this  in the specified order, Closed ]
        "valueCodeableConcept" : { CodeableConcept } // C?Value of extension

      },
      { // 

      { // DNA sequence variant type // C?

        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Type", // R! 
        "

        "valueCodeableConcept" : [ //  sliced by type:$this  in the specified order, Closed ]
        "valueCodeableConcept" : { CodeableConcept } // C?Value of extension

      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant", // R! 
// value[x]: Value of extension. One of these 50:
  }

 

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