Current Build

Extension: AminoAcidChange

Orders and Observations Work Group Maturity Level: 1InformativeUse Context: Any

URL for this extension:

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

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

AminoAcidChange information.

Context of Use: Use on Element ID Observation

Extension Content

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. AminoAcidChange0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange
AminoAcidChange: AminoAcidChange information.


Use on Element ID Observation
... Name0..1CodeableConceptHuman Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference sequence ID used for HGVS naming must be annotated. An amino acid is a sequence feature that corresponds to a single amino acid residue in a polypeptide (SO:0001237). LOINC Code: (48005-3).

... Type0..1CodeableConceptCodified type for associated Amino Acid Change. LOINC Code: (48006-1).


doco Documentation for this format

Full Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange
AminoAcidChange: AminoAcidChange information.


Use on Element ID Observation
... extension I0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... extension:Name I0..1ExtensionHGVS nomenclature for observed Amino Acid Change
.... extension I0..0
.... url 1..1url"Name"
.... value[x] I0..1(Slice Definition)Value of extension
Slice: Unordered, Closed by type:$this
..... value[x]:valueCodeableConcept I0..1CodeableConceptValue of extension
Binding: Clin var (preferred)
... extension:Type I0..1ExtensionAmino Acid Change Type
.... extension I0..0
.... url 1..1url"Type"
.... value[x] I0..1(Slice Definition)Value of extension
Slice: Unordered, Closed by type:$this
..... value[x]:valueCodeableConcept I0..1CodeableConceptValue of extension
... url 1..1url"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"
... value[x] I0..0
.... valueBase64Binarybase64Binary
.... valueBooleanboolean
.... valueCanonicalcanonical()
.... valueCodecode
.... valueDatedate
.... valueDateTimedateTime
.... valueDecimaldecimal
.... valueIdid
.... valueInstantinstant
.... valueIntegerinteger
.... valueMarkdownmarkdown
.... valueOidoid
.... valuePositiveIntpositiveInt
.... valueStringstring
.... valueTimetime
.... valueUnsignedIntunsignedInt
.... valueUriuri
.... valueUrlurl
.... valueUuiduuid
.... valueAddressAddress
.... valueAgeAge
.... valueAnnotationAnnotation
.... valueAttachmentAttachment
.... valueCodeableConceptCodeableConcept
.... valueCodingCoding
.... valueContactPointContactPoint
.... valueCountCount
.... valueDistanceDistance
.... valueDurationDuration
.... valueHumanNameHumanName
.... valueIdentifierIdentifier
.... valueMoneyMoney
.... valuePeriodPeriod
.... valueQuantityQuantity
.... valueRangeRange
.... valueRatioRatio
.... valueReferenceReference()
.... valueSampledDataSampledData
.... valueSignatureSignature
.... valueTimingTiming
.... valueContactDetailContactDetail
.... valueContributorContributor
.... valueDataRequirementDataRequirement
.... valueExpressionExpression
.... valueParameterDefinitionParameterDefinition
.... valueRelatedArtifactRelatedArtifact
.... valueTriggerDefinitionTriggerDefinition
.... valueUsageContextUsageContext
.... valueDosageDosage
.... valueMetaMeta

doco Documentation for this format

XML Template

<!-- AminoAcidChange -->doco

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange" >
 <-- extension sliced by value:url  in the specified orderOpen-->
 <extension url="Name"> ?? 0..1 Extension  <!-- ?? 0..1 HGVS nomenclature for observed Amino Acid Change -->
  <-- valueCodeableConcept sliced by type:$this  in the specified orderClosed-->
  <valueCodeableConcept><!-- ?? 0..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Type"> ?? 0..1 Extension  <!-- ?? 0..1 Amino Acid Change Type -->
  <-- valueCodeableConcept sliced by type:$this  in the specified orderClosed-->
  <valueCodeableConcept><!-- ?? 0..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
</extension>

JSON Template

{ // AminoAcidChange
    "extension" : [ //  sliced by value:url  in the specified order, Open 
      { // HGVS nomenclature for observed Amino Acid Change // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : [ //  sliced by type:$this  in the specified order, Closed ]
        "valueCodeableConcept" : { CodeableConcept } // C?Value of extension
      },
      { // Amino Acid Change Type // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Type", // R! 
        "valueCodeableConcept" : [ //  sliced by type:$this  in the specified order, Closed ]
        "valueCodeableConcept" : { CodeableConcept } // C?Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange", // R! 
// value[x]: Value of extension. One of these 50:
  }

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. AminoAcidChange0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange
AminoAcidChange: AminoAcidChange information.


Use on Element ID Observation
... Name0..1CodeableConceptHuman Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference sequence ID used for HGVS naming must be annotated. An amino acid is a sequence feature that corresponds to a single amino acid residue in a polypeptide (SO:0001237). LOINC Code: (48005-3).

... Type0..1CodeableConceptCodified type for associated Amino Acid Change. LOINC Code: (48006-1).


doco Documentation for this format

Full Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange
AminoAcidChange: AminoAcidChange information.


Use on Element ID Observation
... extension I0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... extension:Name I0..1ExtensionHGVS nomenclature for observed Amino Acid Change
.... extension I0..0
.... url 1..1url"Name"
.... value[x] I0..1(Slice Definition)Value of extension
Slice: Unordered, Closed by type:$this
..... value[x]:valueCodeableConcept I0..1CodeableConceptValue of extension
Binding: Clin var (preferred)
... extension:Type I0..1ExtensionAmino Acid Change Type
.... extension I0..0
.... url 1..1url"Type"
.... value[x] I0..1(Slice Definition)Value of extension
Slice: Unordered, Closed by type:$this
..... value[x]:valueCodeableConcept I0..1CodeableConceptValue of extension
... url 1..1url"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"
... value[x] I0..0
.... valueBase64Binarybase64Binary
.... valueBooleanboolean
.... valueCanonicalcanonical()
.... valueCodecode
.... valueDatedate
.... valueDateTimedateTime
.... valueDecimaldecimal
.... valueIdid
.... valueInstantinstant
.... valueIntegerinteger
.... valueMarkdownmarkdown
.... valueOidoid
.... valuePositiveIntpositiveInt
.... valueStringstring
.... valueTimetime
.... valueUnsignedIntunsignedInt
.... valueUriuri
.... valueUrlurl
.... valueUuiduuid
.... valueAddressAddress
.... valueAgeAge
.... valueAnnotationAnnotation
.... valueAttachmentAttachment
.... valueCodeableConceptCodeableConcept
.... valueCodingCoding
.... valueContactPointContactPoint
.... valueCountCount
.... valueDistanceDistance
.... valueDurationDuration
.... valueHumanNameHumanName
.... valueIdentifierIdentifier
.... valueMoneyMoney
.... valuePeriodPeriod
.... valueQuantityQuantity
.... valueRangeRange
.... valueRatioRatio
.... valueReferenceReference()
.... valueSampledDataSampledData
.... valueSignatureSignature
.... valueTimingTiming
.... valueContactDetailContactDetail
.... valueContributorContributor
.... valueDataRequirementDataRequirement
.... valueExpressionExpression
.... valueParameterDefinitionParameterDefinition
.... valueRelatedArtifactRelatedArtifact
.... valueTriggerDefinitionTriggerDefinition
.... valueUsageContextUsageContext
.... valueDosageDosage
.... valueMetaMeta

doco Documentation for this format

XML Template

<!-- AminoAcidChange -->doco

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange" >
 <-- extension sliced by value:url  in the specified orderOpen-->
 <extension url="Name"> ?? 0..1 Extension  <!-- ?? 0..1 HGVS nomenclature for observed Amino Acid Change -->
  <-- valueCodeableConcept sliced by type:$this  in the specified orderClosed-->
  <valueCodeableConcept><!-- ?? 0..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Type"> ?? 0..1 Extension  <!-- ?? 0..1 Amino Acid Change Type -->
  <-- valueCodeableConcept sliced by type:$this  in the specified orderClosed-->
  <valueCodeableConcept><!-- ?? 0..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
</extension>

JSON Template

{ // AminoAcidChange
    "extension" : [ //  sliced by value:url  in the specified order, Open 
      { // HGVS nomenclature for observed Amino Acid Change // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : [ //  sliced by type:$this  in the specified order, Closed ]
        "valueCodeableConcept" : { CodeableConcept } // C?Value of extension
      },
      { // Amino Acid Change Type // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Type", // R! 
        "valueCodeableConcept" : [ //  sliced by type:$this  in the specified order, Closed ]
        "valueCodeableConcept" : { CodeableConcept } // C?Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange", // 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.value[x]: All FHIR elements must have a @value or children (xpath on Extension.value[x]: @value|f:*|h:div)