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Extension: AminoAcidChange

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
• Full Structure
• XML
• JSON
• All

Summary

Name	Flags	Card.	Type	Description & Constraints
AminoAcidChange		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange AminoAcidChange: AminoAcidChange information. Use on Element ID Observation
Name		0..1	CodeableConcept	Human 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).
Type		0..1	CodeableConcept	Codified type for associated Amino Acid Change. LOINC Code: (48006-1).
Documentation for this format

Full Structure

Name	Flags	Card.	Type	Description & Constraints
extension		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange AminoAcidChange: AminoAcidChange information. Use on Element ID Observation
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
extension:Name		0..1	Extension	HGVS nomenclature for observed Amino Acid Change
id		0..1	string	Unique id for inter-element referencing
extension		0..0
url		1..1	uri	"Name"
value[x]		1..1	CodeableConcept	Value of extension Binding: ClinVar (preferred): NCBI central repository for curating pathogenicity of potentially clinically relevant variants
extension:Type		0..1	Extension	Amino Acid Change Type
id		0..1	string	Unique id for inter-element referencing
extension		0..0
url		1..1	uri	"Type"
value[x]		1..1	CodeableConcept	Value of extension
url		1..1	uri	"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"
value[x]		0..0
valueBase64Binary			base64Binary
valueBoolean			boolean
valueCanonical			canonical(Any)
valueCode			code
valueDate			date
valueDateTime			dateTime
valueDecimal			decimal
valueId			id
valueInstant			instant
valueInteger			integer
valueMarkdown			markdown
valueOid			oid
valuePositiveInt			positiveInt
valueString			string
valueTime			time
valueUnsignedInt			unsignedInt
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(Any)
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
Documentation for this format

XML Template

<!-- AminoAcidChange -->

<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><!--  1..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Type">  0..1 Extension  <!--  0..1 Amino Acid Change Type -->
  <valueCodeableConcept><!--  1..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" : { CodeableConcept } // C? R! 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" : { CodeableConcept } // C? R! Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange", // R! 
// value[x]: Value of extension. One of these 50:
  }

Summary

Name	Flags	Card.	Type	Description & Constraints
AminoAcidChange		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange AminoAcidChange: AminoAcidChange information. Use on Element ID Observation
Name		0..1	CodeableConcept	Human 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).
Type		0..1	CodeableConcept	Codified type for associated Amino Acid Change. LOINC Code: (48006-1).
Documentation for this format

Full Structure

Name	Flags	Card.	Type	Description & Constraints
extension		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange AminoAcidChange: AminoAcidChange information. Use on Element ID Observation
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
extension:Name		0..1	Extension	HGVS nomenclature for observed Amino Acid Change
id		0..1	string	Unique id for inter-element referencing
extension		0..0
url		1..1	uri	"Name"
value[x]		1..1	CodeableConcept	Value of extension Binding: ClinVar (preferred): NCBI central repository for curating pathogenicity of potentially clinically relevant variants
extension:Type		0..1	Extension	Amino Acid Change Type
id		0..1	string	Unique id for inter-element referencing
extension		0..0
url		1..1	uri	"Type"
value[x]		1..1	CodeableConcept	Value of extension
url		1..1	uri	"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"
value[x]		0..0
valueBase64Binary			base64Binary
valueBoolean			boolean
valueCanonical			canonical(Any)
valueCode			code
valueDate			date
valueDateTime			dateTime
valueDecimal			decimal
valueId			id
valueInstant			instant
valueInteger			integer
valueMarkdown			markdown
valueOid			oid
valuePositiveInt			positiveInt
valueString			string
valueTime			time
valueUnsignedInt			unsignedInt
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(Any)
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
Documentation for this format

XML Template

<!-- AminoAcidChange -->

<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><!--  1..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Type">  0..1 Extension  <!--  0..1 Amino Acid Change Type -->
  <valueCodeableConcept><!--  1..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" : { CodeableConcept } // C? R! 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" : { CodeableConcept } // C? R! 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 unless an empty Parameters resource (xpath: @value|f:*|h:div|self::f:Parameters)
• 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: 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.value[x]: All FHIR elements must have a @value or children (xpath on Extension.value[x]: @value|f:*|h:div)