Release 4B

Extension: AminoAcidChange

Orders and Observations Work Group

Maturity Level: 1

Informative

Use 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

Name	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	The material on this page will be removed in a future release. This content is deprecated and SHOULD NOT be used. Implementers are instead directed to the (Genomics Reporting Implementation Guide) for guidance. 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	Card.	Type	Description & Constraints
extension	0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange AminoAcidChange: AminoAcidChange information. Use on Element ID Observation
Slices for 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	id	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	id	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
valueCodeableReference		CodeableReference
valueCoding		Coding
valueContactPoint		ContactPoint
valueCount		Count
valueDistance		Distance
valueDuration		Duration
valueHumanName		HumanName
valueIdentifier		Identifier
valueMoney		Money
valuePeriod		Period
valueQuantity		Quantity
valueRange		Range
valueRatio		Ratio
valueRatioRange		RatioRange
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
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 51:
  }

Summary

Name	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	The material on this page will be removed in a future release. This content is deprecated and SHOULD NOT be used. Implementers are instead directed to the (Genomics Reporting Implementation Guide) for guidance. 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	Card.	Type	Description & Constraints
extension	0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange AminoAcidChange: AminoAcidChange information. Use on Element ID Observation
Slices for 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	id	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	id	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
valueCodeableReference		CodeableReference
valueCoding		Coding
valueContactPoint		ContactPoint
valueCount		Count
valueDistance		Distance
valueDuration		Duration
valueHumanName		HumanName
valueIdentifier		Identifier
valueMoney		Money
valuePeriod		Period
valueQuantity		Quantity
valueRange		Range
valueRatio		Ratio
valueRatioRange		RatioRange
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
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 51:
  }

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)