Release 4 5 Preview #1

This page is part of the FHIR Specification (v4.0.1: R4 - Mixed Normative and STU ) in it's permanent home (it will always be available at this URL). (v4.2.0: R5 Preview #1). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions . Page versions: R4B R4

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 Flags Card. Type Description & Constraints doco
. . 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 ).


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-geneticsAminoAcidChange
AminoAcidChange: AminoAcidChange information.


Use on Element ID Observation
. . . extension I 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
. . . extension:Name I 0..1 Extension HGVS nomenclature for observed Amino Acid Change
. . . . id 0..1 string Unique id for inter-element referencing
.... extension I 0..0
. . . . url 1..1 uri "Name"
. . . . value[x] I 1..1 CodeableConcept Value of extension
Binding: Clin var ( preferred )
. . . extension:Type I 0..1 Extension Amino Acid Change Type
. . . . id 0..1 string Unique id for inter-element referencing
. . . . extension I 0..0
. . . . url 1..1 uri "Type"
. . . . value[x] I 1..1 CodeableConcept Value of extension
. . . value[x] I 0 .. 0
. . . . valueBase64Binary base64Binary
. . . . valueBoolean boolean
. . . . valueCanonical canonical () (Any)
. . . . valueCode code
. . . . valueDate date
. . . . valueDateTime dateTime
. . . . valueDecimal decimal
. . . . valueId id
. . . . valueInstant instant
. . . . valueInteger integer
. . . . valueMarkdown valueInteger64 markdown integer64
. . . . valueOid valueMarkdown oid markdown
. . . . valuePositiveInt valueOid positiveInt oid
. . . . valueString valuePositiveInt string positiveInt
. . . . valueTime valueString time string
. . . . valueUnsignedInt valueTime unsignedInt time
. . . . valueUri valueUnsignedInt uri unsignedInt
. . . . valueUrl valueUri url uri
. . . . valueUuid valueUrl uuid url
. . . valueAddress . valueUuid Address uuid
. . . . valueAge valueAddress Age Address
. . . . valueAnnotation valueAge Annotation Age
. . . . valueAttachment valueAnnotation Attachment Annotation
. . . . valueCodeableConcept valueAttachment CodeableConcept Attachment
. . . . valueCoding valueCodeableConcept Coding CodeableConcept
. . . . valueContactPoint valueCoding ContactPoint Coding
. . . . valueCount valueContactPoint Count ContactPoint
. . . . valueDistance valueCount Distance Count
. . . . valueDuration valueDistance Duration Distance
. . . . valueHumanName valueDuration HumanName Duration
. . . . valueIdentifier valueHumanName Identifier HumanName
. . . . valueMoney valueIdentifier Money Identifier
. . . . valuePeriod valueMoney Period Money
. . . . valueQuantity valuePeriod Quantity Period
. . . . valueRange valueQuantity Range Quantity
. . . . valueRatio valueRange Ratio Range
. . . valueReference . valueRatio Reference Ratio ()
. . . valueSampledData . valueReference SampledData Reference (Any)
. . . . valueSignature valueSampledData Signature SampledData
. . . . valueTiming valueSignature Timing Signature
. . . . valueContactDetail valueTiming ContactDetail Timing
. . . . valueContributor valueContactDetail Contributor ContactDetail
. . . . valueDataRequirement valueContributor DataRequirement Contributor
. . . . valueExpression valueDataRequirement Expression DataRequirement
. . . . valueParameterDefinition valueExpression ParameterDefinition Expression
. . . . valueRelatedArtifact valueParameterDefinition RelatedArtifact ParameterDefinition
. . . . valueTriggerDefinition valueRelatedArtifact TriggerDefinition RelatedArtifact
. . . . valueUsageContext valueTriggerDefinition UsageContext TriggerDefinition
. . . . valueDosage valueUsageContext Dosage UsageContext
. . . . valueMeta valueDosage Dosage
.... valueMeta Meta

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>

  <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 Flags Card. Type Description & Constraints doco
. . 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 ).


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-geneticsAminoAcidChange
AminoAcidChange: AminoAcidChange information.


Use on Element ID Observation
. . . extension I 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
. . . extension:Name I 0..1 Extension HGVS nomenclature for observed Amino Acid Change
. . . . id 0..1 string Unique id for inter-element referencing
.... extension I 0..0
. . . . url 1..1 uri "Name"
. . . . value[x] I 1..1 CodeableConcept Value of extension
Binding: Clin var ( preferred )
. . . extension:Type I 0..1 Extension Amino Acid Change Type
. . . . id 0..1 string Unique id for inter-element referencing
. . . . extension I 0..0
. . . . url 1..1 uri "Type"
. . . . value[x] I 1..1 CodeableConcept Value of extension
. . . value[x] I 0 .. 0
. . . . valueBase64Binary base64Binary
. . . . valueBoolean boolean
. . . . valueCanonical canonical () (Any)
. . . . valueCode code
. . . . valueDate date
. . . . valueDateTime dateTime
. . . . valueDecimal decimal
. . . . valueId id
. . . . valueInstant instant
. . . . valueInteger integer
. . . . valueMarkdown valueInteger64 markdown integer64
. . . . valueOid valueMarkdown oid markdown
. . . . valuePositiveInt valueOid positiveInt oid
. . . . valueString valuePositiveInt string positiveInt
. . . . valueTime valueString time string
. . . . valueUnsignedInt valueTime unsignedInt time
. . . . valueUri valueUnsignedInt uri unsignedInt
. . . . valueUrl valueUri url uri
. . . . valueUuid valueUrl uuid url
. . . valueAddress . valueUuid Address uuid
. . . . valueAge valueAddress Age Address
. . . . valueAnnotation valueAge Annotation Age
. . . . valueAttachment valueAnnotation Attachment Annotation
. . . . valueCodeableConcept valueAttachment CodeableConcept Attachment
. . . . valueCoding valueCodeableConcept Coding CodeableConcept
. . . . valueContactPoint valueCoding ContactPoint Coding
. . . . valueCount valueContactPoint Count ContactPoint
. . . . valueDistance valueCount Distance Count
. . . . valueDuration valueDistance Duration Distance
. . . . valueHumanName valueDuration HumanName Duration
. . . . valueIdentifier valueHumanName Identifier HumanName
. . . . valueMoney valueIdentifier Money Identifier
. . . . valuePeriod valueMoney Period Money
. . . . valueQuantity valuePeriod Quantity Period
. . . . valueRange valueQuantity Range Quantity
. . . . valueRatio valueRange Ratio Range
. . . valueReference . valueRatio Reference Ratio ()
. . . valueSampledData . valueReference SampledData Reference (Any)
. . . . valueSignature valueSampledData Signature SampledData
. . . . valueTiming valueSignature Timing Signature
. . . . valueContactDetail valueTiming ContactDetail Timing
. . . . valueContributor valueContactDetail Contributor ContactDetail
. . . . valueDataRequirement valueContributor DataRequirement Contributor
. . . . valueExpression valueDataRequirement Expression DataRequirement
. . . . valueParameterDefinition valueExpression ParameterDefinition Expression
. . . . valueRelatedArtifact valueParameterDefinition RelatedArtifact ParameterDefinition
. . . . valueTriggerDefinition valueRelatedArtifact TriggerDefinition RelatedArtifact
. . . . valueUsageContext valueTriggerDefinition UsageContext TriggerDefinition
. . . . valueDosage valueUsageContext Dosage UsageContext
. . . . valueMeta valueDosage Dosage
.... valueMeta Meta

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>

  <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 (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: 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 )