FHIR Extensions Pack
5.2.0-ballot - 5.2.0 Ballot - September 2024) International flag

FHIR Extensions Pack, published by HL7 International / FHIR Infrastructure. This guide is not an authorized publication; it is the continuous build for version 5.2.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/fhir-extensions/ and changes regularly. See the Directory of published versions

Extension: Amino Acid Change

Official URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange Version: 5.2.0-ballot
Standards status: Deprecated Maturity Level: 1 Responsible: HL7 International / Orders and Observations Computable Name: AminoAcidChange

AminoAcidChange information.

Context of Use

This extension may be used on the following element(s):

Usage info

Usage:

  • This Extension is not used by any profiles in this Implementation Guide

Changes since version 1.0.0:

  • New Content
  • Formal Views of Extension Content

    Description of Profiles, Differentials, Snapshots, and how the XML and JSON presentations work.

    This structure is derived from Extension

    Summary

    Complex Extension: AminoAcidChange information.

    • Name: 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: CodeableConcept: Codified type for associated Amino Acid Change. LOINC Code: (48006-1).

    Maturity: 1

    This structure is derived from Extension

    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension AminoAcidChange
    ... Slices for extension Content/Rules for all slices
    .... extension:Name 0..1 Extension HGVS nomenclature for observed Amino Acid Change
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description (No ValueSet): (example): NCBI central repository of potentially clinically relevant variants.

    .... extension:Type 0..1 Extension Amino Acid Change Type
    ..... 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

    doco Documentation for this format
    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension AminoAcidChange
    ... id 0..1 id Unique id for inter-element referencing
    ... 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 Description (No ValueSet): (example): NCBI central repository 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"

    doco Documentation for this format

    This structure is derived from Extension

    Summary

    Complex Extension: AminoAcidChange information.

    • Name: 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: CodeableConcept: Codified type for associated Amino Acid Change. LOINC Code: (48006-1).

    Maturity: 1

    Differential View

    This structure is derived from Extension

    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension AminoAcidChange
    ... Slices for extension Content/Rules for all slices
    .... extension:Name 0..1 Extension HGVS nomenclature for observed Amino Acid Change
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description (No ValueSet): (example): NCBI central repository of potentially clinically relevant variants.

    .... extension:Type 0..1 Extension Amino Acid Change Type
    ..... 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

    doco Documentation for this format

    Snapshot View

    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension AminoAcidChange
    ... id 0..1 id Unique id for inter-element referencing
    ... 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 Description (No ValueSet): (example): NCBI central repository 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"

    doco Documentation for this format

     

    Other representations of profile: CSV, Excel, Schematron

    Terminology Bindings

    PathConformanceValueSetURI
    Extension.extension:Name.value[x]example

    Constraints

    IdGradePath(s)DetailsRequirements
    ele-1error**ALL** elementsAll FHIR elements must have a @value or children
    : hasValue() or (children().count() > id.count())
    ext-1error**ALL** extensionsMust have either extensions or value[x], not both
    : extension.exists() != value.exists()

    Search Parameters for this Extension

    (none found)