R4 Ballot #1 (Mixed Normative/Trial use)

This page is part of the FHIR Specification (v3.3.0: R4 Ballot 2). 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: 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

usage info: insert a list of places where this extension is used

Extension Content

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..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 0..1ExtensionHGVS nomenclature for observed Amino Acid Change
.... url 1..1uri"Name"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
Binding: ClinVar (preferred)
... extension 0..1ExtensionAmino Acid Change Type
.... url 1..1uri"Type"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
... url 1..1uri"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"
... value[x] 0..0

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><!-- 0..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Type"> 0..1 Extension  <!-- 0..1 Amino Acid Change Type -->
  <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 //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      },
      { // Amino Acid Change Type //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Type", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange", // R! 
// value[x]: Value of extension. One of these 48:
  }

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..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 0..1ExtensionHGVS nomenclature for observed Amino Acid Change
.... url 1..1uri"Name"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
Binding: ClinVar (preferred)
... extension 0..1ExtensionAmino Acid Change Type
.... url 1..1uri"Type"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
... url 1..1uri"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"
... value[x] 0..0

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><!-- 0..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Type"> 0..1 Extension  <!-- 0..1 Amino Acid Change Type -->
  <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 //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      },
      { // Amino Acid Change Type //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Type", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange", // R! 
// value[x]: Value of extension. One of these 48:
  }

 

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')]))