R4 Draft for Comment

This page is part of the FHIR Specification (v3.2.0: R4 Ballot 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: 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: 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: 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](http://www.sequenceontology.org/browser/current_svn/term/SO:0001237)). LOINC Code: ([48005-3](http://loinc.org/48005-3)).
... Type0..1CodeableConceptCodified type for associated Amino Acid Change. LOINC Code: ([48006-1](http://loinc.org/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: Observation
... extension 0..1ExtensionHGVS nomenclature for observed Amino Acid Change
.... url 1..1uri"Name"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
Binding: ???? (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 46:
  }

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange
AminoAcidChange: AminoAcidChange information.
Use on element: 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](http://www.sequenceontology.org/browser/current_svn/term/SO:0001237)). LOINC Code: ([48005-3](http://loinc.org/48005-3)).
... Type0..1CodeableConceptCodified type for associated Amino Acid Change. LOINC Code: ([48006-1](http://loinc.org/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: Observation
... extension 0..1ExtensionHGVS nomenclature for observed Amino Acid Change
.... url 1..1uri"Name"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
Binding: ???? (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 46:
  }

 

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')]))