STU3 Candidate

This page is part of the FHIR Specification (v1.8.0: STU 3 Draft). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions

Extension: HGVS nomenclature for observed Amino Acid Change

(No assigned work group)

Maturity Level : 0

Context: Any

URL for this extension:


http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName

Status: draft. Extension maintained by: Health Level Seven International (Clinical Genomics)

Human Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference sequence ID used for HGVS naming must be anotated. An amino acid is a sequence feature that corresponds to a single amino acid residue in a polypeptide ( SO:0001237 ). LONIC Code: ( 48005-3 ).

Context of Use: Use on element: Observation

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

Summary

Name	Flags	Card.	Type	Description & Constraints
extension		0..1	CodeableConcept	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName HGVS nomenclature for observed Amino Acid Change: Human Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference sequence ID used for HGVS naming must be anotated. 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)). LONIC Code: ([48005-3](http://loinc.org/48005-3)). Use on element: Observation
Documentation for this format

Fulle Structure

Name	Card.	Type	Description & Constraints
extension	0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName HGVS nomenclature for observed Amino Acid Change: Human Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference sequence ID used for HGVS naming must be anotated. 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)). LONIC Code: ([48005-3](http://loinc.org/48005-3)). Use on element: Observation
extension	0 .. 0
url	1..1	uri	"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName"
valueCodeableConcept	1..1	CodeableConcept	Value of extension Binding: ???? ( preferred )
Documentation for this format

XML Template

<!-- HGVS nomenclature for observed Amino Acid Change -->

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName" >
  <!-- from Element: extension -->
 <valueCodeableConcept><!-- 1..1 CodeableConcept Value of extension --></valueCodeableConcept>
</extension>

JSON Template

{ // HGVS nomenclature for observed Amino Acid Change
  // from Element: extension
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName", // R! 
    "valueCodeableConcept" : { CodeableConcept } // R! Value of extension
  }

Summary

Name	Flags	Card.	Type	Description & Constraints
extension		0..1	CodeableConcept	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName HGVS nomenclature for observed Amino Acid Change: Human Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference sequence ID used for HGVS naming must be anotated. 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)). LONIC Code: ([48005-3](http://loinc.org/48005-3)). Use on element: Observation
Documentation for this format

Full Structure

Name	Card.	Type	Description & Constraints
extension	0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName HGVS nomenclature for observed Amino Acid Change: Human Genome Variation Society (HGVS) nomenclature for an amino acid change. Reference sequence ID used for HGVS naming must be anotated. 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)). LONIC Code: ([48005-3](http://loinc.org/48005-3)). Use on element: Observation
extension	0 .. 0
url	1..1	uri	"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName"
valueCodeableConcept	1..1	CodeableConcept	Value of extension Binding: ???? ( preferred )
Documentation for this format

XML Template

<!-- HGVS nomenclature for observed Amino Acid Change -->

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName" >
  <!-- from Element: extension -->
 <valueCodeableConcept><!-- 1..1 CodeableConcept Value of extension --></valueCodeableConcept>
</extension>

JSON Template

{ // HGVS nomenclature for observed Amino Acid Change
  // from Element: extension
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName", // R! 
    "valueCodeableConcept" : { CodeableConcept } // R! Value of extension
  }

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')]) )