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Extension: HGVS nomenclature for observed Amino Acid Change

(No assigned work group) Maturity Level: 0Context: 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

Extension Content

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1CodeableConceptURL = 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

doco Documentation for this format

Fulle Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = 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..1uri"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName"
... valueCodeableConcept 1..1CodeableConceptValue of extension
Binding: ???? (preferred)

doco Documentation for this format

XML Template

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

<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

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1CodeableConceptURL = 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

doco Documentation for this format

Full Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = 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..1uri"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName"
... valueCodeableConcept 1..1CodeableConceptValue of extension
Binding: ???? (preferred)

doco Documentation for this format

XML Template

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

<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')]))