Connectathon 11 Snapshot

This page is part of the FHIR Specification (v1.2.0: 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: PredictedAminoAcidChange

URL for this extension: 

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

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

HGVS nomenclature for predicted amino acid change.

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..*ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation
PredictedAminoAcidChange: HGVS nomenclature for predicted amino acid change.
Use on element: Observation
... HGVS0..1CodeableConceptProtein variant following HGVS nomenclature on the given ProteinReferenceSequenceId.
... referenceSeq0..1CodeableConceptReference identifier for protein transcript, with version, from NCBI's RefSeq or ENSEMBL.
... predictionModel0..1CodeableConceptPrediction model used for amino acid change.

doco Documentation for this format

Fulle Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..*ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation
PredictedAminoAcidChange: HGVS nomenclature for predicted amino acid change.
Use on element: Observation
... extension 0..1ExtensionHGVSAminoAcidVariation
.... extension 0..0
.... url 1..1uri"HGVS"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
... extension 0..1ExtensionProteinReference SequenceId
.... extension 0..0
.... url 1..1uri"referenceSeq"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
... extension 0..1ExtensionPredictionModel
.... extension 0..0
.... url 1..1uri"predictionModel"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
... url 1..1uri"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation"
... value[x] 0..0

doco Documentation for this format

XML Template

<!-- PredictedAminoAcidChange -->doco

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation" >
 <-- extension sliced by url  in the specified orderOpen-->
 <extension url="HGVS"> 0..1 Extension  <!-- 0..1 HGVSAminoAcidVariation -->
  <valueCodeableConcept><!-- 1..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="referenceSeq"> 0..1 Extension  <!-- 0..1 ProteinReference SequenceId -->
  <valueCodeableConcept><!-- 1..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="predictionModel"> 0..1 Extension  <!-- 0..1 PredictionModel -->
  <valueCodeableConcept><!-- 1..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
</extension>

JSON Template

{ // PredictedAminoAcidChange
    "extension" : [ //  sliced by url  in the specified orderOpen
      { // HGVSAminoAcidVariation //
        // from Element: extension
        "url" : "HGVS", // R! 
        "valueCodeableConcept" : { CodeableConcept } // R! Value of extension
      },
      { // ProteinReference SequenceId //
        // from Element: extension
        "url" : "referenceSeq", // R! 
        "valueCodeableConcept" : { CodeableConcept } // R! Value of extension
      },
      { // PredictionModel //
        // from Element: extension
        "url" : "predictionModel", // R! 
        "valueCodeableConcept" : { CodeableConcept } // R! Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation", // R! 
// value[x]: Value of extension. One of these 33:
  }

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..*ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation
PredictedAminoAcidChange: HGVS nomenclature for predicted amino acid change.
Use on element: Observation
... HGVS0..1CodeableConceptProtein variant following HGVS nomenclature on the given ProteinReferenceSequenceId.
... referenceSeq0..1CodeableConceptReference identifier for protein transcript, with version, from NCBI's RefSeq or ENSEMBL.
... predictionModel0..1CodeableConceptPrediction model used for amino acid change.

doco Documentation for this format

Full Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..*ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation
PredictedAminoAcidChange: HGVS nomenclature for predicted amino acid change.
Use on element: Observation
... extension 0..1ExtensionHGVSAminoAcidVariation
.... extension 0..0
.... url 1..1uri"HGVS"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
... extension 0..1ExtensionProteinReference SequenceId
.... extension 0..0
.... url 1..1uri"referenceSeq"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
... extension 0..1ExtensionPredictionModel
.... extension 0..0
.... url 1..1uri"predictionModel"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
... url 1..1uri"http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation"
... value[x] 0..0

doco Documentation for this format

XML Template

<!-- PredictedAminoAcidChange -->doco

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation" >
 <-- extension sliced by url  in the specified orderOpen-->
 <extension url="HGVS"> 0..1 Extension  <!-- 0..1 HGVSAminoAcidVariation -->
  <valueCodeableConcept><!-- 1..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="referenceSeq"> 0..1 Extension  <!-- 0..1 ProteinReference SequenceId -->
  <valueCodeableConcept><!-- 1..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="predictionModel"> 0..1 Extension  <!-- 0..1 PredictionModel -->
  <valueCodeableConcept><!-- 1..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
</extension>

JSON Template

{ // PredictedAminoAcidChange
    "extension" : [ //  sliced by url  in the specified orderOpen
      { // HGVSAminoAcidVariation //
        // from Element: extension
        "url" : "HGVS", // R! 
        "valueCodeableConcept" : { CodeableConcept } // R! Value of extension
      },
      { // ProteinReference SequenceId //
        // from Element: extension
        "url" : "referenceSeq", // R! 
        "valueCodeableConcept" : { CodeableConcept } // R! Value of extension
      },
      { // PredictionModel //
        // from Element: extension
        "url" : "predictionModel", // R! 
        "valueCodeableConcept" : { CodeableConcept } // R! Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation", // R! 
// value[x]: Value of extension. One of these 33:
  }