Release 4

This page is part of the FHIR Specification (v4.0.1: R4 - Mixed Normative and STU) in it's permanent home (it will always be available at this URL). 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-observation-geneticsaminoacidchange.json

Orders and Observations Work GroupMaturity Level: N/AStandards Status: Informative

Raw JSON (canonical form + also see JSON Format Specification)

AminoAcidChange

{
  "resourceType" : "StructureDefinition",
  "id" : "observation-geneticsAminoAcidChange",
  "extension" : [{
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
    "valueCode" : "oo"
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
    "valueInteger" : 1
  }],
  "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange",
  "version" : "4.0.1",
  "name" : "AminoAcidChange",
  "status" : "draft",
  "date" : "2016-03-14",
  "publisher" : "Health Level Seven International (Clinical Genomics)",
  "contact" : [{
    "telecom" : [{
      "system" : "url",
      "value" : "http://www.hl7.org/Special/committees/clingenomics"
    }]
  }],
  "description" : "AminoAcidChange information.",
  "fhirVersion" : "4.0.1",
  "mapping" : [{
    "identity" : "v2",
    "uri" : "http://hl7.org/v2",
    "name" : "HL7 v2 Mapping"
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    "uri" : "http://hl7.org/v3",
    "name" : "RIM Mapping"
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  "kind" : "complex-type",
  "abstract" : false,
  "context" : [{
    "type" : "element",
    "expression" : "Observation"
  }],
  "type" : "Extension",
  "baseDefinition" : "http://hl7.org/fhir/StructureDefinition/Extension",
  "derivation" : "constraint",
  "snapshot" : {
    "element" : [{
      "id" : "Extension",
      "path" : "Extension",
      "short" : "AminoAcidChange",
      "definition" : "AminoAcidChange information.",
      "min" : 0,
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        "description" : "Extensions are always sliced by (at least) url",
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      "short" : "Additional content defined by implementations",
      "definition" : "May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance  applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.",
      "comment" : "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions.  The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.",
      "alias" : ["extensions",
      "user content"],
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        "path" : "Element.extension",
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    },
    {
      "id" : "Extension.extension:Name",
      "path" : "Extension.extension",
      "sliceName" : "Name",
      "short" : "HGVS nomenclature for observed Amino Acid Change",
      "definition" : "Human 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)).",
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        "source" : "http://hl7.org/fhir/StructureDefinition/Element"
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      {
        "key" : "ext-1",
        "severity" : "error",
        "human" : "Must have either extensions or value[x], not both",
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      "short" : "Unique id for inter-element referencing",
      "definition" : "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
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          "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
          "valueUrl" : "string"
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        "identity" : "rim",
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    },
    {
      "id" : "Extension.extension:Name.extension",
      "path" : "Extension.extension.extension",
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        "discriminator" : [{
          "type" : "value",
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        "description" : "Extensions are always sliced by (at least) url",
        "rules" : "open"
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      "short" : "Extension",
      "definition" : "An Extension",
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        "path" : "Element.extension",
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        "code" : "Extension"
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        "expression" : "hasValue() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "http://hl7.org/fhir/StructureDefinition/Element"
      },
      {
        "key" : "ext-1",
        "severity" : "error",
        "human" : "Must have either extensions or value[x], not both",
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        "xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
        "source" : "http://hl7.org/fhir/StructureDefinition/Extension"
      }],
      "isModifier" : false,
      "isSummary" : false
    },
    {
      "id" : "Extension.extension:Name.url",
      "path" : "Extension.extension.url",
      "representation" : ["xmlAttr"],
      "short" : "identifies the meaning of the extension",
      "definition" : "Source of the definition for the extension code - a logical name or a URL.",
      "comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
      "min" : 1,
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      "base" : {
        "path" : "Extension.url",
        "min" : 1,
        "max" : "1"
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      "type" : [{
        "code" : "uri"
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      "fixedUri" : "Name",
      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
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    },
    {
      "id" : "Extension.extension:Name.value[x]",
      "path" : "Extension.extension.value[x]",
      "short" : "Value of extension",
      "definition" : "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/extensibility.html) for a list).",
      "min" : 1,
      "max" : "1",
      "base" : {
        "path" : "Extension.value[x]",
        "min" : 0,
        "max" : "1"
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      "type" : [{
        "code" : "CodeableConcept"
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      "constraint" : [{
        "key" : "ele-1",
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        "human" : "All FHIR elements must have a @value or children",
        "expression" : "hasValue() or (children().count() > id.count())",
        "xpath" : "@value|f:*|h:div",
        "source" : "http://hl7.org/fhir/StructureDefinition/Element"
      }],
      "isModifier" : false,
      "isSummary" : false,
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "ClinVar-variant-database"
        }],
        "strength" : "preferred",
        "description" : "NCBI central repository of potentially clinically relevant variants.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/clinvar"
      },
      "mapping" : [{
        "identity" : "rim",
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    },
    {
      "id" : "Extension.extension:Type",
      "path" : "Extension.extension",
      "sliceName" : "Type",
      "short" : "Amino Acid Change Type",
      "definition" : "Codified type for associated Amino Acid Change.  LOINC Code: ([48006-1](http://loinc.org/48006-1)).",
      "min" : 0,
      "max" : "1",
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        "path" : "Element.extension",
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    },
    {
      "id" : "Extension.extension:Type.id",
      "path" : "Extension.extension.id",
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      "short" : "Unique id for inter-element referencing",
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      "min" : 0,
      "max" : "1",
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        "path" : "Element.id",
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        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
          "valueUrl" : "string"
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      "isModifier" : false,
      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
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    },
    {
      "id" : "Extension.extension:Type.extension",
      "path" : "Extension.extension.extension",
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        "discriminator" : [{
          "type" : "value",
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        "description" : "Extensions are always sliced by (at least) url",
        "rules" : "open"
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      "short" : "Extension",
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      "isModifier" : false,
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    {
      "id" : "Extension.extension:Type.url",
      "path" : "Extension.extension.url",
      "representation" : ["xmlAttr"],
      "short" : "identifies the meaning of the extension",
      "definition" : "Source of the definition for the extension code - a logical name or a URL.",
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      "isSummary" : false,
      "mapping" : [{
        "identity" : "rim",
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    },
    {
      "id" : "Extension.extension:Type.value[x]",
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      "short" : "Value of extension",
      "definition" : "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/extensibility.html) for a list).",
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      "mapping" : [{
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    },
    {
      "id" : "Extension.url",
      "path" : "Extension.url",
      "representation" : ["xmlAttr"],
      "short" : "identifies the meaning of the extension",
      "definition" : "Source of the definition for the extension code - a logical name or a URL.",
      "comment" : "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
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      "fixedUri" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange",
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    },
    {
      "id" : "Extension.value[x]",
      "path" : "Extension.value[x]",
      "short" : "Value of extension",
      "definition" : "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/extensibility.html) for a list).",
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      {
        "code" : "Timing"
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      {
        "code" : "ContactDetail"
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      {
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        "code" : "RelatedArtifact"
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        "code" : "Dosage"
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      {
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  },
  "differential" : {
    "element" : [{
      "id" : "Extension",
      "path" : "Extension",
      "short" : "AminoAcidChange",
      "definition" : "AminoAcidChange information.",
      "min" : 0,
      "max" : "1",
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      {
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    },
    {
      "id" : "Extension.extension:Name",
      "path" : "Extension.extension",
      "sliceName" : "Name",
      "short" : "HGVS nomenclature for observed Amino Acid Change",
      "definition" : "Human 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)).",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "Extension"
      }],
      "mapping" : [{
        "identity" : "v2",
        "map" : "N/A"
      },
      {
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.extension:Name.extension",
      "path" : "Extension.extension.extension",
      "max" : "0"
    },
    {
      "id" : "Extension.extension:Name.url",
      "path" : "Extension.extension.url",
      "type" : [{
        "code" : "uri"
      }],
      "fixedUri" : "Name"
    },
    {
      "id" : "Extension.extension:Name.value[x]",
      "path" : "Extension.extension.value[x]",
      "min" : 1,
      "type" : [{
        "code" : "CodeableConcept"
      }],
      "binding" : {
        "extension" : [{
          "url" : "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName",
          "valueString" : "ClinVar-variant-database"
        }],
        "strength" : "preferred",
        "description" : "NCBI central repository of potentially clinically relevant variants.",
        "valueSet" : "http://hl7.org/fhir/ValueSet/clinvar"
      }
    },
    {
      "id" : "Extension.extension:Type",
      "path" : "Extension.extension",
      "sliceName" : "Type",
      "short" : "Amino Acid Change Type",
      "definition" : "Codified type for associated Amino Acid Change.  LOINC Code: ([48006-1](http://loinc.org/48006-1)).",
      "min" : 0,
      "max" : "1",
      "type" : [{
        "code" : "Extension"
      }],
      "mapping" : [{
        "identity" : "v2",
        "map" : "N/A"
      },
      {
        "identity" : "rim",
        "map" : "N/A"
      }]
    },
    {
      "id" : "Extension.extension:Type.extension",
      "path" : "Extension.extension.extension",
      "max" : "0"
    },
    {
      "id" : "Extension.extension:Type.url",
      "path" : "Extension.extension.url",
      "type" : [{
        "code" : "uri"
      }],
      "fixedUri" : "Type"
    },
    {
      "id" : "Extension.extension:Type.value[x]",
      "path" : "Extension.extension.value[x]",
      "min" : 1,
      "type" : [{
        "code" : "CodeableConcept"
      }]
    },
    {
      "id" : "Extension.url",
      "path" : "Extension.url",
      "fixedUri" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange"
    },
    {
      "id" : "Extension.value[x]",
      "path" : "Extension.value[x]",
      "min" : 0,
      "max" : "0"
    }]
  }
}

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.