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
Orders and Observations Work Group | Maturity Level: N/A | Standards 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" }, { "identity" : "rim", "uri" : "http://hl7.org/v3", "name" : "RIM Mapping" }], "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, "max" : "1", "base" : { "path" : "Extension", "min" : 0, "max" : "*" }, "condition" : ["ele-1"], "constraint" : [{ "key" : "ele-1", "severity" : "error", "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" }, { "key" : "ext-1", "severity" : "error", "human" : "Must have either extensions or value[x], not both", "expression" : "extension.exists() != value.exists()", "xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])", "source" : "http://hl7.org/fhir/StructureDefinition/Extension" }], "isModifier" : false, "mapping" : [{ "identity" : "v2", "map" : "N/A" }, { "identity" : "rim", "map" : "N/A" }] }, { "id" : "Extension.id", "path" : "Extension.id", "representation" : ["xmlAttr"], "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.", "min" : 0, "max" : "1", "base" : { "path" : "Element.id", "min" : 0, "max" : "1" }, "type" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl" : "string" }], "code" : "http://hl7.org/fhirpath/System.String" }], "isModifier" : false, "isSummary" : false, "mapping" : [{ "identity" : "rim", "map" : "n/a" }] }, { "id" : "Extension.extension", "path" : "Extension.extension", "slicing" : { "discriminator" : [{ "type" : "value", "path" : "url" }], "description" : "Extensions are always sliced by (at least) url", "rules" : "open" }, "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"], "min" : 0, "max" : "*", "base" : { "path" : "Element.extension", "min" : 0, "max" : "*" }, "type" : [{ "code" : "Extension" }], "constraint" : [{ "key" : "ele-1", "severity" : "error", "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" }, { "key" : "ext-1", "severity" : "error", "human" : "Must have either extensions or value[x], not both", "expression" : "extension.exists() != value.exists()", "xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", "source" : "http://hl7.org/fhir/StructureDefinition/Extension" }], "isModifier" : false, "isSummary" : false, "mapping" : [{ "identity" : "rim", "map" : "n/a" }] }, { "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", "base" : { "path" : "Element.extension", "min" : 0, "max" : "*" }, "type" : [{ "code" : "Extension" }], "constraint" : [{ "key" : "ele-1", "severity" : "error", "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" }, { "key" : "ext-1", "severity" : "error", "human" : "Must have either extensions or value[x], not both", "expression" : "extension.exists() != value.exists()", "xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", "source" : "http://hl7.org/fhir/StructureDefinition/Extension" }], "isModifier" : false, "isSummary" : false, "mapping" : [{ "identity" : "v2", "map" : "N/A" }, { "identity" : "rim", "map" : "N/A" }] }, { "id" : "Extension.extension:Name.id", "path" : "Extension.extension.id", "representation" : ["xmlAttr"], "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.", "min" : 0, "max" : "1", "base" : { "path" : "Element.id", "min" : 0, "max" : "1" }, "type" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl" : "string" }], "code" : "http://hl7.org/fhirpath/System.String" }], "isModifier" : false, "isSummary" : false, "mapping" : [{ "identity" : "rim", "map" : "n/a" }] }, { "id" : "Extension.extension:Name.extension", "path" : "Extension.extension.extension", "slicing" : { "discriminator" : [{ "type" : "value", "path" : "url" }], "description" : "Extensions are always sliced by (at least) url", "rules" : "open" }, "short" : "Extension", "definition" : "An Extension", "min" : 0, "max" : "0", "base" : { "path" : "Element.extension", "min" : 0, "max" : "*" }, "type" : [{ "code" : "Extension" }], "constraint" : [{ "key" : "ele-1", "severity" : "error", "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" }, { "key" : "ext-1", "severity" : "error", "human" : "Must have either extensions or value[x], not both", "expression" : "extension.exists() != value.exists()", "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, "max" : "1", "base" : { "path" : "Extension.url", "min" : 1, "max" : "1" }, "type" : [{ "code" : "uri" }], "fixedUri" : "Name", "isModifier" : false, "isSummary" : false, "mapping" : [{ "identity" : "rim", "map" : "N/A" }] }, { "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" }, "type" : [{ "code" : "CodeableConcept" }], "constraint" : [{ "key" : "ele-1", "severity" : "error", "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", "map" : "N/A" }] }, { "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", "base" : { "path" : "Element.extension", "min" : 0, "max" : "*" }, "type" : [{ "code" : "Extension" }], "constraint" : [{ "key" : "ele-1", "severity" : "error", "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" }, { "key" : "ext-1", "severity" : "error", "human" : "Must have either extensions or value[x], not both", "expression" : "extension.exists() != value.exists()", "xpath" : "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", "source" : "http://hl7.org/fhir/StructureDefinition/Extension" }], "isModifier" : false, "isSummary" : false, "mapping" : [{ "identity" : "v2", "map" : "N/A" }, { "identity" : "rim", "map" : "N/A" }] }, { "id" : "Extension.extension:Type.id", "path" : "Extension.extension.id", "representation" : ["xmlAttr"], "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.", "min" : 0, "max" : "1", "base" : { "path" : "Element.id", "min" : 0, "max" : "1" }, "type" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl" : "string" }], "code" : "http://hl7.org/fhirpath/System.String" }], "isModifier" : false, "isSummary" : false, "mapping" : [{ "identity" : "rim", "map" : "n/a" }] }, { "id" : "Extension.extension:Type.extension", "path" : "Extension.extension.extension", "slicing" : { "discriminator" : [{ "type" : "value", "path" : "url" }], "description" : "Extensions are always sliced by (at least) url", "rules" : "open" }, "short" : "Extension", "definition" : "An Extension", "min" : 0, "max" : "0", "base" : { "path" : "Element.extension", "min" : 0, "max" : "*" }, "type" : [{ "code" : "Extension" }], "constraint" : [{ "key" : "ele-1", "severity" : "error", "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" }, { "key" : "ext-1", "severity" : "error", "human" : "Must have either extensions or value[x], not both", "expression" : "extension.exists() != value.exists()", "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: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.", "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, "max" : "1", "base" : { "path" : "Extension.url", "min" : 1, "max" : "1" }, "type" : [{ "code" : "uri" }], "fixedUri" : "Type", "isModifier" : false, "isSummary" : false, "mapping" : [{ "identity" : "rim", "map" : "N/A" }] }, { "id" : "Extension.extension:Type.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" }, "type" : [{ "code" : "CodeableConcept" }], "constraint" : [{ "key" : "ele-1", "severity" : "error", "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, "mapping" : [{ "identity" : "rim", "map" : "N/A" }] }, { "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.", "min" : 1, "max" : "1", "base" : { "path" : "Extension.url", "min" : 1, "max" : "1" }, "type" : [{ "extension" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl" : "uri" }], "code" : "http://hl7.org/fhirpath/System.String" }], "fixedUri" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChange", "isModifier" : false, "isSummary" : false, "mapping" : [{ "identity" : "rim", "map" : "N/A" }] }, { "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).", "min" : 0, "max" : "0", "base" : { "path" : "Extension.value[x]", "min" : 0, "max" : "1" }, "type" : [{ "code" : "base64Binary" }, { "code" : "boolean" }, { "code" : "canonical" }, { "code" : "code" }, { "code" : "date" }, { "code" : "dateTime" }, { "code" : "decimal" }, { "code" : "id" }, { "code" : "instant" }, { "code" : "integer" }, { "code" : "markdown" }, { "code" : "oid" }, { "code" : "positiveInt" }, { "code" : "string" }, { "code" : "time" }, { "code" : "unsignedInt" }, { "code" : "uri" }, { "code" : "url" }, { "code" : "uuid" }, { "code" : "Address" }, { "code" : "Age" }, { "code" : "Annotation" }, { "code" : "Attachment" }, { "code" : "CodeableConcept" }, { "code" : "Coding" }, { "code" : "ContactPoint" }, { "code" : "Count" }, { "code" : "Distance" }, { "code" : "Duration" }, { "code" : "HumanName" }, { "code" : "Identifier" }, { "code" : "Money" }, { "code" : "Period" }, { "code" : "Quantity" }, { "code" : "Range" }, { "code" : "Ratio" }, { "code" : "Reference" }, { "code" : "SampledData" }, { "code" : "Signature" }, { "code" : "Timing" }, { "code" : "ContactDetail" }, { "code" : "Contributor" }, { "code" : "DataRequirement" }, { "code" : "Expression" }, { "code" : "ParameterDefinition" }, { "code" : "RelatedArtifact" }, { "code" : "TriggerDefinition" }, { "code" : "UsageContext" }, { "code" : "Dosage" }, { "code" : "Meta" }], "constraint" : [{ "key" : "ele-1", "severity" : "error", "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, "mapping" : [{ "identity" : "rim", "map" : "N/A" }] }] }, "differential" : { "element" : [{ "id" : "Extension", "path" : "Extension", "short" : "AminoAcidChange", "definition" : "AminoAcidChange information.", "min" : 0, "max" : "1", "mapping" : [{ "identity" : "v2", "map" : "N/A" }, { "identity" : "rim", "map" : "N/A" }] }, { "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.