{ "description": "Allele information.", "_filename": "StructureDefinition-observation-geneticsAllele.json", "package_name": "hl7.fhir.uv.extensions.r4", "date": "2016-03-14", "derivation": "constraint", "publisher": "HL7 International / Orders and Observations", "fhirVersion": "4.0.1", "jurisdiction": [ { "coding": [ { "code": "001", "system": "http://unstats.un.org/unsd/methods/m49/m49.htm" } ] } ], "name": "Allele", "mapping": [ { "uri": "http://hl7.org/v2", "name": "HL7 v2 Mapping", "identity": "v2" }, { "uri": "http://hl7.org/v3", "name": "RIM Mapping", "identity": "rim" } ], "abstract": false, "type": "Extension", "experimental": null, "resourceType": "StructureDefinition", "title": "Allele", "package_version": "5.3.0-ballot", "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/structuredefinition-standards-status", "valueCode": "deprecated", "_valueCode": { "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status-reason", "valueMarkdown": "This extension has been replaced by the profiles and extensions defined in the [Genomics Reporting Guide](https://hl7.org/fhir/uv/genomics-reporting/)" } ] } }, { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-type-characteristics", "valueCode": "can-bind" } ], "snapshot": { "element": [ { "constraint": [ { "key": "ele-1", "human": "All FHIR elements must have a @value or children", "xpath": "@value|f:*|h:div", "source": "http://hl7.org/fhir/StructureDefinition/Element", "severity": "error", "expression": "hasValue() or (children().count() > id.count())" }, { "key": "ext-1", "human": "Must have either extensions or value[x], not both", "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])", "source": "http://hl7.org/fhir/StructureDefinition/Extension", "severity": "error", "expression": "extension.exists() != value.exists()" } ], "path": "Extension", "min": 0, "definition": "Allele information.", "isModifier": false, "short": "Allele", "max": "1", "id": "Extension", "condition": [ "ele-1" ], "base": { "max": "*", "min": 0, "path": "Extension" } }, { "path": "Extension.id", "min": 0, "definition": "Unique id for the element within a resource (for internal references). 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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.", "isModifier": false, "short": "Additional content defined by implementations", "mapping": [ { "map": "n/a", "identity": "rim" } ], "slicing": { "rules": "open", "description": "Extensions are always sliced by (at least) url", "discriminator": [ { "path": "url", "type": "value" } ] }, "type": [ { "code": "Extension" } ], "alias": [ "extensions", "user content" ], "max": "*", "id": "Extension.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. 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This element is the common name for the allele. LOINC Code: ([48008-7](http://loinc.org/48008-7)).", "isModifier": false, "short": "Name of allele", "mapping": [ { "map": "N/A", "identity": "v2" }, { "map": "N/A", "identity": "rim" } ], "type": [ { "code": "Extension" } ], "sliceName": "Name", "max": "1", "id": "Extension.extension:Name", "base": { "max": "*", "min": 0, "path": "Element.extension" }, "isSummary": false }, { "path": "Extension.extension.id", "min": 0, "definition": "Unique id for the element within a resource (for internal references). 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The definition SHALL be a URI for the Structure Definition defining the extension.", "base": { "max": "1", "min": 1, "path": "Extension.url" }, "isSummary": false }, { "constraint": [ { "key": "ele-1", "human": "All FHIR elements must have a @value or children", "xpath": "@value|f:*|h:div", "source": "http://hl7.org/fhir/StructureDefinition/Element", "severity": "error", "expression": "hasValue() or (children().count() > id.count())" } ], "path": "Extension.extension.value[x]", "min": 1, "definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list).", "isModifier": false, "short": "Value of extension", "mapping": [ { "map": "N/A", "identity": "rim" } ], "type": [ { "code": "CodeableConcept" } ], "binding": { "strength": "example", "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "EBI-AlleleName" } ], "description": "EMBL-EBI database of AlleleName." }, "max": "1", "id": "Extension.extension:Name.value[x]", "base": { "max": "1", "min": 0, "path": "Extension.value[x]" }, "isSummary": false }, { "constraint": [ { "key": "ele-1", "human": "All FHIR elements must have a @value or children", "xpath": "@value|f:*|h:div", "source": "http://hl7.org/fhir/StructureDefinition/Element", "severity": "error", "expression": "hasValue() or (children().count() > id.count())" }, { "key": "ext-1", "human": "Must have either extensions or value[x], not both", "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", "source": "http://hl7.org/fhir/StructureDefinition/Extension", "severity": "error", "expression": "extension.exists() != value.exists()" } ], "path": "Extension.extension", "min": 0, "definition": "The level of occurrence of a single DNA Sequence Variant within a set of chromosomes. Heterozygous indicates the DNA sequence variant is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variant is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variant exists in the only single copy of a gene in a non-homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variant is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variant is present in all of the copies of mitochondrial DNA. LOINC Code: ([53034-5](http://loinc.org/53034-5)).", "isModifier": false, "short": "The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous", "type": [ { "code": "Extension" } ], "sliceName": "State", "max": "1", "id": "Extension.extension:State", "base": { "max": "*", "min": 0, "path": "Element.extension" }, "isSummary": false }, { "path": "Extension.extension.id", "min": 0, "definition": "Unique id for the element within a resource (for internal references). 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The definition SHALL be a URI for the Structure Definition defining the extension.", "base": { "max": "1", "min": 1, "path": "Extension.url" }, "isSummary": false }, { "constraint": [ { "key": "ele-1", "human": "All FHIR elements must have a @value or children", "xpath": "@value|f:*|h:div", "source": "http://hl7.org/fhir/StructureDefinition/Element", "severity": "error", "expression": "hasValue() or (children().count() > id.count())" } ], "path": "Extension.extension.value[x]", "min": 1, "definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list).", "isModifier": false, "short": "Value of extension", "mapping": [ { "map": "N/A", "identity": "rim" } ], "type": [ { "code": "CodeableConcept" } ], "max": "1", "id": "Extension.extension:State.value[x]", "base": { "max": "1", "min": 0, "path": "Extension.value[x]" }, "isSummary": false }, { "constraint": [ { "key": "ele-1", "human": "All FHIR elements must have a @value or children", "xpath": "@value|f:*|h:div", "source": "http://hl7.org/fhir/StructureDefinition/Element", "severity": "error", "expression": "hasValue() or (children().count() > id.count())" }, { "key": "ext-1", "human": "Must have either extensions or value[x], not both", "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])", "source": "http://hl7.org/fhir/StructureDefinition/Extension", "severity": "error", "expression": "extension.exists() != value.exists()" } ], "path": "Extension.extension", "min": 0, "definition": "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. LOINC Code: ([81258-6](http://loinc.org/81258-6)).", "isModifier": false, "short": "Allele frequency", "type": [ { "code": "Extension" } ], "sliceName": "Frequency", "max": "1", "id": "Extension.extension:Frequency", "base": { "max": "*", "min": 0, "path": "Element.extension" }, "isSummary": false }, { "path": "Extension.extension.id", "min": 0, "definition": "Unique id for the element within a resource (for internal references). 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The definition SHALL be a URI for the Structure Definition defining the extension.", "base": { "max": "1", "min": 1, "path": "Extension.url" }, "isSummary": false }, { "constraint": [ { "key": "ele-1", "human": "All FHIR elements must have a @value or children", "xpath": "@value|f:*|h:div", "source": "http://hl7.org/fhir/StructureDefinition/Element", "severity": "error", "expression": "hasValue() or (children().count() > id.count())" } ], "path": "Extension.extension.value[x]", "min": 1, "definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list).", "isModifier": false, "short": "Value of extension", "mapping": [ { "map": "N/A", "identity": "rim" } ], "type": [ { "code": "decimal" } ], "max": "1", "id": "Extension.extension:Frequency.value[x]", "base": { "max": "1", "min": 0, "path": "Extension.value[x]" }, "isSummary": false }, { "path": "Extension.url", "min": 1, "definition": "Source of the definition for the extension code - a logical name or a URL.", "isModifier": false, "short": "identifies the meaning of the extension", "fixedUri": "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele", "mapping": [ { "map": "N/A", "identity": "rim" } ], "type": [ { "code": "http://hl7.org/fhirpath/System.String", "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type", "valueUrl": "uri" } ] } ], "representation": [ "xmlAttr" ], "max": "1", "id": "Extension.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.", "base": { "max": "1", "min": 1, "path": "Extension.url" }, "isSummary": false }, { "constraint": [ { "key": "ele-1", "human": "All FHIR elements must have a @value or children", "xpath": "@value|f:*|h:div", "source": "http://hl7.org/fhir/StructureDefinition/Element", "severity": "error", "expression": "hasValue() or (children().count() > id.count())" } ], "path": "Extension.value[x]", "min": 0, "definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list).", "isModifier": false, "short": "Value of extension", "mapping": [ { "map": "N/A", "identity": "rim" } ], "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" } ], "max": "0", "id": "Extension.value[x]", "base": { "max": "1", "min": 0, "path": "Extension.value[x]" }, "isSummary": false } ], "extension": [ { "url": "http://hl7.org/fhir/tools/StructureDefinition/snapshot-base-version", "valueString": "4.0.1" } ] }, "status": "retired", "id": "bcbb45ad-ae6f-4525-b69c-7f7157472fb1", "kind": "complex-type", "url": "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele", "context": [ { "type": "element", "expression": "Observation" } ], "version": "5.3.0-ballot", "differential": { "element": [ { "id": "Extension", "max": "1", "min": 0, "path": "Extension", "short": "Allele", "definition": "Allele information." }, { "path": "Extension.extension", "min": 0, "definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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LOINC Code: ([48008-7](http://loinc.org/48008-7)).", "short": "Name of allele", "mapping": [ { "map": "N/A", "identity": "v2" }, { "map": "N/A", "identity": "rim" } ], "type": [ { "code": "Extension" } ], "sliceName": "Name", "max": "1", "id": "Extension.extension:Name" }, { "id": "Extension.extension:Name.extension", "max": "0", "path": "Extension.extension.extension" }, { "id": "Extension.extension:Name.url", "path": "Extension.extension.url", "type": [ { "code": "uri" } ], "fixedUri": "Name" }, { "id": "Extension.extension:Name.value[x]", "min": 1, "path": "Extension.extension.value[x]", "type": [ { "code": "CodeableConcept" } ], "binding": { "strength": "example", "extension": [ { "url": "http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", "valueString": "EBI-AlleleName" } ], "description": "EMBL-EBI database of AlleleName." } }, { "id": "Extension.extension:State", "max": "1", "min": 0, "path": "Extension.extension", "type": [ { "code": "Extension" } ], "short": "The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous", "sliceName": "State", "definition": "The level of occurrence of a single DNA Sequence Variant within a set of chromosomes. Heterozygous indicates the DNA sequence variant is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variant is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variant exists in the only single copy of a gene in a non-homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variant is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variant is present in all of the copies of mitochondrial DNA. LOINC Code: ([53034-5](http://loinc.org/53034-5))." }, { "id": "Extension.extension:State.extension", "max": "0", "path": "Extension.extension.extension" }, { "id": "Extension.extension:State.url", "path": "Extension.extension.url", "type": [ { "code": "uri" } ], "fixedUri": "State" }, { "id": "Extension.extension:State.value[x]", "min": 1, "path": "Extension.extension.value[x]", "type": [ { "code": "CodeableConcept" } ] }, { "id": "Extension.extension:Frequency", "max": "1", "min": 0, "path": "Extension.extension", "type": [ { "code": "Extension" } ], "short": "Allele frequency", "sliceName": "Frequency", "definition": "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. LOINC Code: ([81258-6](http://loinc.org/81258-6))." }, { "id": "Extension.extension:Frequency.extension", "max": "0", "path": "Extension.extension.extension" }, { "id": "Extension.extension:Frequency.url", "path": "Extension.extension.url", "type": [ { "code": "uri" } ], "fixedUri": "Frequency" }, { "id": "Extension.extension:Frequency.value[x]", "min": 1, "path": "Extension.extension.value[x]", "type": [ { "code": "decimal" } ] }, { "id": "Extension.url", "path": "Extension.url", "fixedUri": "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele" }, { "id": "Extension.value[x]", "max": "0", "min": 0, "path": "Extension.value[x]" } ] }, "contact": [ { "telecom": [ { "value": "http://www.hl7.org/Special/committees/orders", "system": "url" } ] } ], "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension" }