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    Class GenomicStudyAnalysisComponent

    GenomicStudyAnalysisComponent Class

    FHIR Specification

    • Short: Genomic Analysis Event
    • Definition: The details about a specific analysis that was performed in this GenomicStudy.

    FHIR GenomicStudy

    Hierarchy (View Summary)

    Implements

    Index

    Constructors

    constructor

    Properties

    identifier? methodType? changeType? genomeBuild? instantiatesCanonical? instantiatesUri? title? focus? specimen? date? note? protocolPerformed? regionsStudied? regionsCalled? input? output? performer? device?

    Methods

    parse getIdentifier setIdentifier addIdentifier hasIdentifier getMethodType setMethodType addMethodType hasMethodType getChangeType setChangeType addChangeType hasChangeType getGenomeBuild setGenomeBuild hasGenomeBuild getInstantiatesCanonicalElement setInstantiatesCanonicalElement hasInstantiatesCanonicalElement getInstantiatesCanonical setInstantiatesCanonical hasInstantiatesCanonical getInstantiatesUriElement setInstantiatesUriElement hasInstantiatesUriElement getInstantiatesUri setInstantiatesUri hasInstantiatesUri getTitleElement setTitleElement hasTitleElement getTitle setTitle hasTitle getFocus setFocus addFocus hasFocus getSpecimen setSpecimen addSpecimen hasSpecimen getDateElement setDateElement hasDateElement getDate setDate hasDate getNote setNote addNote hasNote getProtocolPerformed setProtocolPerformed hasProtocolPerformed getRegionsStudied setRegionsStudied addRegionsStudied hasRegionsStudied getRegionsCalled setRegionsCalled addRegionsCalled hasRegionsCalled getInput setInput addInput hasInput getOutput setOutput addOutput hasOutput getPerformer setPerformer addPerformer hasPerformer getDevice setDevice addDevice hasDevice fhirType isEmpty copy toJSON getModifierExtension setModifierExtension hasModifierExtension getModifierExtensionByUrl addModifierExtension removeModifierExtension getId setId hasId getExtension setExtension hasExtension getExtensionByUrl addExtension removeExtension isRequiredFieldsEmpty isResource isDataType isComplexDataType isPrimitive isBooleanPrimitive isStringPrimitive isNumberPrimitive isBigIntPrimitive isDateTimePrimitive copyValues initIdentifier initMethodType initChangeType initFocus initSpecimen initNote initRegionsStudied initRegionsCalled initInput initOutput initPerformer initDevice

    Constructors

    Properties

    identifier?: Identifier[]

    GenomicStudy.analysis.identifier Element

    FHIR Specification

    • Short: Identifiers for the analysis event
    • Definition: Identifiers for the analysis event.
    • FHIR Type: Identifier
    • Cardinality: 0..*
    • isModifier: false
    • isSummary: true
    methodType?: CodeableConcept[]

    GenomicStudy.analysis.methodType Element

    FHIR Specification

    • Short: Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI)
    • Definition: Type of the methods used in the analysis, e.g., Fluorescence in situ hybridization (FISH), Karyotyping, or Microsatellite instability testing (MSI).
    • FHIR Type: CodeableConcept
    • Cardinality: 0..*
    • isModifier: false
    • isSummary: true
    changeType?: CodeableConcept[]

    GenomicStudy.analysis.changeType Element

    FHIR Specification

    • Short: Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change)
    • Definition: Type of the genomic changes studied in the analysis, e.g., DNA, RNA, or amino acid change.
    • FHIR Type: CodeableConcept
    • Cardinality: 0..*
    • isModifier: false
    • isSummary: false
    genomeBuild?: CodeableConcept

    GenomicStudy.analysis.genomeBuild Element

    FHIR Specification

    • Short: Genome build that is used in this analysis
    • Definition: The reference genome build that is used in this analysis.
    • FHIR Type: CodeableConcept
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: false
    instantiatesCanonical?: CanonicalType

    GenomicStudy.analysis.instantiatesCanonical Element

    FHIR Specification

    instantiatesUri?: UriType

    GenomicStudy.analysis.instantiatesUri Element

    FHIR Specification

    • Short: The URL pointing to an externally maintained protocol that describes the analysis
    • Definition: The URL pointing to an externally maintained protocol that describes the analysis.
    • FHIR Type: uri
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: false
    title?: StringType

    GenomicStudy.analysis.title Element

    FHIR Specification

    • Short: Name of the analysis event (human friendly)
    • Definition: Name of the analysis event (human friendly).
    • FHIR Type: string
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: true
    focus?: Reference[]

    GenomicStudy.analysis.focus Element

    FHIR Specification

    • Short: What the genomic analysis is about, when it is not about the subject of record
    • Definition: The focus of a genomic analysis when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the GenomicStudy.subject would be the child (proband) and the GenomicStudy.analysis.focus of a specific analysis would be the parent.
    • Comment: If the focus of the analysis is not known, the value of this field SHALL use the data absent extension.
    • FHIR Type: Reference
    • Cardinality: 0..*
    • isModifier: false
    • isSummary: true
    specimen?: Reference[]

    GenomicStudy.analysis.specimen Element

    FHIR Specification

    • Short: The specimen used in the analysis event
    • Definition: The specimen used in the analysis event.
    • FHIR Type: Reference
    • Cardinality: 0..*
    • isModifier: false
    • isSummary: true
    date?: DateTimeType

    GenomicStudy.analysis.date Element

    FHIR Specification

    • Short: The date of the analysis event
    • Definition: The date of the analysis event.
    • FHIR Type: dateTime
    • Cardinality: 0..1
    • isModifier: false
    • isSummary: false
    note?: Annotation[]

    GenomicStudy.analysis.note Element

    FHIR Specification

    • Short: Any notes capture with the analysis event
    • Definition: Any notes capture with the analysis event.
    • FHIR Type: Annotation
    • Cardinality: 0..*
    • isModifier: false
    • isSummary: false
    protocolPerformed?: Reference

    GenomicStudy.analysis.protocolPerformed Element

    FHIR Specification

    regionsStudied?: Reference[]

    GenomicStudy.analysis.regionsStudied Element

    FHIR Specification

    regionsCalled?: Reference[]

    GenomicStudy.analysis.regionsCalled Element

    FHIR Specification

    input?: GenomicStudyAnalysisInputComponent[]

    GenomicStudy.analysis.input Element

    FHIR Specification

    • Short: Inputs for the analysis event
    • Definition: Inputs for the analysis event.
    • FHIR Type: BackboneElement
    • Cardinality: 0..*
    • isModifier: false
    • isSummary: false
    output?: GenomicStudyAnalysisOutputComponent[]

    GenomicStudy.analysis.output Element

    FHIR Specification

    • Short: Outputs for the analysis event
    • Definition: Outputs for the analysis event.
    • FHIR Type: BackboneElement
    • Cardinality: 0..*
    • isModifier: false
    • isSummary: false
    performer?: GenomicStudyAnalysisPerformerComponent[]

    GenomicStudy.analysis.performer Element

    FHIR Specification

    • Short: Performer for the analysis event
    • Definition: Performer for the analysis event.
    • FHIR Type: BackboneElement
    • Cardinality: 0..*
    • isModifier: false
    • isSummary: false
    device?: GenomicStudyAnalysisDeviceComponent[]

    GenomicStudy.analysis.device Element

    FHIR Specification

    • Short: Devices used for the analysis (e.g., instruments, software), with settings and parameters
    • Definition: Devices used for the analysis (e.g., instruments, software), with settings and parameters.
    • FHIR Type: BackboneElement
    • Cardinality: 0..*
    • isModifier: false
    • isSummary: false

    Methods

    • Parse the provided GenomicStudyAnalysisComponent JSON to instantiate the GenomicStudyAnalysisComponent data model.

      Parameters

      • sourceJson: Value

        JSON representing FHIR GenomicStudyAnalysisComponent

      • OptionaloptSourceField: string

        Optional data source field (e.g. <complexTypeName>.<complexTypeFieldName>); defaults to GenomicStudyAnalysisComponent

      Returns undefined | GenomicStudyAnalysisComponent

      GenomicStudyAnalysisComponent data model or undefined for GenomicStudyAnalysisComponent

      JsonError if the provided JSON is not a valid JSON object

    • Assigns the provided ProtocolPerformed object value to the protocolPerformed property.

      Parameters

      • value: undefined | Reference

        the protocolPerformed object value

      Returns this

      this

      @ReferenceTargets('GenomicStudy.analysis.protocolPerformed', ['Procedure','Task',])

      InvalidTypeError for invalid data type or reference value

    • Assigns the provided Reference array value to the regionsStudied property.

      Parameters

      • value: undefined | Reference[]

        the regionsStudied array value

      Returns this

      this

      @ReferenceTargets('GenomicStudy.analysis.regionsStudied', ['DocumentReference','Observation',])

      InvalidTypeError for invalid data type or reference value

    • Determines if the modifierExtension property exists.

      Parameters

      • Optionalurl: string

        the url that identifies a specific Extension

      Returns boolean

      true if an Extension has the provided url; false otherwise

      If the url is provided, determines if an Extension having the provided url exists. If the url is not provided, determines if the modifierExtension property exists and has any values.

      AssertionError for invalid url

    • Returns undefined | string

      the id property value

    • Assigns the provided value to the id property.

      Parameters

      • value: undefined | string

        the id value

      Returns this

      this

      PrimitiveTypeError for invalid value

    • Returns boolean

      true if id exists and has a value; false otherwise

    • Determines if the extension property exists.

      Parameters

      • Optionalurl: string

        the url that identifies a specific Extension

      Returns boolean

      true if an Extension has the provided url; false otherwise

      If the url is provided, determines if an Extension having the provided url exists. If the url is not provided, determines if the extension property exists and has any values.

      AssertionError for invalid url

    • Determines if the extension property exists.

      Parameters

      • url: string

        the url that identifies a specific Extension

      Returns undefined | IExtension

      an Extension having the provided url

      If the url is provided, determines if an Extension having the provided url exists. If the url is not provided, determines if the extension property exists and has any values.

      AssertionError for invalid url

    • Adds the provided Extension to the extension property array.

      Parameters

      • extension: undefined | IExtension

        the Extension value to add to the extension property array

      Returns this

      this

    • Removes the Extension having the provided url from the extension property array.

      Parameters

      • url: string

        the url that identifies a specific Extension to remove

      Returns void

      AssertionError for invalid url

    • Returns boolean

      true if and only if the data model has required fields (min cardinality > 0) and at least one of those required fields in the instance is empty; false otherwise

    • Returns boolean

      true if the instance is a FHIR complex or primitive datatype; false otherwise

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