Class: FunctionalAssayResult

The result of assessing a genetic variant's effect under a single instance of a functional assay.

Slots

Name	Range	Cardinality	Description	Info
result	string	1..1	The measured value of this variant's effect on function. The value must be consistent with the `range` of the referenced `assay`.	.
result_assertion	string	0..1	An assertion as to the categorized impact of the variant's effect, as described by the authors reporting the `assay` (if provided).	.
assay	FunctionalAssay	0..1	None	.
variant	Variant	0..1	None	.
units	unit	0..1	For qualtitatve assays, the units of the `result`. This may be omitted if the referenced `assay` provides a default value for the units of its measurements. Values must be from the Units of Measurement Ontology (UO)	.
validation_control	ValidationControlType	0..1	Optional field used to indicate if this result is for a variant that was used as a validation control for the `assay` either as a `benign` or `pathogenic` variant.	.
replicate_count	integer	0..1	The number of times the `variant` was evaluated using the `assay` to produce the reported `result`.	.
standard_deviation	decimal	0..1	None	.
standard_error_of_mean	decimal	0..1	None	.
range	string	0..1	None	.
intraquartile_range	string	0..1	None	.
p_value	decimal	0..1	None	.
is_approximation_by_curator	boolean	0..1	A flag to indicate that the curator had to use some method of approximation of the `result` (e.g., by reading the value from a graph when numerical values were not provided by the authors reporting the `assay`).	.

Usages

Identifier and Mapping Information

LinkML Specification

Direct

name: FunctionalAssayResult
description: The result of assessing a genetic variant's effect under a single instance
  of a functional assay.
from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
attributes:
  result:
    name: result
    description: The measured value of this variant's effect on function. The value
      must be consistent with the `range` of the referenced `assay`.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    required: true
  result assertion:
    name: result assertion
    description: An assertion as to the categorized impact of the variant's effect,
      as described by the authors reporting the `assay` (if provided).
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
  assay:
    name: assay
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: FunctionalAssay
  variant:
    name: variant
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: Variant
  units:
    name: units
    description: For qualtitatve assays, the units of the `result`. This may be omitted
      if the referenced `assay` provides a default value for the units of its measurements.
      Values must be from the Units of Measurement Ontology (UO)
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: unit
  validation control:
    name: validation control
    description: Optional field used to indicate if this result is for a variant that
      was used as a validation control for the `assay` either as a `benign` or `pathogenic`
      variant.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: ValidationControlType
  replicate count:
    name: replicate count
    description: The number of times the `variant` was evaluated using the `assay`
      to produce the reported `result`.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: integer
    minimum_value: 0
  standard deviation:
    name: standard deviation
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: decimal
    minimum_value: 0
  standard error of mean:
    name: standard error of mean
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: decimal
    minimum_value: 0
  range:
    name: range
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    pattern: ^[<>]?[-\d]+(.\d+)? - [<>]?[-\d]+(.\d+)?
  intraquartile range:
    name: intraquartile range
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    pattern: ^[<>]?[-\d]+(.\d+)? - [<>]?[-\d]+(.\d+)?
  p value:
    name: p value
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: decimal
    minimum_value: 0
    maximum_value: 1
  is approximation by curator:
    name: is approximation by curator
    description: A flag to indicate that the curator had to use some method of approximation
      of the `result` (e.g., by reading the value from a graph when numerical values
      were not provided by the authors reporting the `assay`).
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: boolean

Induced

name: FunctionalAssayResult
description: The result of assessing a genetic variant's effect under a single instance
  of a functional assay.
from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
attributes:
  result:
    name: result
    description: The measured value of this variant's effect on function. The value
      must be consistent with the `range` of the referenced `assay`.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: result
    owner: FunctionalAssayResult
    range: string
    required: true
  result assertion:
    name: result assertion
    description: An assertion as to the categorized impact of the variant's effect,
      as described by the authors reporting the `assay` (if provided).
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: result_assertion
    owner: FunctionalAssayResult
    range: string
  assay:
    name: assay
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: assay
    owner: FunctionalAssayResult
    range: FunctionalAssay
  variant:
    name: variant
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: variant
    owner: FunctionalAssayResult
    range: Variant
  units:
    name: units
    description: For qualtitatve assays, the units of the `result`. This may be omitted
      if the referenced `assay` provides a default value for the units of its measurements.
      Values must be from the Units of Measurement Ontology (UO)
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: units
    owner: FunctionalAssayResult
    range: unit
  validation control:
    name: validation control
    description: Optional field used to indicate if this result is for a variant that
      was used as a validation control for the `assay` either as a `benign` or `pathogenic`
      variant.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: validation_control
    owner: FunctionalAssayResult
    range: ValidationControlType
  replicate count:
    name: replicate count
    description: The number of times the `variant` was evaluated using the `assay`
      to produce the reported `result`.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: replicate_count
    owner: FunctionalAssayResult
    range: integer
    minimum_value: 0
  standard deviation:
    name: standard deviation
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: standard_deviation
    owner: FunctionalAssayResult
    range: decimal
    minimum_value: 0
  standard error of mean:
    name: standard error of mean
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: standard_error_of_mean
    owner: FunctionalAssayResult
    range: decimal
    minimum_value: 0
  range:
    name: range
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: range
    owner: FunctionalAssayResult
    range: string
    pattern: ^[<>]?[-\d]+(.\d+)? - [<>]?[-\d]+(.\d+)?
  intraquartile range:
    name: intraquartile range
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: intraquartile_range
    owner: FunctionalAssayResult
    range: string
    pattern: ^[<>]?[-\d]+(.\d+)? - [<>]?[-\d]+(.\d+)?
  p value:
    name: p value
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: p_value
    owner: FunctionalAssayResult
    range: decimal
    minimum_value: 0
    maximum_value: 1
  is approximation by curator:
    name: is approximation by curator
    description: A flag to indicate that the curator had to use some method of approximation
      of the `result` (e.g., by reading the value from a graph when numerical values
      were not provided by the authors reporting the `assay`).
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: is_approximation_by_curator
    owner: FunctionalAssayResult
    range: boolean