Class: FunctionalAssay

Experimental evaluation of the functional effect of one or more genetic variants.

Slots

Name	Range	Cardinality	Description	Info
general_class	string	0..*	The type or class of assay as identified using structured language or ontology terms. BAO or ECO terms are preferred when available.	.
material_used	string	0..*	Reagents (biological or non-biological) that were use as comparators or other inputs to an assay. CLO, CO and BAI terms are preferred when available.	.
patient_derived_material_used	string	0..*	Material used as inputs or comparators within an assay that were derived/sourced from a patient. These are differentiated from other materials used in an assay because of the possibility that use of such materials may involved confounding variables (e.g., other genetic variants) that may be difficult to account for in validation. CLO, CO and BAI terms are preferred when available.	.
description	string	0..1	Free-text description/summary of the assay	.
document	string	0..1	The primary document or manuscript in which the assay and its results are described. Supplementary descriptions can be recorded in "additional publication"	.
additional_document	string	0..*	External document referenced in this document as providing details about the assay	.
read_out_description	string	0..1	Free-text description of the type of readout of the assay	.
range	string	0..1	Range of all possible output values of the assay. If qualitative this will comprise a list of terms indicating the observable results. If quantitative, this will indicate the units used.	.
normal_range	string	0..1	The subset of possible output values which the authors of an assay classify as indicative of normal function.	.
abnormal_range	string	0..1	The subset of possible output values which the authors of an assay classify as indicative of abnormal function.	.
indeterminate_range	string	0..1	The subset of possible output values which the authors of an assay classify as indeterminante with respect to function.	.
validation_control_pathogenic	string	0..1	None	.
validation_control_benign	string	0..1	None	.
replication	string	1..1	Description of the process for replication of an assay as provided by the document, or "not reported" if not specified.	.
statistical_analysis_description	string	1..1	Description of the statistical analysis performed for validation and determination of thresholds of the assay, or "not reported" if the document does not specify.	.
significance_threshold	string	0..1	The threshold for significance of measurements under this assay, as defined by the authors of the document (if provided).	.
comment	string	0..*	Any additional information that a curator would like to provide about the FunctionalAssay that is not adequately captured by other fields	.
range_type	RangeType	0..1	The type of values that can be expected from results of this assay (quantitative or qualitative). This could be inferred from the assay's range, but is encoded here to simplify searches.	.
units	unit	0..1	For quantitative assays, the default unit to be applied to individual results if not overridden.	.

Usages

used by	used in	type	used
FunctionalAssayResult	assay	range	FunctionalAssay

Identifier and Mapping Information

LinkML Specification

Direct

name: FunctionalAssay
description: Experimental evaluation of the functional effect of one or more genetic
  variants.
from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
attributes:
  general class:
    name: general class
    description: The type or class of assay as identified using structured language
      or ontology terms. BAO or ECO terms are preferred when available.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    multivalued: true
  material used:
    name: material used
    description: Reagents (biological or non-biological) that were use as comparators
      or other inputs to an assay. CLO, CO and BAI terms are preferred when available.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    multivalued: true
  patient derived material used:
    name: patient derived material used
    description: Material used as inputs or comparators within an assay that were
      derived/sourced from a patient. These are differentiated from other materials
      used in an assay because of the possibility that use of such materials may involved
      confounding variables (e.g.,  other genetic variants) that may be difficult
      to account for in validation. CLO, CO and BAI terms are preferred when available.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    multivalued: true
  description:
    name: description
    description: Free-text description/summary of the assay
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    slot_uri: dc:description
  document:
    name: document
    description: The primary document or manuscript in which the assay and its results
      are described. Supplementary descriptions can be recorded in "additional publication"
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
  additional document:
    name: additional document
    description: External document referenced in this document as providing details
      about the assay
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    multivalued: true
  read out description:
    name: read out description
    description: Free-text description of the type of readout of the assay
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
  range:
    name: range
    description: Range of all possible output values of the assay. If qualitative
      this will comprise a list of terms indicating the observable results. If quantitative,
      this will indicate the units used.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
  normal range:
    name: normal range
    description: The subset of possible output values which the authors of an assay
      classify as indicative of normal function.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
  abnormal range:
    name: abnormal range
    description: The subset of possible output values which the authors of an assay
      classify as indicative of abnormal function.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
  indeterminate range:
    name: indeterminate range
    description: The subset of possible output values which the authors of an assay
      classify as indeterminante with respect to function.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
  validation control pathogenic:
    name: validation control pathogenic
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
  validation control benign:
    name: validation control benign
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
  replication:
    name: replication
    description: Description of the process for replication of an assay as provided
      by the document, or "not reported" if not specified.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: string
    required: true
  statistical analysis description:
    name: statistical analysis description
    description: Description of the statistical analysis performed for validation
      and determination of thresholds of the assay, or "not reported" if the document
      does not specify.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: string
    required: true
  significance threshold:
    name: significance threshold
    description: The threshold for significance of measurements under this assay,
      as defined by the authors of the document (if provided).
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
  comment:
    name: comment
    description: Any additional information that a curator would like to provide about
      the FunctionalAssay that is not adequately captured by other fields
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    multivalued: true
  range type:
    name: range type
    description: The type of values that can be expected from results of this assay
      (quantitative or qualitative). This could be inferred from the assay's range,
      but is encoded here to simplify searches.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: RangeType
  units:
    name: units
    description: For quantitative assays, the default unit to be applied to individual
      results if not overridden.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    range: unit

Induced

name: FunctionalAssay
description: Experimental evaluation of the functional effect of one or more genetic
  variants.
from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
attributes:
  general class:
    name: general class
    description: The type or class of assay as identified using structured language
      or ontology terms. BAO or ECO terms are preferred when available.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    multivalued: true
    alias: general_class
    owner: FunctionalAssay
    range: string
  material used:
    name: material used
    description: Reagents (biological or non-biological) that were use as comparators
      or other inputs to an assay. CLO, CO and BAI terms are preferred when available.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    multivalued: true
    alias: material_used
    owner: FunctionalAssay
    range: string
  patient derived material used:
    name: patient derived material used
    description: Material used as inputs or comparators within an assay that were
      derived/sourced from a patient. These are differentiated from other materials
      used in an assay because of the possibility that use of such materials may involved
      confounding variables (e.g.,  other genetic variants) that may be difficult
      to account for in validation. CLO, CO and BAI terms are preferred when available.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    multivalued: true
    alias: patient_derived_material_used
    owner: FunctionalAssay
    range: string
  description:
    name: description
    description: Free-text description/summary of the assay
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    slot_uri: dc:description
    alias: description
    owner: FunctionalAssay
    range: string
  document:
    name: document
    description: The primary document or manuscript in which the assay and its results
      are described. Supplementary descriptions can be recorded in "additional publication"
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: document
    owner: FunctionalAssay
    range: string
  additional document:
    name: additional document
    description: External document referenced in this document as providing details
      about the assay
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    multivalued: true
    alias: additional_document
    owner: FunctionalAssay
    range: string
  read out description:
    name: read out description
    description: Free-text description of the type of readout of the assay
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: read_out_description
    owner: FunctionalAssay
    range: string
  range:
    name: range
    description: Range of all possible output values of the assay. If qualitative
      this will comprise a list of terms indicating the observable results. If quantitative,
      this will indicate the units used.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: range
    owner: FunctionalAssay
    range: string
  normal range:
    name: normal range
    description: The subset of possible output values which the authors of an assay
      classify as indicative of normal function.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: normal_range
    owner: FunctionalAssay
    range: string
  abnormal range:
    name: abnormal range
    description: The subset of possible output values which the authors of an assay
      classify as indicative of abnormal function.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: abnormal_range
    owner: FunctionalAssay
    range: string
  indeterminate range:
    name: indeterminate range
    description: The subset of possible output values which the authors of an assay
      classify as indeterminante with respect to function.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: indeterminate_range
    owner: FunctionalAssay
    range: string
  validation control pathogenic:
    name: validation control pathogenic
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: validation_control_pathogenic
    owner: FunctionalAssay
    range: string
  validation control benign:
    name: validation control benign
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: validation_control_benign
    owner: FunctionalAssay
    range: string
  replication:
    name: replication
    description: Description of the process for replication of an assay as provided
      by the document, or "not reported" if not specified.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: replication
    owner: FunctionalAssay
    range: string
    required: true
  statistical analysis description:
    name: statistical analysis description
    description: Description of the statistical analysis performed for validation
      and determination of thresholds of the assay, or "not reported" if the document
      does not specify.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: statistical_analysis_description
    owner: FunctionalAssay
    range: string
    required: true
  significance threshold:
    name: significance threshold
    description: The threshold for significance of measurements under this assay,
      as defined by the authors of the document (if provided).
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: significance_threshold
    owner: FunctionalAssay
    range: string
  comment:
    name: comment
    description: Any additional information that a curator would like to provide about
      the FunctionalAssay that is not adequately captured by other fields
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    multivalued: true
    alias: comment
    owner: FunctionalAssay
    range: string
  range type:
    name: range type
    description: The type of values that can be expected from results of this assay
      (quantitative or qualitative). This could be inferred from the assay's range,
      but is encoded here to simplify searches.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: range_type
    owner: FunctionalAssay
    range: RangeType
  units:
    name: units
    description: For quantitative assays, the default unit to be applied to individual
      results if not overridden.
    from_schema: https://dataexchange.clinicalgenome.org/variant-functional-assay
    alias: units
    owner: FunctionalAssay
    range: unit