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Class: Assay

A planned process with the objective to produce information about biological state relevant to a Key Event in an Adverse Outcome Pathway. Assays are organized by the functional domain they assess (e.g., ciliary function, oxidative stress), and each domain-specific assay class contains named slots for the specific measurements it can produce. Assays inform on key events and contain the measurement data as named slots.

  • NOTE: this is an abstract class and should not be instantiated directly

URI: OBI:0000070

 classDiagram
    class Assay
    click Assay href "../Assay/"
      NamedThing <|-- Assay
        click NamedThing href "../NamedThing/"


      Assay <|-- CiliaryFunctionAssay
        click CiliaryFunctionAssay href "../CiliaryFunctionAssay/"
      Assay <|-- ASLAssay
        click ASLAssay href "../ASLAssay/"
      Assay <|-- MucociliaryClearanceAssay
        click MucociliaryClearanceAssay href "../MucociliaryClearanceAssay/"
      Assay <|-- OxidativeStressAssay
        click OxidativeStressAssay href "../OxidativeStressAssay/"
      Assay <|-- CFTRFunctionAssay
        click CFTRFunctionAssay href "../CFTRFunctionAssay/"
      Assay <|-- EGFRSignalingAssay
        click EGFRSignalingAssay href "../EGFRSignalingAssay/"
      Assay <|-- GobletCellAssay
        click GobletCellAssay href "../GobletCellAssay/"
      Assay <|-- BALFSputumAssay
        click BALFSputumAssay href "../BALFSputumAssay/"
      Assay <|-- LungFunctionAssay
        click LungFunctionAssay href "../LungFunctionAssay/"
      Assay <|-- FoxJExpressionAssay
        click FoxJExpressionAssay href "../FoxJExpressionAssay/"
      Assay <|-- GeneExpressionAssay
        click GeneExpressionAssay href "../GeneExpressionAssay/"


      Assay : assay_date

      Assay : description

      Assay : follows_protocols





        Assay --> "*" Protocol : follows_protocols
        click Protocol href "../Protocol/"



      Assay : has_exposure_condition





        Assay --> "*" ExposureCondition : has_exposure_condition
        click ExposureCondition href "../ExposureCondition/"



      Assay : has_specified_output





        Assay --> "0..1" AssayOutputMeasurement : has_specified_output
        click AssayOutputMeasurement href "../AssayOutputMeasurement/"



      Assay : id

      Assay : informs_on_key_event





        Assay --> "0..1" KeyEvent : informs_on_key_event
        click KeyEvent href "../KeyEvent/"



      Assay : name

      Assay : study_subject





        Assay --> "0..1" StudySubject : study_subject
        click StudySubject href "../StudySubject/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
informs_on_key_event 0..1
KeyEvent		 The Key Event that this assay provides evidence for direct
study_subject 0..1
StudySubject		 The subject of the study — what the assay is performed on direct
has_exposure_condition *
ExposureCondition		 The exposure condition(s) applied to the study subject direct
follows_protocols *
Protocol		 The Protocol(s) that this assay follows direct
has_specified_output 0..1
AssayOutputMeasurement		 The measurement results produced by this assay — the specified output of a pl... direct
assay_date 0..1
Date		 Date when the assay was performed direct
id 1
Uriorcurie		 A unique identifier for the entity NamedThing
name 0..1
String		 A human-readable name for the entity NamedThing
description 0..1
String		 A detailed description of the entity NamedThing

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/EHS-Data-Standards/soma

Mappings

Mapping Type Mapped Value
self OBI:0000070
native soma:Assay

LinkML Source

Direct

name: Assay
description: A planned process with the objective to produce information about biological
  state relevant to a Key Event in an Adverse Outcome Pathway. Assays are organized
  by the functional domain they assess (e.g., ciliary function, oxidative stress),
  and each domain-specific assay class contains named slots for the specific measurements
  it can produce. Assays inform on key events and contain the measurement data as
  named slots.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: NamedThing
abstract: true
slots:
- informs_on_key_event
- study_subject
- has_exposure_condition
- follows_protocols
- has_specified_output
- assay_date
class_uri: OBI:0000070

Induced

name: Assay
description: A planned process with the objective to produce information about biological
  state relevant to a Key Event in an Adverse Outcome Pathway. Assays are organized
  by the functional domain they assess (e.g., ciliary function, oxidative stress),
  and each domain-specific assay class contains named slots for the specific measurements
  it can produce. Assays inform on key events and contain the measurement data as
  named slots.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: NamedThing
abstract: true
attributes:
  informs_on_key_event:
    name: informs_on_key_event
    description: The Key Event that this assay provides evidence for. This establishes
      the mechanistic connection between the assay measurements and the Adverse Outcome
      Pathway framework. Multiple assays can inform on the same key event, providing
      converging evidence.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: informs_on_key_event
    owner: Assay
    domain_of:
    - Assay
    range: KeyEvent
    inlined: true
  study_subject:
    name: study_subject
    description: The subject of the study — what the assay is performed on. Can be
      a ModelSystem (e.g., CellularSystem), an InVivoSubject, or a PopulationSubject.
      The type of subject determines which context slots are available.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: study_subject
    owner: Assay
    domain_of:
    - Assay
    range: StudySubject
    inlined: true
  has_exposure_condition:
    name: has_exposure_condition
    description: The exposure condition(s) applied to the study subject. Captures
      the agent, concentration, duration, and timing of exposure/treatment. Multivalued
      to support co-exposures or dose-response series.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: has_exposure_condition
    owner: Assay
    domain_of:
    - Assay
    range: ExposureCondition
    multivalued: true
    inlined: true
    inlined_as_list: true
  follows_protocols:
    name: follows_protocols
    description: The Protocol(s) that this assay follows. Any Protocol or Protocol
      subclass (ImagingProtocol, StainingProtocol, SpirometryProtocol, MolecularAssayProtocol)
      is valid. Use this for general protocol references; assay subclasses also have
      typed protocol slots for domain-specific protocols.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: follows_protocols
    owner: Assay
    domain_of:
    - Assay
    range: Protocol
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_specified_output:
    name: has_specified_output
    description: The measurement results produced by this assay — the specified output
      of a planned process (OBI). Contains the domain-specific measurement values
      (e.g., beat frequency, cilia length for CiliaryFunctionAssay).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    exact_mappings:
    - OBI:0000299
    rank: 1000
    alias: has_specified_output
    owner: Assay
    domain_of:
    - Assay
    range: AssayOutputMeasurement
    inlined: true
  assay_date:
    name: assay_date
    description: Date when the assay was performed.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: assay_date
    owner: Assay
    domain_of:
    - Assay
    range: date
  id:
    name: id
    description: A unique identifier for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    identifier: true
    alias: id
    owner: Assay
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: uriorcurie
    required: true
  name:
    name: name
    description: A human-readable name for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: Assay
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: string
  description:
    name: description
    description: A detailed description of the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: Assay
    domain_of:
    - NamedThing
    range: string
class_uri: OBI:0000070