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Class: MucociliaryClearanceAssay

Assay for measuring mucociliary clearance and transport. Informs on Key Event: "Impaired mucociliary clearance" in respiratory AOPs. TIER 1 slots (critical): transport_rate, directionality.

URI: soma:MucociliaryClearanceAssay

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

      MucociliaryClearanceAssay : assay_date

      MucociliaryClearanceAssay : description

      MucociliaryClearanceAssay : follows_protocols





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



      MucociliaryClearanceAssay : has_exposure_condition





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



      MucociliaryClearanceAssay : has_specified_output





        MucociliaryClearanceAssay --> "0..1" MucociliaryClearanceOutput : has_specified_output
        click MucociliaryClearanceOutput href "../MucociliaryClearanceOutput/"



      MucociliaryClearanceAssay : id

      MucociliaryClearanceAssay : informs_on_key_event





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



      MucociliaryClearanceAssay : mucus_composition

      MucociliaryClearanceAssay : name

      MucociliaryClearanceAssay : study_subject





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

Inheritance

Slots

Name Cardinality and Range Description Inheritance
mucus_composition 0..1
String		 Composition of mucus direct
informs_on_key_event 0..1
KeyEvent		 The Key Event that this assay provides evidence for Assay
study_subject 0..1
StudySubject		 The subject of the study — what the assay is performed on Assay
has_exposure_condition *
ExposureCondition		 The exposure condition(s) applied to the study subject Assay
follows_protocols *
Protocol		 The Protocol(s) that this assay follows Assay
has_specified_output 0..1
MucociliaryClearanceOutput		 The measurement results produced by this assay — the specified output of a pl... Assay
assay_date 0..1
Date		 Date when the assay was performed Assay
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

Usages

used by used in type used
Container mcc_assays range MucociliaryClearanceAssay

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self soma:MucociliaryClearanceAssay
native soma:MucociliaryClearanceAssay

LinkML Source

Direct

name: MucociliaryClearanceAssay
description: 'Assay for measuring mucociliary clearance and transport. Informs on
  Key Event: "Impaired mucociliary clearance" in respiratory AOPs. TIER 1 slots (critical):
  transport_rate, directionality.'
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slots:
- mucus_composition
slot_usage:
  has_specified_output:
    name: has_specified_output
    range: MucociliaryClearanceOutput

Induced

name: MucociliaryClearanceAssay
description: 'Assay for measuring mucociliary clearance and transport. Informs on
  Key Event: "Impaired mucociliary clearance" in respiratory AOPs. TIER 1 slots (critical):
  transport_rate, directionality.'
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slot_usage:
  has_specified_output:
    name: has_specified_output
    range: MucociliaryClearanceOutput
attributes:
  mucus_composition:
    name: mucus_composition
    description: Composition of mucus. TIER 2 per feedback.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: mucus_composition
    owner: MucociliaryClearanceAssay
    domain_of:
    - MucociliaryClearanceAssay
    range: string
  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: MucociliaryClearanceAssay
    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: MucociliaryClearanceAssay
    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: MucociliaryClearanceAssay
    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: MucociliaryClearanceAssay
    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: MucociliaryClearanceAssay
    domain_of:
    - Assay
    range: MucociliaryClearanceOutput
    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: MucociliaryClearanceAssay
    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: MucociliaryClearanceAssay
    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: MucociliaryClearanceAssay
    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: MucociliaryClearanceAssay
    domain_of:
    - NamedThing
    range: string