Class: CiliaryFunctionAssay

Assay for measuring ciliary function including beat frequency, active area, cilia morphology, and ciliated cell populations. Informs on Key Event: "Decreased ciliary function" in respiratory AOPs.

CONTEXT: Can be performed in vitro (tissue slices, spheroids) or in vivo (often using optical coherence tomography).

TIER 1 slots (critical): beat_frequency_hz, active_area_percentage, cilia_length, cilia_per_cell, percentage_ciliated_cells, cell_type_ratios,

URI: soma:CiliaryFunctionAssay

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

      CiliaryFunctionAssay : airway_region

      CiliaryFunctionAssay : analysis_software

      CiliaryFunctionAssay : assay_date

      CiliaryFunctionAssay : description

      CiliaryFunctionAssay : follows_protocols





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



      CiliaryFunctionAssay : has_exposure_condition





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



      CiliaryFunctionAssay : has_specified_output





        CiliaryFunctionAssay --> "0..1" CiliaryFunctionOutput : has_specified_output
        click CiliaryFunctionOutput href "../CiliaryFunctionOutput/"



      CiliaryFunctionAssay : id

      CiliaryFunctionAssay : informs_on_key_event





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



      CiliaryFunctionAssay : name

      CiliaryFunctionAssay : study_subject





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

Inheritance

NamedThing
- Assay
  - CiliaryFunctionAssay

Slots

Name	Cardinality and Range	Description	Inheritance
analysis_software	0..1 String	Software used for analysis (e	direct
airway_region	0..1 String	Region of airway from which cells originated	direct
informs_on_key_event	0..1 KeyEvent	The Key Event that this assay provides evidence for	Assay
study_subject	0..1 StudySubject	Can be ModelSystem (in vitro - ALI cultures, tissue slices, spheroids) or InV...	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 CiliaryFunctionOutput	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	ciliary_function_assays	range	CiliaryFunctionAssay

Identifier and Mapping Information

Annotations

property	value
supported_contexts	in_vitro_or_in_vivo

Schema Source

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

Mappings

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

LinkML Source

Direct

name: CiliaryFunctionAssay
annotations:
  supported_contexts:
    tag: supported_contexts
    value: in_vitro_or_in_vivo
description: 'Assay for measuring ciliary function including beat frequency, active
  area, cilia morphology, and ciliated cell populations. Informs on Key Event: "Decreased
  ciliary function" in respiratory AOPs.

  CONTEXT: Can be performed in vitro (tissue slices, spheroids) or in vivo (often
  using optical coherence tomography).

  TIER 1 slots (critical): beat_frequency_hz, active_area_percentage, cilia_length,
  cilia_per_cell, percentage_ciliated_cells, cell_type_ratios,'
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slots:
- analysis_software
- airway_region
slot_usage:
  study_subject:
    name: study_subject
    description: Can be ModelSystem (in vitro - ALI cultures, tissue slices, spheroids)
      or InVivoSubject (in vivo - OCT measurements)
    range: StudySubject
  has_specified_output:
    name: has_specified_output
    range: CiliaryFunctionOutput

Induced

name: CiliaryFunctionAssay
annotations:
  supported_contexts:
    tag: supported_contexts
    value: in_vitro_or_in_vivo
description: 'Assay for measuring ciliary function including beat frequency, active
  area, cilia morphology, and ciliated cell populations. Informs on Key Event: "Decreased
  ciliary function" in respiratory AOPs.

  CONTEXT: Can be performed in vitro (tissue slices, spheroids) or in vivo (often
  using optical coherence tomography).

  TIER 1 slots (critical): beat_frequency_hz, active_area_percentage, cilia_length,
  cilia_per_cell, percentage_ciliated_cells, cell_type_ratios,'
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slot_usage:
  study_subject:
    name: study_subject
    description: Can be ModelSystem (in vitro - ALI cultures, tissue slices, spheroids)
      or InVivoSubject (in vivo - OCT measurements)
    range: StudySubject
  has_specified_output:
    name: has_specified_output
    range: CiliaryFunctionOutput
attributes:
  analysis_software:
    name: analysis_software
    description: Software used for analysis (e.g., SAVA, Cilia FA).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: analysis_software
    owner: CiliaryFunctionAssay
    domain_of:
    - CiliaryFunctionAssay
    range: string
  airway_region:
    name: airway_region
    description: Region of airway from which cells originated.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: airway_region
    owner: CiliaryFunctionAssay
    domain_of:
    - CiliaryFunctionAssay
    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: CiliaryFunctionAssay
    domain_of:
    - Assay
    range: KeyEvent
    inlined: true
  study_subject:
    name: study_subject
    description: Can be ModelSystem (in vitro - ALI cultures, tissue slices, spheroids)
      or InVivoSubject (in vivo - OCT measurements)
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: study_subject
    owner: CiliaryFunctionAssay
    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: CiliaryFunctionAssay
    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: CiliaryFunctionAssay
    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: CiliaryFunctionAssay
    domain_of:
    - Assay
    range: CiliaryFunctionOutput
    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: CiliaryFunctionAssay
    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: CiliaryFunctionAssay
    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: CiliaryFunctionAssay
    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: CiliaryFunctionAssay
    domain_of:
    - NamedThing
    range: string