Class: BALFSputumAssay

Assay for measuring bronchoalveolar lavage fluid (BALF) or sputum composition. Informs on Key Event: "Airway inflammation" and provides evidence for inflammatory cell populations and cytokine levels.

This assay is IN VIVO ONLY - requires samples from human or animal subjects.

URI: soma:BALFSputumAssay

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

      BALFSputumAssay : assay_date

      BALFSputumAssay : description

      BALFSputumAssay : follows_protocols





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



      BALFSputumAssay : has_exposure_condition





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



      BALFSputumAssay : has_specified_output





        BALFSputumAssay --> "0..1" BALFSputumOutput : has_specified_output
        click BALFSputumOutput href "../BALFSputumOutput/"



      BALFSputumAssay : id

      BALFSputumAssay : informs_on_key_event





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



      BALFSputumAssay : name

      BALFSputumAssay : study_subject





        BALFSputumAssay --> "0..1" InVivoSubject : study_subject
        click InVivoSubject href "../InVivoSubject/"



      BALFSputumAssay : target_cell_type





        BALFSputumAssay --> "0..1" CellTypeReference : target_cell_type
        click CellTypeReference href "../CellTypeReference/"

Inheritance

NamedThing
- Assay
  - BALFSputumAssay

Slots

Name	Cardinality and Range	Description	Inheritance
target_cell_type	0..1 CellTypeReference	The specific cell type that is the primary focus of this assay's analysis, wh...	direct
informs_on_key_event	0..1 KeyEvent	The Key Event that this assay provides evidence for	Assay
study_subject	0..1 InVivoSubject	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 BALFSputumOutput	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	balf_sputum_assays	range	BALFSputumAssay

Identifier and Mapping Information

Annotations

property	value
supported_contexts	in_vivo_only

Schema Source

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

Mappings

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

LinkML Source

Direct

name: BALFSputumAssay
annotations:
  supported_contexts:
    tag: supported_contexts
    value: in_vivo_only
description: 'Assay for measuring bronchoalveolar lavage fluid (BALF) or sputum composition.
  Informs on Key Event: "Airway inflammation" and provides evidence for inflammatory
  cell populations and cytokine levels.

  This assay is IN VIVO ONLY - requires samples from human or animal subjects.'
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slots:
- target_cell_type
slot_usage:
  study_subject:
    name: study_subject
    range: InVivoSubject
  has_specified_output:
    name: has_specified_output
    range: BALFSputumOutput

Induced

name: BALFSputumAssay
annotations:
  supported_contexts:
    tag: supported_contexts
    value: in_vivo_only
description: 'Assay for measuring bronchoalveolar lavage fluid (BALF) or sputum composition.
  Informs on Key Event: "Airway inflammation" and provides evidence for inflammatory
  cell populations and cytokine levels.

  This assay is IN VIVO ONLY - requires samples from human or animal subjects.'
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slot_usage:
  study_subject:
    name: study_subject
    range: InVivoSubject
  has_specified_output:
    name: has_specified_output
    range: BALFSputumOutput
attributes:
  target_cell_type:
    name: target_cell_type
    description: The specific cell type that is the primary focus of this assay's
      analysis, when the assay examines multiple cell populations in a sample (e.g.,
      neutrophils in a BALF differential).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: target_cell_type
    owner: BALFSputumAssay
    domain_of:
    - BALFSputumAssay
    range: CellTypeReference
    inlined: true
  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: BALFSputumAssay
    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: BALFSputumAssay
    domain_of:
    - Assay
    range: InVivoSubject
    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: BALFSputumAssay
    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: BALFSputumAssay
    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: BALFSputumAssay
    domain_of:
    - Assay
    range: BALFSputumOutput
    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: BALFSputumAssay
    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: BALFSputumAssay
    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: BALFSputumAssay
    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: BALFSputumAssay
    domain_of:
    - NamedThing
    range: string