Class: LungFunctionAssay

Clinical assay for measuring lung function. Informs on Adverse Outcome: "Decreased lung function" - the composite clinical outcome.

IMPORTANT per domain feedback: - Subject characteristics (sex, species, age, height) are critical -

_ often reported as % of predicted baseline_

- Reference dataset (GLI-2012 for humans) is essential for interpretation - Hemoglobin levels pair with DLCO measurements - Recent respiratory illness affects spirometry results

TIER 1 slots (critical): fev1, fvc, subject_characteristics, reference_dataset. This assay is IN VIVO ONLY.

URI: soma:LungFunctionAssay

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

      LungFunctionAssay : assay_date

      LungFunctionAssay : description

      LungFunctionAssay : follows_protocols





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



      LungFunctionAssay : has_exposure_condition





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



      LungFunctionAssay : has_specified_output





        LungFunctionAssay --> "0..1" LungFunctionOutput : has_specified_output
        click LungFunctionOutput href "../LungFunctionOutput/"



      LungFunctionAssay : hemoglobin_level





        LungFunctionAssay --> "0..1" QuantityValue : hemoglobin_level
        click QuantityValue href "../QuantityValue/"



      LungFunctionAssay : id

      LungFunctionAssay : informs_on_key_event





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



      LungFunctionAssay : name

      LungFunctionAssay : recent_respiratory_illness

      LungFunctionAssay : reference_dataset

      LungFunctionAssay : study_subject





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

Inheritance

NamedThing
- Assay
  - LungFunctionAssay

Slots

Name	Cardinality and Range	Description	Inheritance
reference_dataset	0..1 String	Reference dataset for interpretation (GLI-2012 for humans)	direct
hemoglobin_level	0..1 QuantityValue	Hemoglobin level	direct
recent_respiratory_illness	0..1 String	Recent respiratory illness (affects spirometry)	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 LungFunctionOutput	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	lung_function_assays	range	LungFunctionAssay

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:LungFunctionAssay
native	soma:LungFunctionAssay

LinkML Source

Direct

name: LungFunctionAssay
annotations:
  supported_contexts:
    tag: supported_contexts
    value: in_vivo_only
description: "Clinical assay for measuring lung function. Informs on Adverse Outcome:\
  \ \"Decreased lung function\" - the composite clinical outcome.\nIMPORTANT per domain\
  \ feedback: - Subject characteristics (sex, species, age, height) are critical -\n\
  \  often reported as % of predicted baseline\n- Reference dataset (GLI-2012 for\
  \ humans) is essential for interpretation - Hemoglobin levels pair with DLCO measurements\
  \ - Recent respiratory illness affects spirometry results\nTIER 1 slots (critical):\
  \ fev1, fvc, subject_characteristics, reference_dataset. This assay is IN VIVO ONLY."
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slots:
- reference_dataset
- hemoglobin_level
- recent_respiratory_illness
slot_usage:
  study_subject:
    name: study_subject
    range: InVivoSubject
  has_specified_output:
    name: has_specified_output
    range: LungFunctionOutput

Induced

name: LungFunctionAssay
annotations:
  supported_contexts:
    tag: supported_contexts
    value: in_vivo_only
description: "Clinical assay for measuring lung function. Informs on Adverse Outcome:\
  \ \"Decreased lung function\" - the composite clinical outcome.\nIMPORTANT per domain\
  \ feedback: - Subject characteristics (sex, species, age, height) are critical -\n\
  \  often reported as % of predicted baseline\n- Reference dataset (GLI-2012 for\
  \ humans) is essential for interpretation - Hemoglobin levels pair with DLCO measurements\
  \ - Recent respiratory illness affects spirometry results\nTIER 1 slots (critical):\
  \ fev1, fvc, subject_characteristics, reference_dataset. This assay is IN VIVO ONLY."
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: LungFunctionOutput
attributes:
  reference_dataset:
    name: reference_dataset
    description: Reference dataset for interpretation (GLI-2012 for humans). TIER
      1 - essential for interpretation.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: reference_dataset
    owner: LungFunctionAssay
    domain_of:
    - LungFunctionAssay
    range: string
  hemoglobin_level:
    name: hemoglobin_level
    description: Hemoglobin level. TIER 2 - pairs with DLCO.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: hemoglobin_level
    owner: LungFunctionAssay
    domain_of:
    - LungFunctionAssay
    range: QuantityValue
    inlined: true
  recent_respiratory_illness:
    name: recent_respiratory_illness
    description: Recent respiratory illness (affects spirometry). TIER 2.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: recent_respiratory_illness
    owner: LungFunctionAssay
    domain_of:
    - LungFunctionAssay
    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: LungFunctionAssay
    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: LungFunctionAssay
    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: LungFunctionAssay
    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: LungFunctionAssay
    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: LungFunctionAssay
    domain_of:
    - Assay
    range: LungFunctionOutput
    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: LungFunctionAssay
    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: LungFunctionAssay
    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: LungFunctionAssay
    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: LungFunctionAssay
    domain_of:
    - NamedThing
    range: string