Class: EGFRSignalingAssay

Assay for measuring EGFR phosphorylation and downstream signaling. Informs on Key Event: "EGFR activation" in mucus hypersecretion AOPs.

IMPORTANT: EGFR phosphorylation is the MOST SPECIFIC evidence for activation. Downstream kinase data alone is insufficient - needs phosphorylation measure OR inhibitor reversal for strong evidence. Cell type matters due to receptor location in ALI cultures.

TIER 1 slots (critical): egfr_phosphorylation with site specification.

URI: soma:EGFRSignalingAssay

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

      EGFRSignalingAssay : assay_date

      EGFRSignalingAssay : description

      EGFRSignalingAssay : follows_protocols





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



      EGFRSignalingAssay : has_exposure_condition





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



      EGFRSignalingAssay : has_specified_output





        EGFRSignalingAssay --> "0..1" EGFRSignalingOutput : has_specified_output
        click EGFRSignalingOutput href "../EGFRSignalingOutput/"



      EGFRSignalingAssay : id

      EGFRSignalingAssay : informs_on_key_event





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



      EGFRSignalingAssay : name

      EGFRSignalingAssay : normalization_reference

      EGFRSignalingAssay : phosphorylation_site

      EGFRSignalingAssay : study_subject





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

Inheritance

NamedThing
- Assay
  - EGFRSignalingAssay

Slots

Name	Cardinality and Range	Description	Inheritance
normalization_reference	0..1 String	Normalization reference (beta-actin, GAPDH, total EGFR)	direct
phosphorylation_site	0..1 String	Specific phosphorylation site being measured	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 EGFRSignalingOutput	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	egfr_signaling_assays	range	EGFRSignalingAssay

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: EGFRSignalingAssay
description: 'Assay for measuring EGFR phosphorylation and downstream signaling. Informs
  on Key Event: "EGFR activation" in mucus hypersecretion AOPs.

  IMPORTANT: EGFR phosphorylation is the MOST SPECIFIC evidence for activation. Downstream
  kinase data alone is insufficient - needs phosphorylation measure OR inhibitor reversal
  for strong evidence. Cell type matters due to receptor location in ALI cultures.

  TIER 1 slots (critical): egfr_phosphorylation with site specification.'
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slots:
- normalization_reference
- phosphorylation_site
slot_usage:
  has_specified_output:
    name: has_specified_output
    range: EGFRSignalingOutput

Induced

name: EGFRSignalingAssay
description: 'Assay for measuring EGFR phosphorylation and downstream signaling. Informs
  on Key Event: "EGFR activation" in mucus hypersecretion AOPs.

  IMPORTANT: EGFR phosphorylation is the MOST SPECIFIC evidence for activation. Downstream
  kinase data alone is insufficient - needs phosphorylation measure OR inhibitor reversal
  for strong evidence. Cell type matters due to receptor location in ALI cultures.

  TIER 1 slots (critical): egfr_phosphorylation with site specification.'
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Assay
slot_usage:
  has_specified_output:
    name: has_specified_output
    range: EGFRSignalingOutput
attributes:
  normalization_reference:
    name: normalization_reference
    description: Normalization reference (beta-actin, GAPDH, total EGFR).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: normalization_reference
    owner: EGFRSignalingAssay
    domain_of:
    - EGFRSignalingAssay
    - GeneExpressionAssay
    range: string
  phosphorylation_site:
    name: phosphorylation_site
    description: Specific phosphorylation site being measured.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: phosphorylation_site
    owner: EGFRSignalingAssay
    domain_of:
    - EGFRSignalingAssay
    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: EGFRSignalingAssay
    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: EGFRSignalingAssay
    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: EGFRSignalingAssay
    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: EGFRSignalingAssay
    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: EGFRSignalingAssay
    domain_of:
    - Assay
    range: EGFRSignalingOutput
    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: EGFRSignalingAssay
    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: EGFRSignalingAssay
    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: EGFRSignalingAssay
    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: EGFRSignalingAssay
    domain_of:
    - NamedThing
    range: string