Class: EGFRSignalingOutput

Measurement results from an EGFR signaling assay. Contains the measured values for EGFR phosphorylation, total protein, and downstream kinase activation.

URI: soma:EGFRSignalingOutput

 classDiagram
    class EGFRSignalingOutput
    click EGFRSignalingOutput href "../EGFRSignalingOutput/"
      AssayOutputMeasurement <|-- EGFRSignalingOutput
        click AssayOutputMeasurement href "../AssayOutputMeasurement/"

      EGFRSignalingOutput : akt_phosphorylation





        EGFRSignalingOutput --> "0..1" QuantityValue : akt_phosphorylation
        click QuantityValue href "../QuantityValue/"



      EGFRSignalingOutput : description

      EGFRSignalingOutput : downstream_kinase_activation

      EGFRSignalingOutput : egfr_ligand_expression





        EGFRSignalingOutput --> "0..1" QuantityValue : egfr_ligand_expression
        click QuantityValue href "../QuantityValue/"



      EGFRSignalingOutput : egfr_membrane_localization





        EGFRSignalingOutput --> "0..1" QuantityValue : egfr_membrane_localization
        click QuantityValue href "../QuantityValue/"



      EGFRSignalingOutput : egfr_phosphorylation_y1068





        EGFRSignalingOutput --> "0..1" QuantityValue : egfr_phosphorylation_y1068
        click QuantityValue href "../QuantityValue/"



      EGFRSignalingOutput : egfr_phosphorylation_y1173





        EGFRSignalingOutput --> "0..1" QuantityValue : egfr_phosphorylation_y1173
        click QuantityValue href "../QuantityValue/"



      EGFRSignalingOutput : erk_phosphorylation





        EGFRSignalingOutput --> "0..1" QuantityValue : erk_phosphorylation
        click QuantityValue href "../QuantityValue/"



      EGFRSignalingOutput : id

      EGFRSignalingOutput : name

      EGFRSignalingOutput : pathway_biomarkers

      EGFRSignalingOutput : total_egfr_protein





        EGFRSignalingOutput --> "0..1" QuantityValue : total_egfr_protein
        click QuantityValue href "../QuantityValue/"

Inheritance

NamedThing
- AssayOutputMeasurement
  - EGFRSignalingOutput

Slots

Name	Cardinality and Range	Description	Inheritance
egfr_phosphorylation_y1068	0..1 QuantityValue	EGFR phosphorylation at Y1068 residue (fold change)	direct
egfr_phosphorylation_y1173	0..1 QuantityValue	EGFR phosphorylation at Y1173 residue (fold change)	direct
total_egfr_protein	0..1 QuantityValue	Total EGFR protein level (loading control)	direct
downstream_kinase_activation	0..1 String	Activation levels of downstream kinases	direct
erk_phosphorylation	0..1 QuantityValue	ERK phosphorylation level	direct
akt_phosphorylation	0..1 QuantityValue	AKT phosphorylation level	direct
pathway_biomarkers	* String	Pathway-specific biomarker signatures	direct
egfr_ligand_expression	0..1 QuantityValue	Expression of EGFR ligands (EGF, TGF-alpha, amphiregulin)	direct
egfr_membrane_localization	0..1 QuantityValue	EGFR membrane localization percentage	direct
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
EGFRSignalingAssay	has_specified_output	range	EGFRSignalingOutput

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: EGFRSignalingOutput
description: Measurement results from an EGFR signaling assay. Contains the measured
  values for EGFR phosphorylation, total protein, and downstream kinase activation.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: AssayOutputMeasurement
slots:
- egfr_phosphorylation_y1068
- egfr_phosphorylation_y1173
- total_egfr_protein
- downstream_kinase_activation
- erk_phosphorylation
- akt_phosphorylation
- pathway_biomarkers
- egfr_ligand_expression
- egfr_membrane_localization

Induced

name: EGFRSignalingOutput
description: Measurement results from an EGFR signaling assay. Contains the measured
  values for EGFR phosphorylation, total protein, and downstream kinase activation.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: AssayOutputMeasurement
attributes:
  egfr_phosphorylation_y1068:
    name: egfr_phosphorylation_y1068
    description: EGFR phosphorylation at Y1068 residue (fold change). TIER 1 - MOST
      SPECIFIC evidence for EGFR activation.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: egfr_phosphorylation_y1068
    owner: EGFRSignalingOutput
    domain_of:
    - EGFRSignalingOutput
    range: QuantityValue
    inlined: true
  egfr_phosphorylation_y1173:
    name: egfr_phosphorylation_y1173
    description: EGFR phosphorylation at Y1173 residue (fold change). TIER 1.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: egfr_phosphorylation_y1173
    owner: EGFRSignalingOutput
    domain_of:
    - EGFRSignalingOutput
    range: QuantityValue
    inlined: true
  total_egfr_protein:
    name: total_egfr_protein
    description: Total EGFR protein level (loading control). TIER 1.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: total_egfr_protein
    owner: EGFRSignalingOutput
    domain_of:
    - EGFRSignalingOutput
    range: QuantityValue
    inlined: true
  downstream_kinase_activation:
    name: downstream_kinase_activation
    description: Activation levels of downstream kinases. TIER 2 - not specific to
      EGFR alone without phosphorylation data.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: downstream_kinase_activation
    owner: EGFRSignalingOutput
    domain_of:
    - EGFRSignalingOutput
    range: string
  erk_phosphorylation:
    name: erk_phosphorylation
    description: ERK phosphorylation level. TIER 2.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: erk_phosphorylation
    owner: EGFRSignalingOutput
    domain_of:
    - EGFRSignalingOutput
    range: QuantityValue
    inlined: true
  akt_phosphorylation:
    name: akt_phosphorylation
    description: AKT phosphorylation level. TIER 2.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: akt_phosphorylation
    owner: EGFRSignalingOutput
    domain_of:
    - EGFRSignalingOutput
    range: QuantityValue
    inlined: true
  pathway_biomarkers:
    name: pathway_biomarkers
    description: Pathway-specific biomarker signatures. TIER 2 - relationship to outcome
      needs further investigation.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: pathway_biomarkers
    owner: EGFRSignalingOutput
    domain_of:
    - EGFRSignalingOutput
    range: string
    multivalued: true
  egfr_ligand_expression:
    name: egfr_ligand_expression
    description: Expression of EGFR ligands (EGF, TGF-alpha, amphiregulin).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: egfr_ligand_expression
    owner: EGFRSignalingOutput
    domain_of:
    - EGFRSignalingOutput
    range: QuantityValue
    inlined: true
  egfr_membrane_localization:
    name: egfr_membrane_localization
    description: EGFR membrane localization percentage.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: egfr_membrane_localization
    owner: EGFRSignalingOutput
    domain_of:
    - EGFRSignalingOutput
    range: QuantityValue
    inlined: true
  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: EGFRSignalingOutput
    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: EGFRSignalingOutput
    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: EGFRSignalingOutput
    domain_of:
    - NamedThing
    range: string