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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 : data_in_figure_only

      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 : evidence





        EGFRSignalingOutput --> "* _recommended_" EvidenceItem : evidence
        click EvidenceItem href "../EvidenceItem/"



      EGFRSignalingOutput : experimental_group





        EGFRSignalingOutput --> "0..1" ExperimentalGroupEnum : experimental_group
        click ExperimentalGroupEnum href "../ExperimentalGroupEnum/"



      EGFRSignalingOutput : id

      EGFRSignalingOutput : measured_under





        EGFRSignalingOutput --> "0..1" ExposureCondition : measured_under
        click ExposureCondition href "../ExposureCondition/"



      EGFRSignalingOutput : name

      EGFRSignalingOutput : pathway_biomarkers

      EGFRSignalingOutput : total_egfr_protein





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

Inheritance

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
evidence * recommended
EvidenceItem		 Evidence items backing this object's claims AssayOutputMeasurement
experimental_group 0..1
ExperimentalGroupEnum		 The role of this output record's group in the experimental design: control, v... AssayOutputMeasurement
measured_under 0..1
ExposureCondition		 Reference (by id) to the specific ExposureCondition this output record was me... AssayOutputMeasurement
data_in_figure_only 0..1
Boolean		 True when the quantitative values for this output record are reported only in... AssayOutputMeasurement
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
  evidence:
    name: evidence
    description: Evidence items backing this object's claims. Each one carries an
      exact quote from a cited publication.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: evidence
    owner: EGFRSignalingOutput
    domain_of:
    - KeyEvent
    - KeyEventRelationship
    - Assay
    - AssayOutputMeasurement
    range: EvidenceItem
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  experimental_group:
    name: experimental_group
    description: 'The role of this output record''s group in the experimental design:
      control, vehicle control, baseline, treated, recovery, or sham. Lets extraction
      distinguish the control/baseline response from the treated response so a change
      relative to control can be assembled downstream.'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: experimental_group
    owner: EGFRSignalingOutput
    domain_of:
    - AssayOutputMeasurement
    range: ExperimentalGroupEnum
  measured_under:
    name: measured_under
    description: Reference (by id) to the specific ExposureCondition this output record
      was measured under. Links each set of response values to the concentration/treatment
      it corresponds to, so a dose-response series keeps each response paired with
      its exposure level. The referenced condition should be listed in the assay's
      has_exposure_condition.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: measured_under
    owner: EGFRSignalingOutput
    domain_of:
    - AssayOutputMeasurement
    range: ExposureCondition
    inlined: false
  data_in_figure_only:
    name: data_in_figure_only
    description: True when the quantitative values for this output record are reported
      only in a figure or chart and could not be read from the text. The record then
      documents that the endpoint was measured and where its data lives (via an evidence
      item's figure_reference and article_section), without numeric values. This keeps
      figure-only results visible to reviewers in the workbook instead of silently
      dropping them.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: data_in_figure_only
    owner: EGFRSignalingOutput
    domain_of:
    - AssayOutputMeasurement
    range: boolean
  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