Class: Container

Root container for outcomes research data. Organized around ASSAYS that inform on Key Events in Adverse Outcome Pathways (AOPs).

The schema is assay-centric: each assay class contains named slots for its specific measurements, with an explicit connection to the Key Event it informs via the informs_on_key_event slot.

URI: soma:Container

 classDiagram
    class Container
    click Container href "../Container/"
      Container : adverse_outcome_pathways





        Container --> "*" AdverseOutcomePathway : adverse_outcome_pathways
        click AdverseOutcomePathway href "../AdverseOutcomePathway/"



      Container : asl_assays





        Container --> "*" ASLAssay : asl_assays
        click ASLAssay href "../ASLAssay/"



      Container : balf_sputum_assays





        Container --> "*" BALFSputumAssay : balf_sputum_assays
        click BALFSputumAssay href "../BALFSputumAssay/"



      Container : cftr_assays





        Container --> "*" CFTRFunctionAssay : cftr_assays
        click CFTRFunctionAssay href "../CFTRFunctionAssay/"



      Container : ciliary_function_assays





        Container --> "*" CiliaryFunctionAssay : ciliary_function_assays
        click CiliaryFunctionAssay href "../CiliaryFunctionAssay/"



      Container : egfr_signaling_assays





        Container --> "*" EGFRSignalingAssay : egfr_signaling_assays
        click EGFRSignalingAssay href "../EGFRSignalingAssay/"



      Container : foxj_assays





        Container --> "*" FoxJExpressionAssay : foxj_assays
        click FoxJExpressionAssay href "../FoxJExpressionAssay/"



      Container : gene_expression_assays





        Container --> "*" GeneExpressionAssay : gene_expression_assays
        click GeneExpressionAssay href "../GeneExpressionAssay/"



      Container : goblet_cell_assays





        Container --> "*" GobletCellAssay : goblet_cell_assays
        click GobletCellAssay href "../GobletCellAssay/"



      Container : key_events





        Container --> "*" KeyEvent : key_events
        click KeyEvent href "../KeyEvent/"



      Container : lung_function_assays





        Container --> "*" LungFunctionAssay : lung_function_assays
        click LungFunctionAssay href "../LungFunctionAssay/"



      Container : mcc_assays





        Container --> "*" MucociliaryClearanceAssay : mcc_assays
        click MucociliaryClearanceAssay href "../MucociliaryClearanceAssay/"



      Container : oxidative_stress_assays





        Container --> "*" OxidativeStressAssay : oxidative_stress_assays
        click OxidativeStressAssay href "../OxidativeStressAssay/"



      Container : protocols





        Container --> "*" Protocol : protocols
        click Protocol href "../Protocol/"

Slots

Name	Cardinality and Range	Description	Inheritance
key_events	* KeyEvent	The key events in this AOP (intermediate events between MIE and AO)	direct
adverse_outcome_pathways	* AdverseOutcomePathway	Collection of Adverse Outcome Pathways	direct
ciliary_function_assays	* CiliaryFunctionAssay	Collection of ciliary function assays	direct
asl_assays	* ASLAssay	Collection of airway surface liquid assays	direct
mcc_assays	* MucociliaryClearanceAssay	Collection of mucociliary clearance assays	direct
oxidative_stress_assays	* OxidativeStressAssay	Collection of oxidative stress assays	direct
cftr_assays	* CFTRFunctionAssay	Collection of CFTR function assays	direct
egfr_signaling_assays	* EGFRSignalingAssay	Collection of EGFR signaling assays	direct
goblet_cell_assays	* GobletCellAssay	Collection of goblet cell and mucin assays	direct
balf_sputum_assays	* BALFSputumAssay	Collection of BALF and sputum assays	direct
lung_function_assays	* LungFunctionAssay	Collection of lung function assays	direct
foxj_assays	* FoxJExpressionAssay	Collection of FoxJ1/ciliogenesis assays	direct
gene_expression_assays	* GeneExpressionAssay	Collection of gene expression assays	direct
protocols	* Protocol	Collection of protocols	direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Container
description: 'Root container for outcomes research data. Organized around ASSAYS that
  inform on Key Events in Adverse Outcome Pathways (AOPs).

  The schema is assay-centric: each assay class contains named slots for its specific
  measurements, with an explicit connection to the Key Event it informs via the informs_on_key_event
  slot.'
from_schema: https://w3id.org/EHS-Data-Standards/soma
slots:
- key_events
- adverse_outcome_pathways
- ciliary_function_assays
- asl_assays
- mcc_assays
- oxidative_stress_assays
- cftr_assays
- egfr_signaling_assays
- goblet_cell_assays
- balf_sputum_assays
- lung_function_assays
- foxj_assays
- gene_expression_assays
- protocols
tree_root: true

Induced

name: Container
description: 'Root container for outcomes research data. Organized around ASSAYS that
  inform on Key Events in Adverse Outcome Pathways (AOPs).

  The schema is assay-centric: each assay class contains named slots for its specific
  measurements, with an explicit connection to the Key Event it informs via the informs_on_key_event
  slot.'
from_schema: https://w3id.org/EHS-Data-Standards/soma
attributes:
  key_events:
    name: key_events
    description: The key events in this AOP (intermediate events between MIE and AO).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: key_events
    owner: Container
    domain_of:
    - Container
    - AdverseOutcomePathway
    range: KeyEvent
    multivalued: true
    inlined_as_list: true
  adverse_outcome_pathways:
    name: adverse_outcome_pathways
    description: Collection of Adverse Outcome Pathways. AOPs describe sequences of
      causally linked events from molecular initiating events to adverse outcomes.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: adverse_outcome_pathways
    owner: Container
    domain_of:
    - Container
    range: AdverseOutcomePathway
    multivalued: true
    inlined_as_list: true
  ciliary_function_assays:
    name: ciliary_function_assays
    description: 'Collection of ciliary function assays. Informs on Key Event: "Decreased
      ciliary function". Contains named slots for beat frequency, active area, cilia
      length, etc.'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: ciliary_function_assays
    owner: Container
    domain_of:
    - Container
    range: CiliaryFunctionAssay
    multivalued: true
    inlined_as_list: true
  asl_assays:
    name: asl_assays
    description: 'Collection of airway surface liquid assays. Informs on Key Event:
      "Decreased ASL height" or "Altered airway hydration".'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: asl_assays
    owner: Container
    domain_of:
    - Container
    range: ASLAssay
    multivalued: true
    inlined_as_list: true
  mcc_assays:
    name: mcc_assays
    description: 'Collection of mucociliary clearance assays. Informs on Key Event:
      "Impaired mucociliary clearance".'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: mcc_assays
    owner: Container
    domain_of:
    - Container
    range: MucociliaryClearanceAssay
    multivalued: true
    inlined_as_list: true
  oxidative_stress_assays:
    name: oxidative_stress_assays
    description: 'Collection of oxidative stress assays. Informs on Key Event: "Increased
      oxidative stress" - often a Molecular Initiating Event.'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: oxidative_stress_assays
    owner: Container
    domain_of:
    - Container
    range: OxidativeStressAssay
    multivalued: true
    inlined_as_list: true
  cftr_assays:
    name: cftr_assays
    description: 'Collection of CFTR function assays. Informs on Key Event: "Decreased
      CFTR function".'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: cftr_assays
    owner: Container
    domain_of:
    - Container
    range: CFTRFunctionAssay
    multivalued: true
    inlined_as_list: true
  egfr_signaling_assays:
    name: egfr_signaling_assays
    description: 'Collection of EGFR signaling assays. Informs on Key Event: "EGFR
      activation". Note: EGFR phosphorylation is the most specific evidence for activation.'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: egfr_signaling_assays
    owner: Container
    domain_of:
    - Container
    range: EGFRSignalingAssay
    multivalued: true
    inlined_as_list: true
  goblet_cell_assays:
    name: goblet_cell_assays
    description: 'Collection of goblet cell and mucin assays. Informs on Key Event:
      "Goblet cell hyperplasia" or "Mucin hypersecretion". Combined from previous
      GobletCellMeasurement and MucinProductionMeasurement.'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: goblet_cell_assays
    owner: Container
    domain_of:
    - Container
    range: GobletCellAssay
    multivalued: true
    inlined_as_list: true
  balf_sputum_assays:
    name: balf_sputum_assays
    description: 'Collection of BALF and sputum assays. In vivo only. Informs on Key
      Event: "Airway inflammation".'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: balf_sputum_assays
    owner: Container
    domain_of:
    - Container
    range: BALFSputumAssay
    multivalued: true
    inlined_as_list: true
  lung_function_assays:
    name: lung_function_assays
    description: 'Collection of lung function assays. In vivo only. Informs on Adverse
      Outcome: "Decreased lung function" - the composite clinical outcome.'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: lung_function_assays
    owner: Container
    domain_of:
    - Container
    range: LungFunctionAssay
    multivalued: true
    inlined_as_list: true
  foxj_assays:
    name: foxj_assays
    description: 'Collection of FoxJ1/ciliogenesis assays. Informs on Key Event: "Altered
      ciliogenesis".'
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: foxj_assays
    owner: Container
    domain_of:
    - Container
    range: FoxJExpressionAssay
    multivalued: true
    inlined_as_list: true
  gene_expression_assays:
    name: gene_expression_assays
    description: Collection of gene expression assays. Generic assay for gene/protein
      expression measurements.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: gene_expression_assays
    owner: Container
    domain_of:
    - Container
    range: GeneExpressionAssay
    multivalued: true
    inlined_as_list: true
  protocols:
    name: protocols
    description: Collection of protocols. Contains Tier 2/3 procedural details important
      for reproducibility.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: protocols
    owner: Container
    domain_of:
    - Container
    range: Protocol
    multivalued: true
    inlined_as_list: true
tree_root: true