Skip to content

Class: CellularSystem

Cell-based model systems that use living cells to model biological processes. Includes 2D cultures, 3D systems, and co-cultures.

  • NOTE: this is an abstract class and should not be instantiated directly

URI: namo:CellularSystem

classDiagram class CellularSystem click CellularSystem href "../CellularSystem/" NAMModel <|-- CellularSystem click NAMModel href "../NAMModel/" CellularSystem <|-- TwoDCellCulture click TwoDCellCulture href "../TwoDCellCulture/" CellularSystem <|-- ThreeDCellCulture click ThreeDCellCulture href "../ThreeDCellCulture/" CellularSystem <|-- CoCulture click CoCulture href "../CoCulture/" CellularSystem : biological_organization_level CellularSystem --> "0..1" BiologicalOrganizationLevelEnum : biological_organization_level click BiologicalOrganizationLevelEnum href "../BiologicalOrganizationLevelEnum/" CellularSystem : cell_source CellularSystem : cell_types CellularSystem --> "*" Term : cell_types click Term href "../Term/" CellularSystem : complexity_level CellularSystem --> "0..1" ComplexityLevelEnum : complexity_level click ComplexityLevelEnum href "../ComplexityLevelEnum/" CellularSystem : culture_conditions CellularSystem : description CellularSystem : id CellularSystem : models CellularSystem --> "*" ModelsRelationship : models click ModelsRelationship href "../ModelsRelationship/" CellularSystem : name CellularSystem : references CellularSystem --> "*" Reference : references click Reference href "../Reference/" CellularSystem : spatial_context CellularSystem : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
cell_types *
Term		 Cell types present in the cellular system direct
cell_source 0..1
String		 Source of cells (e direct
culture_conditions 0..1
String		 Standard culture conditions and media used direct
biological_organization_level 0..1
BiologicalOrganizationLevelEnum		 The level of biological organization represented by the model NAMModel
spatial_context 0..1
String		 Description of spatial organization and context captured by the model NAMModel
complexity_level 0..1
ComplexityLevelEnum		 Level of biological complexity represented (subcellular, cellular, tissue, or... NAMModel
references *
Reference		 Literature references that describe, validate, or support this model NAMModel
models *
ModelsRelationship		 ModelSystem
id 1
Uriorcurie		 A unique identifier for a thing NamedThing
name 0..1
String		 A human-readable name for a thing NamedThing
description 0..1
String		 A human-readable description for a thing NamedThing
type 0..1
String		 NamedThing

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/monarch-initiative/namo

Mappings

Mapping Type Mapped Value
self namo:CellularSystem
native namo:CellularSystem

LinkML Source

Direct

name: CellularSystem
description: Cell-based model systems that use living cells to model biological processes.
  Includes 2D cultures, 3D systems, and co-cultures.
from_schema: https://w3id.org/monarch-initiative/namo
is_a: NAMModel
abstract: true
attributes:
  cell_types:
    name: cell_types
    description: Cell types present in the cellular system
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - CellularSystem
    - OrganOnChip
    range: Term
    bindings:
    - range: CellTypeEnum
      obligation_level: REQUIRED
      binds_value_of: id
    multivalued: true
    inlined: true
    inlined_as_list: true
  cell_source:
    name: cell_source
    description: Source of cells (e.g., primary, iPSC-derived, immortalized cell lines)
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - CellularSystem
    - OrganOnChip
  culture_conditions:
    name: culture_conditions
    description: Standard culture conditions and media used
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - CellularSystem

Induced

name: CellularSystem
description: Cell-based model systems that use living cells to model biological processes.
  Includes 2D cultures, 3D systems, and co-cultures.
from_schema: https://w3id.org/monarch-initiative/namo
is_a: NAMModel
abstract: true
attributes:
  cell_types:
    name: cell_types
    description: Cell types present in the cellular system
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: cell_types
    owner: CellularSystem
    domain_of:
    - CellularSystem
    - OrganOnChip
    range: Term
    bindings:
    - range: CellTypeEnum
      obligation_level: REQUIRED
      binds_value_of: id
    multivalued: true
    inlined: true
    inlined_as_list: true
  cell_source:
    name: cell_source
    description: Source of cells (e.g., primary, iPSC-derived, immortalized cell lines)
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: cell_source
    owner: CellularSystem
    domain_of:
    - CellularSystem
    - OrganOnChip
    range: string
  culture_conditions:
    name: culture_conditions
    description: Standard culture conditions and media used
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: culture_conditions
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: string
  biological_organization_level:
    name: biological_organization_level
    description: The level of biological organization represented by the model
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: biological_organization_level
    owner: CellularSystem
    domain_of:
    - NAMModel
    range: BiologicalOrganizationLevelEnum
  spatial_context:
    name: spatial_context
    description: Description of spatial organization and context captured by the model
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: spatial_context
    owner: CellularSystem
    domain_of:
    - NAMModel
    range: string
  complexity_level:
    name: complexity_level
    description: Level of biological complexity represented (subcellular, cellular,
      tissue, organ, system)
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: complexity_level
    owner: CellularSystem
    domain_of:
    - NAMModel
    range: ComplexityLevelEnum
  references:
    name: references
    description: Literature references that describe, validate, or support this model
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: references
    owner: CellularSystem
    domain_of:
    - NAMModel
    range: Reference
    multivalued: true
    inlined: true
    inlined_as_list: true
  models:
    name: models
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: models
    owner: CellularSystem
    domain_of:
    - ModelSystem
    range: ModelsRelationship
    multivalued: true
  id:
    name: id
    description: A unique identifier for a thing
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: id
    owner: CellularSystem
    domain_of:
    - NamedThing
    - Reference
    range: uriorcurie
    required: true
  name:
    name: name
    description: A human-readable name for a thing
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: CellularSystem
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    description: A human-readable description for a thing
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: CellularSystem
    domain_of:
    - NamedThing
    range: string
  type:
    name: type
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    designates_type: true
    alias: type
    owner: CellularSystem
    domain_of:
    - NamedThing
    range: string