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Class: Organoid

A 3D cell culture system that self-organizes to recapitulate key structural and functional aspects of an organ or tissue

URI: namo:Organoid

classDiagram class Organoid click Organoid href "../Organoid/" ThreeDCellCulture <|-- Organoid click ThreeDCellCulture href "../ThreeDCellCulture/" Organoid : biological_organization_level Organoid --> "0..1" BiologicalOrganizationLevelEnum : biological_organization_level click BiologicalOrganizationLevelEnum href "../BiologicalOrganizationLevelEnum/" Organoid : cell_source Organoid : cell_types Organoid --> "*" Term : cell_types click Term href "../Term/" Organoid : complexity_level Organoid --> "0..1" ComplexityLevelEnum : complexity_level click ComplexityLevelEnum href "../ComplexityLevelEnum/" Organoid : culture_conditions Organoid : culture_system Organoid : description Organoid : differentiation_method Organoid : id Organoid : matrix_composition Organoid : models Organoid --> "*" ModelsRelationship : models click ModelsRelationship href "../ModelsRelationship/" Organoid : name Organoid : organ_modeled Organoid --> "0..1" Term : organ_modeled click Term href "../Term/" Organoid : references Organoid --> "*" Reference : references click Reference href "../Reference/" Organoid : size_range Organoid : spatial_context Organoid : three_d_architecture Organoid --> "0..1" ThreeDArchitectureEnum : three_d_architecture click ThreeDArchitectureEnum href "../ThreeDArchitectureEnum/" Organoid : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
organ_modeled 0..1
Term		 The organ or tissue being modeled direct
differentiation_method 0..1
String		 Method used to differentiate cells into organoid (e direct
culture_system 0..1
String		 Culture system used (e direct
three_d_architecture 0..1
ThreeDArchitectureEnum		 Type of 3D architecture (spheroid, organoid, scaffold-based, etc ThreeDCellCulture
matrix_composition 0..1
String		 Composition of extracellular matrix or scaffold material ThreeDCellCulture
size_range 0..1
String		 Typical size range of 3D structures ThreeDCellCulture
cell_types *
Term		 Cell types present in the cellular system CellularSystem
cell_source 0..1
String		 Source of cells (e CellularSystem
culture_conditions 0..1
String		 Standard culture conditions and media used CellularSystem
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:Organoid
native namo:Organoid

LinkML Source

Direct

name: Organoid
description: A 3D cell culture system that self-organizes to recapitulate key structural
  and functional aspects of an organ or tissue
from_schema: https://w3id.org/monarch-initiative/namo
is_a: ThreeDCellCulture
attributes:
  organ_modeled:
    name: organ_modeled
    description: The organ or tissue being modeled
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - Organoid
    - OrganOnChip
    range: Term
    bindings:
    - range: OrganEnum
      obligation_level: REQUIRED
      binds_value_of: id
    inlined: true
  differentiation_method:
    name: differentiation_method
    description: Method used to differentiate cells into organoid (e.g., directed
      differentiation protocol)
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - Organoid
  culture_system:
    name: culture_system
    description: Culture system used (e.g., Matrigel dome, suspension culture, air-liquid
      interface)
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - Organoid

Induced

name: Organoid
description: A 3D cell culture system that self-organizes to recapitulate key structural
  and functional aspects of an organ or tissue
from_schema: https://w3id.org/monarch-initiative/namo
is_a: ThreeDCellCulture
attributes:
  organ_modeled:
    name: organ_modeled
    description: The organ or tissue being modeled
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: organ_modeled
    owner: Organoid
    domain_of:
    - Organoid
    - OrganOnChip
    range: Term
    bindings:
    - range: OrganEnum
      obligation_level: REQUIRED
      binds_value_of: id
    inlined: true
  differentiation_method:
    name: differentiation_method
    description: Method used to differentiate cells into organoid (e.g., directed
      differentiation protocol)
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: differentiation_method
    owner: Organoid
    domain_of:
    - Organoid
    range: string
  culture_system:
    name: culture_system
    description: Culture system used (e.g., Matrigel dome, suspension culture, air-liquid
      interface)
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: culture_system
    owner: Organoid
    domain_of:
    - Organoid
    range: string
  three_d_architecture:
    name: three_d_architecture
    description: Type of 3D architecture (spheroid, organoid, scaffold-based, etc.)
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: three_d_architecture
    owner: Organoid
    domain_of:
    - ThreeDCellCulture
    range: ThreeDArchitectureEnum
  matrix_composition:
    name: matrix_composition
    description: Composition of extracellular matrix or scaffold material
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: matrix_composition
    owner: Organoid
    domain_of:
    - ThreeDCellCulture
    range: string
  size_range:
    name: size_range
    description: Typical size range of 3D structures
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: size_range
    owner: Organoid
    domain_of:
    - ThreeDCellCulture
    range: string
  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: Organoid
    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: Organoid
    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: Organoid
    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: Organoid
    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: Organoid
    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: Organoid
    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: Organoid
    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: Organoid
    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: Organoid
    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: Organoid
    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: Organoid
    domain_of:
    - NamedThing
    range: string
  type:
    name: type
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    designates_type: true
    alias: type
    owner: Organoid
    domain_of:
    - NamedThing
    range: string