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Class: CellularSystem

Cell-based model systems that use living cells to model biological processes.

URI: soma:CellularSystem

 classDiagram
    class CellularSystem
    click CellularSystem href "../CellularSystem/"
      ModelSystem <|-- CellularSystem
        click ModelSystem href "../ModelSystem/"

      CellularSystem : anatomical_origin





        CellularSystem --> "0..1" AnatomicalEntityReference : anatomical_origin
        click AnatomicalEntityReference href "../AnatomicalEntityReference/"



      CellularSystem : cell_culture_growth_mode





        CellularSystem --> "0..1" CellCultureGrowthModeEnum : cell_culture_growth_mode
        click CellCultureGrowthModeEnum href "../CellCultureGrowthModeEnum/"



      CellularSystem : cell_line





        CellularSystem --> "0..1" CellLine : cell_line
        click CellLine href "../CellLine/"



      CellularSystem : cell_type





        CellularSystem --> "0..1" CellTypeReference : cell_type
        click CellTypeReference href "../CellTypeReference/"



      CellularSystem : cell_type_ratios

      CellularSystem : coating

      CellularSystem : confluence_level





        CellularSystem --> "0..1" QuantityValue : confluence_level
        click QuantityValue href "../QuantityValue/"



      CellularSystem : culture_conditions





        CellularSystem --> "0..1" CellCultureConditions : culture_conditions
        click CellCultureConditions href "../CellCultureConditions/"



      CellularSystem : culture_media





        CellularSystem --> "0..1" CellCultureMedium : culture_media
        click CellCultureMedium href "../CellCultureMedium/"



      CellularSystem : days_at_differentiation

      CellularSystem : description

      CellularSystem : donor_info

      CellularSystem : id

      CellularSystem : matrix_composition

      CellularSystem : model_species





        CellularSystem --> "0..1" SpeciesReference : model_species
        click SpeciesReference href "../SpeciesReference/"



      CellularSystem : name

      CellularSystem : organoid_type

      CellularSystem : passage_number

      CellularSystem : primary_cell





        CellularSystem --> "0..1" CellTypeReference : primary_cell
        click CellTypeReference href "../CellTypeReference/"



      CellularSystem : replicates_per_donor

      CellularSystem : seeding_density





        CellularSystem --> "0..1" QuantityValue : seeding_density
        click QuantityValue href "../QuantityValue/"



      CellularSystem : size_range





        CellularSystem --> "0..1" QuantityRange : size_range
        click QuantityRange href "../QuantityRange/"



      CellularSystem : subject_type

      CellularSystem : substrate_type





        CellularSystem --> "0..1" SubstrateTypeEnum : substrate_type
        click SubstrateTypeEnum href "../SubstrateTypeEnum/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
cell_line 0..1
CellLine		 direct
primary_cell 0..1
CellTypeReference		 direct
cell_type 0..1
CellTypeReference		 The cell type being studied direct
anatomical_origin 0..1
AnatomicalEntityReference		 direct
cell_culture_growth_mode 0..1
CellCultureGrowthModeEnum		 direct
substrate_type 0..1
SubstrateTypeEnum		 direct
confluence_level 0..1
QuantityValue		 direct
passage_number 0..1
Integer		 direct
seeding_density 0..1
QuantityValue		 direct
coating 0..1
String		 direct
matrix_composition 0..1
String		 direct
size_range 0..1
QuantityRange		 direct
organoid_type 0..1
String		 direct
cell_type_ratios *
String		 direct
culture_conditions 0..1
CellCultureConditions		 direct
culture_media 0..1
CellCultureMedium		 direct
days_at_differentiation 0..1
Integer		 Days at air-liquid interface or differentiation stage direct
donor_info 0..1
String		 Information about cell donor (e direct
replicates_per_donor 0..1
Integer		 Number of biological replicates per donor direct
subject_type 0..1
String		 The specific type of study subject StudySubject
model_species 0..1
SpeciesReference		 The species of origin for the cells or organism being studied StudySubject
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

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: CellularSystem
description: Cell-based model systems that use living cells to model biological processes.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: ModelSystem
slots:
- cell_line
- primary_cell
- cell_type
- anatomical_origin
- cell_culture_growth_mode
- substrate_type
- confluence_level
- passage_number
- seeding_density
- coating
- matrix_composition
- size_range
- organoid_type
- cell_type_ratios
- culture_conditions
- culture_media
- days_at_differentiation
- donor_info
- replicates_per_donor

Induced

name: CellularSystem
description: Cell-based model systems that use living cells to model biological processes.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: ModelSystem
attributes:
  cell_line:
    name: cell_line
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: cell_line
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: CellLine
    inlined: true
  primary_cell:
    name: primary_cell
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: primary_cell
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: CellTypeReference
    inlined: true
  cell_type:
    name: cell_type
    description: The cell type being studied. Reference to a Cell Ontology (CL) term.
      Used on CellularSystem and CellLine to describe the cell identity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: EFO:0000324
    alias: cell_type
    owner: CellularSystem
    domain_of:
    - CellularSystem
    - CellLine
    range: CellTypeReference
    inlined: true
  anatomical_origin:
    name: anatomical_origin
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: anatomical_origin
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: AnatomicalEntityReference
    inlined: true
  cell_culture_growth_mode:
    name: cell_culture_growth_mode
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: cell_culture_growth_mode
    owner: CellularSystem
    domain_of:
    - CellularSystem
    - CellCultureConditions
    range: CellCultureGrowthModeEnum
  substrate_type:
    name: substrate_type
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: substrate_type
    owner: CellularSystem
    domain_of:
    - CellularSystem
    - CellCultureConditions
    range: SubstrateTypeEnum
  confluence_level:
    name: confluence_level
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: confluence_level
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: QuantityValue
    inlined: true
  passage_number:
    name: passage_number
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: passage_number
    owner: CellularSystem
    domain_of:
    - CellularSystem
    - CellCultureConditions
    range: integer
  seeding_density:
    name: seeding_density
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: seeding_density
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: QuantityValue
    inlined: true
  coating:
    name: coating
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: coating
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: string
  matrix_composition:
    name: matrix_composition
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: matrix_composition
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: string
  size_range:
    name: size_range
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: size_range
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: QuantityRange
    inlined: true
  organoid_type:
    name: organoid_type
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: organoid_type
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: string
  cell_type_ratios:
    name: cell_type_ratios
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: cell_type_ratios
    owner: CellularSystem
    domain_of:
    - CellularSystem
    - CiliaryFunctionOutput
    range: string
    multivalued: true
  culture_conditions:
    name: culture_conditions
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: culture_conditions
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: CellCultureConditions
    inlined: true
  culture_media:
    name: culture_media
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: culture_media
    owner: CellularSystem
    domain_of:
    - CellularSystem
    - CellCultureConditions
    range: CellCultureMedium
    inlined: true
  days_at_differentiation:
    name: days_at_differentiation
    description: Days at air-liquid interface or differentiation stage.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: days_at_differentiation
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: integer
  donor_info:
    name: donor_info
    description: Information about cell donor (e.g., healthy non-smoker, CF patient,
      age, anatomical region).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: donor_info
    owner: CellularSystem
    domain_of:
    - CellularSystem
    range: string
  replicates_per_donor:
    name: replicates_per_donor
    description: Number of biological replicates per donor.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: replicates_per_donor
    owner: CellularSystem
    domain_of:
    - CellularSystem
    - CellCultureConditions
    range: integer
  subject_type:
    name: subject_type
    description: The specific type of study subject. Used to designate which concrete
      class (e.g., CellularSystem, InVivoSubject) is instantiated for polymorphic
      study_subject slots.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    designates_type: true
    alias: subject_type
    owner: CellularSystem
    domain_of:
    - StudySubject
    range: string
  model_species:
    name: model_species
    description: The species of origin for the cells or organism being studied. Reference
      to NCBITaxon term.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: model_species
    owner: CellularSystem
    domain_of:
    - StudySubject
    - CellLine
    range: SpeciesReference
    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: CellularSystem
    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: CellularSystem
    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: CellularSystem
    domain_of:
    - NamedThing
    range: string