Class: InSilicoModel

Computational models that simulate biological processes without physical biological components.

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

classDiagram class InSilicoModel click InSilicoModel href "../InSilicoModel/" NAMModel <|-- InSilicoModel click NAMModel href "../NAMModel/" InSilicoModel <|-- QSARModel click QSARModel href "../QSARModel/" InSilicoModel <|-- PBPKModel click PBPKModel href "../PBPKModel/" InSilicoModel <|-- DigitalTwin click DigitalTwin href "../DigitalTwin/" InSilicoModel <|-- MLModel click MLModel href "../MLModel/" InSilicoModel <|-- MetabolicModel click MetabolicModel href "../MetabolicModel/" InSilicoModel : biological_organization_level InSilicoModel --> "0..1" BiologicalOrganizationLevelEnum : biological_organization_level click BiologicalOrganizationLevelEnum href "../BiologicalOrganizationLevelEnum/" InSilicoModel : complexity_level InSilicoModel --> "0..1" ComplexityLevelEnum : complexity_level click ComplexityLevelEnum href "../ComplexityLevelEnum/" InSilicoModel : computational_method InSilicoModel : description InSilicoModel : id InSilicoModel : models InSilicoModel --> "*" ModelsRelationship : models click ModelsRelationship href "../ModelsRelationship/" InSilicoModel : name InSilicoModel : prediction_scope InSilicoModel : references InSilicoModel --> "*" Reference : references click Reference href "../Reference/" InSilicoModel : software_platform InSilicoModel : spatial_context InSilicoModel : type InSilicoModel : validation_datasets

Inheritance

NamedThing
- ModelSystem
  - NAMModel
    - InSilicoModel

Slots

Name	Cardinality and Range	Description	Inheritance
computational_method	0..1 String	Primary computational method or algorithm used	direct
software_platform	0..1 String	Software platform or programming language used	direct
validation_datasets	* String	Datasets used for model training and validation	direct
prediction_scope	0..1 String	Scope and limitations of model predictions	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:InSilicoModel
native	namo:InSilicoModel

LinkML Source

Direct

name: InSilicoModel
description: Computational models that simulate biological processes without physical
  biological components.
from_schema: https://w3id.org/monarch-initiative/namo
is_a: NAMModel
abstract: true
attributes:
  computational_method:
    name: computational_method
    description: Primary computational method or algorithm used
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - InSilicoModel
  software_platform:
    name: software_platform
    description: Software platform or programming language used
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - InSilicoModel
  validation_datasets:
    name: validation_datasets
    description: Datasets used for model training and validation
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - InSilicoModel
    multivalued: true
  prediction_scope:
    name: prediction_scope
    description: Scope and limitations of model predictions
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - InSilicoModel

Induced

name: InSilicoModel
description: Computational models that simulate biological processes without physical
  biological components.
from_schema: https://w3id.org/monarch-initiative/namo
is_a: NAMModel
abstract: true
attributes:
  computational_method:
    name: computational_method
    description: Primary computational method or algorithm used
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: computational_method
    owner: InSilicoModel
    domain_of:
    - InSilicoModel
    range: string
  software_platform:
    name: software_platform
    description: Software platform or programming language used
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: software_platform
    owner: InSilicoModel
    domain_of:
    - InSilicoModel
    range: string
  validation_datasets:
    name: validation_datasets
    description: Datasets used for model training and validation
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: validation_datasets
    owner: InSilicoModel
    domain_of:
    - InSilicoModel
    range: string
    multivalued: true
  prediction_scope:
    name: prediction_scope
    description: Scope and limitations of model predictions
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: prediction_scope
    owner: InSilicoModel
    domain_of:
    - InSilicoModel
    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: InSilicoModel
    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: InSilicoModel
    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: InSilicoModel
    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: InSilicoModel
    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: InSilicoModel
    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: InSilicoModel
    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: InSilicoModel
    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: InSilicoModel
    domain_of:
    - NamedThing
    range: string
  type:
    name: type
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    designates_type: true
    alias: type
    owner: InSilicoModel
    domain_of:
    - NamedThing
    range: string