Class: PBPKModel

Physiologically Based Pharmacokinetic models that simulate drug absorption, distribution, metabolism, and excretion.

classDiagram class PBPKModel click PBPKModel href "../PBPKModel/" InSilicoModel <|-- PBPKModel click InSilicoModel href "../InSilicoModel/" PBPKModel : biological_organization_level PBPKModel --> "0..1" BiologicalOrganizationLevelEnum : biological_organization_level click BiologicalOrganizationLevelEnum href "../BiologicalOrganizationLevelEnum/" PBPKModel : compartments PBPKModel --> "*" PBPKCompartment : compartments click PBPKCompartment href "../PBPKCompartment/" PBPKModel : complexity_level PBPKModel --> "0..1" ComplexityLevelEnum : complexity_level click ComplexityLevelEnum href "../ComplexityLevelEnum/" PBPKModel : computational_method PBPKModel : description PBPKModel : drug_properties PBPKModel --> "0..1" DrugProperties : drug_properties click DrugProperties href "../DrugProperties/" PBPKModel : elimination_pathways PBPKModel : id PBPKModel : models PBPKModel --> "*" ModelsRelationship : models click ModelsRelationship href "../ModelsRelationship/" PBPKModel : name PBPKModel : prediction_scope PBPKModel : references PBPKModel --> "*" Reference : references click Reference href "../Reference/" PBPKModel : software_platform PBPKModel : spatial_context PBPKModel : species_modeled PBPKModel --> "0..1" Term : species_modeled click Term href "../Term/" PBPKModel : type PBPKModel : validation_datasets

Inheritance

NamedThing
- ModelSystem
  - NAMModel
    - InSilicoModel
      - PBPKModel

Slots

Name	Cardinality and Range	Description	Inheritance
compartments	* PBPKCompartment	Physiological compartments included in the model	direct
species_modeled	0..1 Term	Species for which the model is designed	direct
drug_properties	0..1 DrugProperties	Physicochemical and pharmacological properties modeled	direct
elimination_pathways	* String	Drug elimination and metabolism pathways included	direct
computational_method	0..1 String	Primary computational method or algorithm used	InSilicoModel
software_platform	0..1 String	Software platform or programming language used	InSilicoModel
validation_datasets	* String	Datasets used for model training and validation	InSilicoModel
prediction_scope	0..1 String	Scope and limitations of model predictions	InSilicoModel
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:PBPKModel
native	namo:PBPKModel

LinkML Source

Direct

name: PBPKModel
description: Physiologically Based Pharmacokinetic models that simulate drug  absorption,
  distribution, metabolism, and excretion.
from_schema: https://w3id.org/monarch-initiative/namo
is_a: InSilicoModel
attributes:
  compartments:
    name: compartments
    description: Physiological compartments included in the model
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - PBPKModel
    range: PBPKCompartment
    multivalued: true
    inlined: true
    inlined_as_list: true
  species_modeled:
    name: species_modeled
    description: Species for which the model is designed
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - PBPKModel
    range: Term
    inlined: true
  drug_properties:
    name: drug_properties
    description: Physicochemical and pharmacological properties modeled
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - PBPKModel
    range: DrugProperties
    inlined: true
  elimination_pathways:
    name: elimination_pathways
    description: Drug elimination and metabolism pathways included
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    domain_of:
    - PBPKModel
    multivalued: true

Induced

name: PBPKModel
description: Physiologically Based Pharmacokinetic models that simulate drug  absorption,
  distribution, metabolism, and excretion.
from_schema: https://w3id.org/monarch-initiative/namo
is_a: InSilicoModel
attributes:
  compartments:
    name: compartments
    description: Physiological compartments included in the model
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: compartments
    owner: PBPKModel
    domain_of:
    - PBPKModel
    range: PBPKCompartment
    multivalued: true
    inlined: true
    inlined_as_list: true
  species_modeled:
    name: species_modeled
    description: Species for which the model is designed
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: species_modeled
    owner: PBPKModel
    domain_of:
    - PBPKModel
    range: Term
    inlined: true
  drug_properties:
    name: drug_properties
    description: Physicochemical and pharmacological properties modeled
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: drug_properties
    owner: PBPKModel
    domain_of:
    - PBPKModel
    range: DrugProperties
    inlined: true
  elimination_pathways:
    name: elimination_pathways
    description: Drug elimination and metabolism pathways included
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    alias: elimination_pathways
    owner: PBPKModel
    domain_of:
    - PBPKModel
    range: string
    multivalued: true
  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: PBPKModel
    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: PBPKModel
    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: PBPKModel
    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: PBPKModel
    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: PBPKModel
    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: PBPKModel
    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: PBPKModel
    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: PBPKModel
    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: PBPKModel
    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: PBPKModel
    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: PBPKModel
    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: PBPKModel
    domain_of:
    - NamedThing
    range: string
  type:
    name: type
    from_schema: https://w3id.org/monarch-initiative/namo
    rank: 1000
    designates_type: true
    alias: type
    owner: PBPKModel
    domain_of:
    - NamedThing
    range: string