Skip to content

Class: ComputationalModel

A computational or in-silico model relevant to understanding disease mechanisms

URI: dismech:class/ComputationalModel

 classDiagram
    class ComputationalModel
    click ComputationalModel href "../../classes/ComputationalModel/"
      ComputationalModel : base_model

      ComputationalModel : description

      ComputationalModel : evidence





        ComputationalModel --> "* _recommended_" EvidenceItem : evidence
        click EvidenceItem href "../../classes/EvidenceItem/"



      ComputationalModel : findings





        ComputationalModel --> "*" Finding : findings
        click Finding href "../../classes/Finding/"



      ComputationalModel : model_format

      ComputationalModel : model_id

      ComputationalModel : model_software

      ComputationalModel : model_type





        ComputationalModel --> "0..1" ComputationalModelTypeEnum : model_type
        click ComputationalModelTypeEnum href "../../enums/ComputationalModelTypeEnum/"



      ComputationalModel : modeled_mechanisms





        ComputationalModel --> "*" ModelMechanismLink : modeled_mechanisms
        click ModelMechanismLink href "../../classes/ModelMechanismLink/"



      ComputationalModel : name

      ComputationalModel : notes

      ComputationalModel : perturbations





        ComputationalModel --> "*" GeneDescriptor : perturbations
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      ComputationalModel : publication

      ComputationalModel : repository_url

      ComputationalModel : variables





        ComputationalModel --> "*" ModelVariable : variables
        click ModelVariable href "../../classes/ModelVariable/"

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
description 0..1
String		 direct
model_type 0..1
ComputationalModelTypeEnum		 Type of computational model direct
repository_url 0..1
Uri		 URL to model repository (GitHub, BiGG, VMH, BioModels) direct
model_id 0..1
String		 Identifier within the repository (e direct
base_model 0..1
String		 Parent/base model this is derived from (e direct
perturbations *
GeneDescriptor		 Gene knockouts, reaction deletions, or parameter changes modeling the disease direct
variables *
ModelVariable		 Variables/outputs of a computational model with ontology mappings direct
modeled_mechanisms *
ModelMechanismLink		 Pathophysiology mechanism nodes/assertions that this experimental model is in... direct
model_software 0..1
String		 Software/toolbox for running the model (e direct
model_format 0..1
String		 File format (e direct
publication 0..1
PMID		 Associated publication (PMID) direct
findings *
Finding		 Key findings or claims extracted from this source (publication or dataset) direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct

Usages

used by used in type used
Disease computational_models range ComputationalModel

Comments

  • Covers genome-scale metabolic models, FBA, kinetic models, digital twins, and ML models
  • Perturbations track gene knockouts or parameter changes used to simulate the disease
  • Findings capture key predictions or insights the model can generate

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self dismech:ComputationalModel
native dismech:ComputationalModel

LinkML Source

Direct

name: ComputationalModel
description: A computational or in-silico model relevant to understanding disease
  mechanisms
comments:
- Covers genome-scale metabolic models, FBA, kinetic models, digital twins, and ML
  models
- Perturbations track gene knockouts or parameter changes used to simulate the disease
- Findings capture key predictions or insights the model can generate
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- description
- model_type
- repository_url
- model_id
- base_model
- perturbations
- variables
- modeled_mechanisms
- model_software
- model_format
- publication
- findings
- evidence
- notes

Induced

name: ComputationalModel
description: A computational or in-silico model relevant to understanding disease
  mechanisms
comments:
- Covers genome-scale metabolic models, FBA, kinetic models, digital twins, and ML
  models
- Perturbations track gene knockouts or parameter changes used to simulate the disease
- Findings capture key predictions or insights the model can generate
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: ComputationalModel
    domain_of:
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycleStage
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ComorbidityAssociation
    range: string
    required: true
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: ComputationalModel
    domain_of:
    - Descriptor
    - DietaryModification
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    range: string
  model_type:
    name: model_type
    description: Type of computational model
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: model_type
    owner: ComputationalModel
    domain_of:
    - ComputationalModel
    range: ComputationalModelTypeEnum
  repository_url:
    name: repository_url
    description: URL to model repository (GitHub, BiGG, VMH, BioModels)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: repository_url
    owner: ComputationalModel
    domain_of:
    - ComputationalModel
    range: uri
  model_id:
    name: model_id
    description: Identifier within the repository (e.g., Recon3D, BIOMD0000000123)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: model_id
    owner: ComputationalModel
    domain_of:
    - ComputationalModel
    range: string
  base_model:
    name: base_model
    description: Parent/base model this is derived from (e.g., Recon3D, Harvey 1.0)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: base_model
    owner: ComputationalModel
    domain_of:
    - ComputationalModel
    range: string
  perturbations:
    name: perturbations
    description: Gene knockouts, reaction deletions, or parameter changes modeling
      the disease
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: perturbations
    owner: ComputationalModel
    domain_of:
    - ComputationalModel
    range: GeneDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  variables:
    name: variables
    description: Variables/outputs of a computational model with ontology mappings
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: variables
    owner: ComputationalModel
    domain_of:
    - ComputationalModel
    range: ModelVariable
    multivalued: true
    inlined: true
    inlined_as_list: true
  modeled_mechanisms:
    name: modeled_mechanisms
    description: Pathophysiology mechanism nodes/assertions that this experimental
      model is intended to recapitulate, perturb, or measure within the disease pathograph.
    comments:
    - Target names should match pathophysiology entry names in the same disease file
    - Use description to capture the specific assayable or modeled assertion, not
      just the node label
    - Kept intentionally lightweight so it can later align more explicitly with NAMO
      relations
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: modeled_mechanisms
    owner: ComputationalModel
    domain_of:
    - ExperimentalModel
    - ComputationalModel
    range: ModelMechanismLink
    multivalued: true
    inlined: true
    inlined_as_list: true
  model_software:
    name: model_software
    description: Software/toolbox for running the model (e.g., COBRApy, COBRA Toolbox)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: model_software
    owner: ComputationalModel
    domain_of:
    - ComputationalModel
    range: string
  model_format:
    name: model_format
    description: File format (e.g., SBML, MATLAB, JSON, ONNX)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: model_format
    owner: ComputationalModel
    domain_of:
    - ComputationalModel
    range: string
  publication:
    name: publication
    description: Associated publication (PMID)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: publication
    owner: ComputationalModel
    domain_of:
    - Dataset
    - ExperimentalModel
    - ComputationalModel
    - ProteinStructure
    range: PMID
  findings:
    name: findings
    description: Key findings or claims extracted from this source (publication or
      dataset)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: findings
    owner: ComputationalModel
    domain_of:
    - Dataset
    - ExperimentalModel
    - ComputationalModel
    - PublicationReference
    range: Finding
    multivalued: true
    inlined: true
    inlined_as_list: true
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: ComputationalModel
    domain_of:
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - ExternalAssertion
    - Finding
    - Prevalence
    - ProgressionInfo
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    range: EvidenceItem
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  notes:
    name: notes
    examples:
    - value: Contagious stage where symptoms appear and the bacteria can be spread
        to others.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: notes
    owner: ComputationalModel
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - ExternalAssertion
    - TrackedIssue
    - Prevalence
    - ProgressionInfo
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    - Transmission
    - Diagnosis
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    range: string