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Class: ExperimentalModel

A disease-relevant non-animal experimental model system. This is a disease-centric bridge class inspired by NAMO, intended to capture the model itself while keeping dismech focused on disease mechanisms rather than study-level model registries.

URI: dismech:class/ExperimentalModel

 classDiagram
    class ExperimentalModel
    click ExperimentalModel href "../../classes/ExperimentalModel/"
      ExperimentalModel : cell_source

      ExperimentalModel : cell_types





        ExperimentalModel --> "*" CellTypeDescriptor : cell_types
        click CellTypeDescriptor href "../../classes/CellTypeDescriptor/"



      ExperimentalModel : conditions

      ExperimentalModel : culture_system

      ExperimentalModel : description

      ExperimentalModel : evidence





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



      ExperimentalModel : experimental_model_type





        ExperimentalModel --> "0..1" ExperimentalModelTypeEnum : experimental_model_type
        click ExperimentalModelTypeEnum href "../../enums/ExperimentalModelTypeEnum/"



      ExperimentalModel : findings





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



      ExperimentalModel : modeled_mechanisms





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



      ExperimentalModel : name

      ExperimentalModel : namo_type

      ExperimentalModel : notes

      ExperimentalModel : organism





        ExperimentalModel --> "0..1" OrganismDescriptor : organism
        click OrganismDescriptor href "../../classes/OrganismDescriptor/"



      ExperimentalModel : publication

      ExperimentalModel : tissue_term





        ExperimentalModel --> "0..1" AnatomicalEntityDescriptor : tissue_term
        click AnatomicalEntityDescriptor href "../../classes/AnatomicalEntityDescriptor/"

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
description 0..1
String		 direct
experimental_model_type 0..1
ExperimentalModelTypeEnum		 Broad category for an experimental model system direct
namo_type 0..1
Uriorcurie		 Optional mapping to the corresponding NAMO class, such as namo:Organoid or ... direct
organism 0..1
OrganismDescriptor		 The organism from which samples were derived direct
tissue_term 0..1
AnatomicalEntityDescriptor		 UBERON term for the tissue direct
cell_types *
CellTypeDescriptor		 direct
conditions *
String		 Experimental conditions or disease states represented direct
cell_source 0..1
String		 Source of cells used in the experimental model direct
culture_system 0..1
String		 Culture format or device context used by the experimental model direct
publication 0..1
PMID		 Associated publication (PMID) direct
modeled_mechanisms *
ModelMechanismLink		 Pathophysiology mechanism nodes/assertions that this experimental model is in... 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 experimental_models range ExperimentalModel

Comments

  • Use namo_type to map to a corresponding NAMO class when applicable
  • Prefer experimental_model_type for broad local categorization and description or notes for disease-specific nuance
  • Use cell_source to record whether the system is patient-derived, iPSC-derived, primary, immortalized, or mixed

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ExperimentalModel
description: A disease-relevant non-animal experimental model system. This is a disease-centric
  bridge class inspired by NAMO, intended to capture the model itself while keeping
  dismech focused on disease mechanisms rather than study-level model registries.
comments:
- Use `namo_type` to map to a corresponding NAMO class when applicable
- Prefer `experimental_model_type` for broad local categorization and `description`
  or `notes` for disease-specific nuance
- Use `cell_source` to record whether the system is patient-derived, iPSC-derived,
  primary, immortalized, or mixed
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- description
- experimental_model_type
- namo_type
- organism
- tissue_term
- cell_types
- conditions
- cell_source
- culture_system
- publication
- modeled_mechanisms
- findings
- evidence
- notes

Induced

name: ExperimentalModel
description: A disease-relevant non-animal experimental model system. This is a disease-centric
  bridge class inspired by NAMO, intended to capture the model itself while keeping
  dismech focused on disease mechanisms rather than study-level model registries.
comments:
- Use `namo_type` to map to a corresponding NAMO class when applicable
- Prefer `experimental_model_type` for broad local categorization and `description`
  or `notes` for disease-specific nuance
- Use `cell_source` to record whether the system is patient-derived, iPSC-derived,
  primary, immortalized, or mixed
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: ExperimentalModel
    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: ExperimentalModel
    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
  experimental_model_type:
    name: experimental_model_type
    description: Broad category for an experimental model system
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: experimental_model_type
    owner: ExperimentalModel
    domain_of:
    - ExperimentalModel
    range: ExperimentalModelTypeEnum
  namo_type:
    name: namo_type
    description: Optional mapping to the corresponding NAMO class, such as `namo:Organoid`
      or `namo:OrganOnChip`.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: namo_type
    owner: ExperimentalModel
    domain_of:
    - ExperimentalModel
    range: uriorcurie
  organism:
    name: organism
    description: The organism from which samples were derived
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: organism
    owner: ExperimentalModel
    domain_of:
    - Dataset
    - ExperimentalModel
    range: OrganismDescriptor
    inlined: true
  tissue_term:
    name: tissue_term
    description: UBERON term for the tissue
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: tissue_term
    owner: ExperimentalModel
    domain_of:
    - SampleTypeDescriptor
    - ExperimentalModel
    range: AnatomicalEntityDescriptor
    inlined: true
  cell_types:
    name: cell_types
    examples:
    - value: '[{preferred_term: Macrophage}, {preferred_term: T Cell}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: cell_types
    owner: ExperimentalModel
    domain_of:
    - ExperimentalModel
    - Pathophysiology
    - Biochemical
    range: CellTypeDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  conditions:
    name: conditions
    description: Experimental conditions or disease states represented
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: conditions
    owner: ExperimentalModel
    domain_of:
    - Dataset
    - ExperimentalModel
    range: string
    multivalued: true
  cell_source:
    name: cell_source
    description: Source of cells used in the experimental model
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: cell_source
    owner: ExperimentalModel
    domain_of:
    - ExperimentalModel
    range: string
  culture_system:
    name: culture_system
    description: Culture format or device context used by the experimental model
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: culture_system
    owner: ExperimentalModel
    domain_of:
    - ExperimentalModel
    range: string
  publication:
    name: publication
    description: Associated publication (PMID)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: publication
    owner: ExperimentalModel
    domain_of:
    - Dataset
    - ExperimentalModel
    - ComputationalModel
    - ProteinStructure
    range: PMID
  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: ExperimentalModel
    domain_of:
    - ExperimentalModel
    - ComputationalModel
    range: ModelMechanismLink
    multivalued: true
    inlined: true
    inlined_as_list: true
  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: ExperimentalModel
    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: ExperimentalModel
    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: ExperimentalModel
    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