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Class: ExperimentalPerturbation

A structured perturbation, intervention, or exposure used in an experiment. Prefer ontology-backed descriptors for genes, chemicals, treatments, exposures, triggers, and biological processes rather than plain string lists.

URI: dismech:class/ExperimentalPerturbation

 classDiagram
    class ExperimentalPerturbation
    click ExperimentalPerturbation href "../../classes/ExperimentalPerturbation/"
      ExperimentalPerturbation : biological_processes





        ExperimentalPerturbation --> "*" BiologicalProcessDescriptor : biological_processes
        click BiologicalProcessDescriptor href "../../classes/BiologicalProcessDescriptor/"



      ExperimentalPerturbation : chemical_entities





        ExperimentalPerturbation --> "*" ChemicalEntityDescriptor : chemical_entities
        click ChemicalEntityDescriptor href "../../classes/ChemicalEntityDescriptor/"



      ExperimentalPerturbation : description

      ExperimentalPerturbation : effect

      ExperimentalPerturbation : evidence





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



      ExperimentalPerturbation : exposure_term





        ExperimentalPerturbation --> "0..1" ExposureDescriptor : exposure_term
        click ExposureDescriptor href "../../classes/ExposureDescriptor/"



      ExperimentalPerturbation : gene





        ExperimentalPerturbation --> "0..1" GeneDescriptor : gene
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      ExperimentalPerturbation : genes





        ExperimentalPerturbation --> "*" GeneDescriptor : genes
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      ExperimentalPerturbation : name

      ExperimentalPerturbation : notes

      ExperimentalPerturbation : target

      ExperimentalPerturbation : treatment_term





        ExperimentalPerturbation --> "0..1" TreatmentDescriptor : treatment_term
        click TreatmentDescriptor href "../../classes/TreatmentDescriptor/"



      ExperimentalPerturbation : triggers





        ExperimentalPerturbation --> "*" TriggerDescriptor : triggers
        click TriggerDescriptor href "../../classes/TriggerDescriptor/"

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
description 0..1
String		 direct
target 1
String		 Entity reference for the pathograph node, phenotype, gene, or other modeled o... direct
gene 0..1
GeneDescriptor		 direct
genes *
GeneDescriptor		 direct
chemical_entities *
ChemicalEntityDescriptor		 direct
treatment_term 0..1
TreatmentDescriptor		 The MAXO term for this treatment/medical action direct
exposure_term 0..1
ExposureDescriptor		 The ECTO/XCO term for this exposure event direct
triggers *
TriggerDescriptor		 direct
biological_processes *
BiologicalProcessDescriptor		 direct
effect 0..1
String		 direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct

Usages

used by used in type used
Experiment perturbations range ExperimentalPerturbation
ExperimentalControl perturbations range ExperimentalPerturbation

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ExperimentalPerturbation
description: A structured perturbation, intervention, or exposure used in an experiment.
  Prefer ontology-backed descriptors for genes, chemicals, treatments, exposures,
  triggers, and biological processes rather than plain string lists.
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- description
- target
- gene
- genes
- chemical_entities
- treatment_term
- exposure_term
- triggers
- biological_processes
- effect
- evidence
- notes
slot_usage:
  target:
    name: target
    description: Entity reference for the pathograph node, phenotype, gene, or other
      modeled object being perturbed. Uses the same hash-anchor grammar as `attaches_to`
      when pointing into a disease entry.

Induced

name: ExperimentalPerturbation
description: A structured perturbation, intervention, or exposure used in an experiment.
  Prefer ontology-backed descriptors for genes, chemicals, treatments, exposures,
  triggers, and biological processes rather than plain string lists.
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  target:
    name: target
    description: Entity reference for the pathograph node, phenotype, gene, or other
      modeled object being perturbed. Uses the same hash-anchor grammar as `attaches_to`
      when pointing into a disease entry.
attributes:
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: ExperimentalPerturbation
    domain_of:
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - SurrogateEndpointCollection
    - 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: ExperimentalPerturbation
    domain_of:
    - Descriptor
    - DietaryModification
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - BiomarkerReadout
    - SurrogateEndpointCollection
    - 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
  target:
    name: target
    description: Entity reference for the pathograph node, phenotype, gene, or other
      modeled object being perturbed. Uses the same hash-anchor grammar as `attaches_to`
      when pointing into a disease entry.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: target
    owner: ExperimentalPerturbation
    domain_of:
    - ExperimentalPerturbation
    - ExperimentalReadout
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - BiomarkerReadout
    range: string
    required: true
  gene:
    name: gene
    examples:
    - value: '{preferred_term: MEFV}'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: gene
    owner: ExperimentalPerturbation
    domain_of:
    - GeneticContext
    - ExperimentalPerturbation
    - Pathophysiology
    - Variant
    range: GeneDescriptor
    inlined: true
  genes:
    name: genes
    examples:
    - value: '[{preferred_term: HLA-DQ2}, {preferred_term: INS}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: genes
    owner: ExperimentalPerturbation
    domain_of:
    - GeneticContext
    - Dataset
    - ExperimentalPerturbation
    - Subtype
    - Pathophysiology
    - AnimalModel
    range: GeneDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  chemical_entities:
    name: chemical_entities
    examples:
    - value: '[{preferred_term: Plasmalogen}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: chemical_entities
    owner: ExperimentalPerturbation
    domain_of:
    - ExperimentalPerturbation
    - Pathophysiology
    range: ChemicalEntityDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  treatment_term:
    name: treatment_term
    description: The MAXO term for this treatment/medical action
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: treatment_term
    owner: ExperimentalPerturbation
    domain_of:
    - ExperimentalPerturbation
    - Treatment
    range: TreatmentDescriptor
    inlined: true
  exposure_term:
    name: exposure_term
    description: The ECTO/XCO term for this exposure event
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: exposure_term
    owner: ExperimentalPerturbation
    domain_of:
    - ExperimentalPerturbation
    - Environmental
    range: ExposureDescriptor
    inlined: true
  triggers:
    name: triggers
    examples:
    - value: '[{preferred_term: Viral Infections}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: triggers
    owner: ExperimentalPerturbation
    domain_of:
    - ExperimentalPerturbation
    - Pathophysiology
    range: TriggerDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  biological_processes:
    name: biological_processes
    examples:
    - value: '[{preferred_term: TNF-alpha Production}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: biological_processes
    owner: ExperimentalPerturbation
    domain_of:
    - ExperimentalPerturbation
    - ExperimentalReadout
    - Pathophysiology
    range: BiologicalProcessDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  effect:
    name: effect
    examples:
    - value: Potential trigger for flare-ups
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: effect
    owner: ExperimentalPerturbation
    domain_of:
    - ExperimentalPerturbation
    - Environmental
    - Transmission
    range: string
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: ExperimentalPerturbation
    domain_of:
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - BiomarkerReadout
    - ReferenceRange
    - SurrogateEndpoint
    - 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
    - Discussion
    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: ExperimentalPerturbation
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - ReferenceRange
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - 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
    - Discussion
    range: string