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Class: Experiment

A structured experiment or protocol-level study design that can be proposed to resolve a knowledge gap, or later reused to represent experiments that have been carried out. The object itself is intentionally status-neutral: proposal, execution, and evidentiary status are expressed by the containing slot or future evidence context.

URI: dismech:class/Experiment

 classDiagram
    class Experiment
    click Experiment href "../../classes/Experiment/"
      Experiment : assays





        Experiment --> "*" AssayDescriptor : assays
        click AssayDescriptor href "../../classes/AssayDescriptor/"



      Experiment : controls





        Experiment --> "*" ExperimentalControl : controls
        click ExperimentalControl href "../../classes/ExperimentalControl/"



      Experiment : datasets





        Experiment --> "* _recommended_" Dataset : datasets
        click Dataset href "../../classes/Dataset/"



      Experiment : decision_criterion

      Experiment : description

      Experiment : evidence





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



      Experiment : experiment_id

      Experiment : experiment_type





        Experiment --> "0..1" Descriptor : experiment_type
        click Descriptor href "../../classes/Descriptor/"



      Experiment : model_systems





        Experiment --> "*" ExperimentalModel : model_systems
        click ExperimentalModel href "../../classes/ExperimentalModel/"



      Experiment : name

      Experiment : notes

      Experiment : perturbations





        Experiment --> "*" ExperimentalPerturbation : perturbations
        click ExperimentalPerturbation href "../../classes/ExperimentalPerturbation/"



      Experiment : protocol_reference

      Experiment : readouts





        Experiment --> "*" ExperimentalReadout : readouts
        click ExperimentalReadout href "../../classes/ExperimentalReadout/"



      Experiment : would_refute

      Experiment : would_support

Slots

Name Cardinality and Range Description Inheritance
experiment_id 1
String		 Stable identifier for an Experiment within a disease entry direct
name 1
String		 direct
description 0..1
String		 direct
experiment_type 0..1
Descriptor		 Ontology-backed descriptor for the overall experiment or study design direct
model_systems *
ExperimentalModel		 Experimental model systems used or proposed for an experiment, using the Expe... direct
perturbations *
ExperimentalPerturbation		 Interventions or manipulations applied in the experiment direct
assays *
AssayDescriptor		 Ontology-backed assays used by the experiment; prefer OBI terms when availabl... direct
readouts *
ExperimentalReadout		 Measurements or outcomes interpreted against disease pathograph nodes, phenot... direct
controls *
ExperimentalControl		 Experimental controls, comparators, or counterfactual arms direct
decision_criterion 0..1
String		 Pre-specified qualitative or quantitative criterion for interpreting the expe... direct
would_support *
String		 Entity references that would be supported if the experiment meets its decisio... direct
would_refute *
String		 Entity references that would be weakened or refuted if the experiment meets a... direct
protocol_reference 0..1
String		 Optional protocol, methods paper, or registry reference for the experimental ... direct
datasets * recommended
Dataset		 Publicly available datasets relevant to disease research direct
evidence *
EvidenceItem		 Literature, protocol papers, or dataset evidence supporting the feasibility, ... direct
notes 0..1
String		 direct

Usages

used by used in type used
Discussion proposed_experiments range Experiment

Comments

  • In Discussion.proposed_experiments, the containing slot means the experiment is proposed as a response to an open question or knowledge gap.
  • Use model_systems for NAMO-aligned models, perturbations for pathograph/gene/chemical/exposure manipulations, and readouts for ontology-backed outcome or mechanism measurements.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Experiment
description: 'A structured experiment or protocol-level study design that can be proposed
  to resolve a knowledge gap, or later reused to represent experiments that have been
  carried out. The object itself is intentionally status-neutral: proposal, execution,
  and evidentiary status are expressed by the containing slot or future evidence context.'
comments:
- In `Discussion.proposed_experiments`, the containing slot means the experiment is
  proposed as a response to an open question or knowledge gap.
- Use `model_systems` for NAMO-aligned models, `perturbations` for pathograph/gene/chemical/exposure
  manipulations, and `readouts` for ontology-backed outcome or mechanism measurements.
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- experiment_id
- name
- description
- experiment_type
- model_systems
- perturbations
- assays
- readouts
- controls
- decision_criterion
- would_support
- would_refute
- protocol_reference
- datasets
- evidence
- notes
slot_usage:
  experiment_id:
    name: experiment_id
    required: true
  perturbations:
    name: perturbations
    description: Interventions or manipulations applied in the experiment. These may
      target disease pathograph nodes, genes, chemical entities, treatments, exposures,
      triggers, or biological processes.
    range: ExperimentalPerturbation
    inlined_as_list: true
  readouts:
    name: readouts
    description: Measurements or outcomes interpreted against disease pathograph nodes,
      phenotypes, biomarkers, or biological processes.
    range: ExperimentalReadout
    inlined_as_list: true
  assays:
    name: assays
    description: Ontology-backed assays used by the experiment; prefer OBI terms when
      available.
  evidence:
    name: evidence
    description: Literature, protocol papers, or dataset evidence supporting the feasibility,
      precedent, or design rationale for this experiment.
    recommended: false

Induced

name: Experiment
description: 'A structured experiment or protocol-level study design that can be proposed
  to resolve a knowledge gap, or later reused to represent experiments that have been
  carried out. The object itself is intentionally status-neutral: proposal, execution,
  and evidentiary status are expressed by the containing slot or future evidence context.'
comments:
- In `Discussion.proposed_experiments`, the containing slot means the experiment is
  proposed as a response to an open question or knowledge gap.
- Use `model_systems` for NAMO-aligned models, `perturbations` for pathograph/gene/chemical/exposure
  manipulations, and `readouts` for ontology-backed outcome or mechanism measurements.
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  experiment_id:
    name: experiment_id
    required: true
  perturbations:
    name: perturbations
    description: Interventions or manipulations applied in the experiment. These may
      target disease pathograph nodes, genes, chemical entities, treatments, exposures,
      triggers, or biological processes.
    range: ExperimentalPerturbation
    inlined_as_list: true
  readouts:
    name: readouts
    description: Measurements or outcomes interpreted against disease pathograph nodes,
      phenotypes, biomarkers, or biological processes.
    range: ExperimentalReadout
    inlined_as_list: true
  assays:
    name: assays
    description: Ontology-backed assays used by the experiment; prefer OBI terms when
      available.
  evidence:
    name: evidence
    description: Literature, protocol papers, or dataset evidence supporting the feasibility,
      precedent, or design rationale for this experiment.
    recommended: false
attributes:
  experiment_id:
    name: experiment_id
    description: Stable identifier for an Experiment within a disease entry
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: experiment_id
    owner: Experiment
    domain_of:
    - Experiment
    range: string
    required: true
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: Experiment
    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: Experiment
    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
  experiment_type:
    name: experiment_type
    description: Ontology-backed descriptor for the overall experiment or study design.
      Prefer OBI terms when available; assay-level details should go in the `assays`
      slot.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: experiment_type
    owner: Experiment
    domain_of:
    - Experiment
    range: Descriptor
    inlined: true
  model_systems:
    name: model_systems
    description: Experimental model systems used or proposed for an experiment, using
      the ExperimentalModel pattern and optional NAMO alignment.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: model_systems
    owner: Experiment
    domain_of:
    - Experiment
    - ExperimentalControl
    range: ExperimentalModel
    multivalued: true
    inlined: true
    inlined_as_list: true
  perturbations:
    name: perturbations
    description: Interventions or manipulations applied in the experiment. These may
      target disease pathograph nodes, genes, chemical entities, treatments, exposures,
      triggers, or biological processes.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: perturbations
    owner: Experiment
    domain_of:
    - Experiment
    - ExperimentalControl
    - ComputationalModel
    range: ExperimentalPerturbation
    multivalued: true
    inlined: true
    inlined_as_list: true
  assays:
    name: assays
    description: Ontology-backed assays used by the experiment; prefer OBI terms when
      available.
    examples:
    - value: '[{preferred_term: Elevated Blood Glucose}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: assays
    owner: Experiment
    domain_of:
    - Experiment
    - ExperimentalReadout
    - Pathophysiology
    - Biochemical
    range: AssayDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  readouts:
    name: readouts
    description: Measurements or outcomes interpreted against disease pathograph nodes,
      phenotypes, biomarkers, or biological processes.
    comments:
    - Target names should match pathophysiology or phenotype entry names in the same
      disease file
    - Readout links are observational/associative, not causal disease-progression
      edges
    - Use evidence on the readout link when the biomarker-to-mechanism mapping is
      distinct from the biomarker's own evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: readouts
    owner: Experiment
    domain_of:
    - Experiment
    - Biochemical
    range: ExperimentalReadout
    multivalued: true
    inlined: true
    inlined_as_list: true
  controls:
    name: controls
    description: Experimental controls, comparators, or counterfactual arms
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: controls
    owner: Experiment
    domain_of:
    - Experiment
    range: ExperimentalControl
    multivalued: true
    inlined: true
    inlined_as_list: true
  decision_criterion:
    name: decision_criterion
    description: Pre-specified qualitative or quantitative criterion for interpreting
      the experiment relative to the attached discussion or knowledge gap.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: decision_criterion
    owner: Experiment
    domain_of:
    - Experiment
    range: string
  would_support:
    name: would_support
    description: Entity references that would be supported if the experiment meets
      its decision criterion. Uses the same hash-anchor grammar as `attaches_to`.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: would_support
    owner: Experiment
    domain_of:
    - Experiment
    range: string
    multivalued: true
  would_refute:
    name: would_refute
    description: Entity references that would be weakened or refuted if the experiment
      meets a contrary result. Uses the same hash-anchor grammar as `attaches_to`.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: would_refute
    owner: Experiment
    domain_of:
    - Experiment
    range: string
    multivalued: true
  protocol_reference:
    name: protocol_reference
    description: Optional protocol, methods paper, or registry reference for the experimental
      workflow. May be a PMID, DOI, protocols.io DOI, URL, or other stable identifier.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: protocol_reference
    owner: Experiment
    domain_of:
    - Experiment
    range: string
  datasets:
    name: datasets
    description: Publicly available datasets relevant to disease research
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: datasets
    owner: Experiment
    domain_of:
    - Experiment
    - Disease
    range: Dataset
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  evidence:
    name: evidence
    description: Literature, protocol papers, or dataset evidence supporting the feasibility,
      precedent, or design rationale for this experiment.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Experiment
    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: false
    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: Experiment
    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