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Class: ExperimentalReadout

A structured readout or outcome measured in an experiment. Use descriptor slots to ground readouts to phenotypes, biomarkers, biological processes, and assays.

URI: dismech:class/ExperimentalReadout

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





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



      ExperimentalReadout : biological_processes





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



      ExperimentalReadout : biomarker_term





        ExperimentalReadout --> "0..1" BiomarkerDescriptor : biomarker_term
        click BiomarkerDescriptor href "../../classes/BiomarkerDescriptor/"



      ExperimentalReadout : description

      ExperimentalReadout : direction





        ExperimentalReadout --> "0..1" BiomarkerReadoutDirectionEnum : direction
        click BiomarkerReadoutDirectionEnum href "../../enums/BiomarkerReadoutDirectionEnum/"



      ExperimentalReadout : evidence





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



      ExperimentalReadout : interpretation

      ExperimentalReadout : name

      ExperimentalReadout : notes

      ExperimentalReadout : phenotype_term





        ExperimentalReadout --> "0..1" PhenotypeDescriptor : phenotype_term
        click PhenotypeDescriptor href "../../classes/PhenotypeDescriptor/"



      ExperimentalReadout : target

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, or other modeled object ... direct
phenotype_term 0..1
PhenotypeDescriptor		 The HP term for this phenotype direct
biomarker_term 0..1
BiomarkerDescriptor		 Ontology term for a biomarker (from NCIT) direct
biological_processes *
BiologicalProcessDescriptor		 direct
assays *
AssayDescriptor		 direct
direction 0..1
BiomarkerReadoutDirectionEnum		 Direction of association between the biomarker value/presence and the linked ... direct
interpretation 0..1
String		 Curator-facing explanation of how this readout would be interpreted relative ... direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct

Usages

used by used in type used
Experiment readouts range ExperimentalReadout

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ExperimentalReadout
description: A structured readout or outcome measured in an experiment. Use descriptor
  slots to ground readouts to phenotypes, biomarkers, biological processes, and assays.
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- description
- target
- phenotype_term
- biomarker_term
- biological_processes
- assays
- direction
- interpretation
- evidence
- notes
slot_usage:
  target:
    name: target
    description: Entity reference for the pathograph node, phenotype, or other modeled
      object that this readout measures or adjudicates.
  interpretation:
    name: interpretation
    description: Curator-facing explanation of how this readout would be interpreted
      relative to the experiment's decision criterion.

Induced

name: ExperimentalReadout
description: A structured readout or outcome measured in an experiment. Use descriptor
  slots to ground readouts to phenotypes, biomarkers, biological processes, and assays.
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  target:
    name: target
    description: Entity reference for the pathograph node, phenotype, or other modeled
      object that this readout measures or adjudicates.
  interpretation:
    name: interpretation
    description: Curator-facing explanation of how this readout would be interpreted
      relative to the experiment's decision criterion.
attributes:
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: ExperimentalReadout
    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: ExperimentalReadout
    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, or other modeled
      object that this readout measures or adjudicates.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: target
    owner: ExperimentalReadout
    domain_of:
    - ExperimentalPerturbation
    - ExperimentalReadout
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - BiomarkerReadout
    range: string
    required: true
  phenotype_term:
    name: phenotype_term
    description: The HP term for this phenotype
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: phenotype_term
    owner: ExperimentalReadout
    domain_of:
    - ExperimentalReadout
    - Phenotype
    range: PhenotypeDescriptor
    inlined: true
  biomarker_term:
    name: biomarker_term
    description: Ontology term for a biomarker (from NCIT)
    comments:
    - Use NCIT terms for biomarkers (proteins, genes, fusion products)
    - NCIT:C16342 (Biomarker) is the root class for validation
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: biomarker_term
    owner: ExperimentalReadout
    domain_of:
    - ExperimentalReadout
    - Biochemical
    range: BiomarkerDescriptor
    inlined: 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: ExperimentalReadout
    domain_of:
    - ExperimentalPerturbation
    - ExperimentalReadout
    - Pathophysiology
    range: BiologicalProcessDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  assays:
    name: assays
    examples:
    - value: '[{preferred_term: Elevated Blood Glucose}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: assays
    owner: ExperimentalReadout
    domain_of:
    - Experiment
    - ExperimentalReadout
    - Pathophysiology
    - Biochemical
    range: AssayDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  direction:
    name: direction
    description: Direction of association between the biomarker value/presence and
      the linked pathograph node
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: direction
    owner: ExperimentalReadout
    domain_of:
    - ExperimentalReadout
    - BiomarkerReadout
    range: BiomarkerReadoutDirectionEnum
  interpretation:
    name: interpretation
    description: Curator-facing explanation of how this readout would be interpreted
      relative to the experiment's decision criterion.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: interpretation
    owner: ExperimentalReadout
    domain_of:
    - ExperimentalReadout
    - BiomarkerReadout
    range: string
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: ExperimentalReadout
    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: ExperimentalReadout
    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