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Class: BiomarkerReadout

Links a biochemical biomarker to a pathograph node that it measures, reflects, predicts, or pharmacodynamically reports on. This is an observational readout link, not a causal claim that the biomarker causes the target mechanism or phenotype.

URI: dismech:class/BiomarkerReadout

 classDiagram
    class BiomarkerReadout
    click BiomarkerReadout href "../../classes/BiomarkerReadout/"
      BiomarkerReadout : description

      BiomarkerReadout : direction





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



      BiomarkerReadout : endpoint_context





        BiomarkerReadout --> "0..1" BiomarkerEndpointContextEnum : endpoint_context
        click BiomarkerEndpointContextEnum href "../../enums/BiomarkerEndpointContextEnum/"



      BiomarkerReadout : evidence





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



      BiomarkerReadout : interpretation

      BiomarkerReadout : regulatory_endpoint_refs

      BiomarkerReadout : relationship





        BiomarkerReadout --> "1" BiomarkerReadoutRelationshipEnum : relationship
        click BiomarkerReadoutRelationshipEnum href "../../enums/BiomarkerReadoutRelationshipEnum/"



      BiomarkerReadout : target

Slots

Name Cardinality and Range Description Inheritance
target 1
String		 Name of the pathograph node this biomarker reports on direct
relationship 1
BiomarkerReadoutRelationshipEnum		 How the biomarker relates to the linked pathograph node direct
direction 0..1
BiomarkerReadoutDirectionEnum		 Direction of association between biomarker level/presence and the linked even... direct
endpoint_context 0..1
BiomarkerEndpointContextEnum		 Diagnostic, prognostic, monitoring, pharmacodynamic, or candidate-surrogate u... direct
regulatory_endpoint_refs *
String		 Source-table regulatory endpoint row IDs linked to this readout direct
interpretation 0..1
String		 Human-readable interpretation of the link for display and curation review direct
description 0..1
String		 direct
evidence * recommended
EvidenceItem		 Evidence supporting this biomarker-to-pathograph-node readout link direct

Usages

used by used in type used
Biochemical readouts range BiomarkerReadout

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: BiomarkerReadout
description: Links a biochemical biomarker to a pathograph node that it measures,
  reflects, predicts, or pharmacodynamically reports on. This is an observational
  readout link, not a causal claim that the biomarker causes the target mechanism
  or phenotype.
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- target
- relationship
- direction
- endpoint_context
- regulatory_endpoint_refs
- interpretation
- description
- evidence
slot_usage:
  target:
    name: target
    description: Name of the pathograph node this biomarker reports on. Prefer a pathophysiology
      entry; phenotype targets are also allowed when the biomarker is explicitly tied
      to a clinical manifestation.
    required: true
  relationship:
    name: relationship
    description: How the biomarker relates to the linked pathograph node.
    required: true
  direction:
    name: direction
    description: Direction of association between biomarker level/presence and the
      linked event or endpoint.
  endpoint_context:
    name: endpoint_context
    description: Diagnostic, prognostic, monitoring, pharmacodynamic, or candidate-surrogate
      use context.
  regulatory_endpoint_refs:
    name: regulatory_endpoint_refs
    description: Source-table regulatory endpoint row IDs linked to this readout.
      Keep regulatory details in the source table; use this field only as a local
      bridge from disease biology to regulatory context.
  interpretation:
    name: interpretation
    description: Human-readable interpretation of the link for display and curation
      review.
  evidence:
    name: evidence
    description: Evidence supporting this biomarker-to-pathograph-node readout link

Induced

name: BiomarkerReadout
description: Links a biochemical biomarker to a pathograph node that it measures,
  reflects, predicts, or pharmacodynamically reports on. This is an observational
  readout link, not a causal claim that the biomarker causes the target mechanism
  or phenotype.
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  target:
    name: target
    description: Name of the pathograph node this biomarker reports on. Prefer a pathophysiology
      entry; phenotype targets are also allowed when the biomarker is explicitly tied
      to a clinical manifestation.
    required: true
  relationship:
    name: relationship
    description: How the biomarker relates to the linked pathograph node.
    required: true
  direction:
    name: direction
    description: Direction of association between biomarker level/presence and the
      linked event or endpoint.
  endpoint_context:
    name: endpoint_context
    description: Diagnostic, prognostic, monitoring, pharmacodynamic, or candidate-surrogate
      use context.
  regulatory_endpoint_refs:
    name: regulatory_endpoint_refs
    description: Source-table regulatory endpoint row IDs linked to this readout.
      Keep regulatory details in the source table; use this field only as a local
      bridge from disease biology to regulatory context.
  interpretation:
    name: interpretation
    description: Human-readable interpretation of the link for display and curation
      review.
  evidence:
    name: evidence
    description: Evidence supporting this biomarker-to-pathograph-node readout link
attributes:
  target:
    name: target
    description: Name of the pathograph node this biomarker reports on. Prefer a pathophysiology
      entry; phenotype targets are also allowed when the biomarker is explicitly tied
      to a clinical manifestation.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: target
    owner: BiomarkerReadout
    domain_of:
    - ExperimentalPerturbation
    - ExperimentalReadout
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - BiomarkerReadout
    range: string
    required: true
  relationship:
    name: relationship
    description: How the biomarker relates to the linked pathograph node.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: relationship
    owner: BiomarkerReadout
    domain_of:
    - BiomarkerReadout
    range: BiomarkerReadoutRelationshipEnum
    required: true
  direction:
    name: direction
    description: Direction of association between biomarker level/presence and the
      linked event or endpoint.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: direction
    owner: BiomarkerReadout
    domain_of:
    - ExperimentalReadout
    - BiomarkerReadout
    range: BiomarkerReadoutDirectionEnum
  endpoint_context:
    name: endpoint_context
    description: Diagnostic, prognostic, monitoring, pharmacodynamic, or candidate-surrogate
      use context.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: endpoint_context
    owner: BiomarkerReadout
    domain_of:
    - BiomarkerReadout
    range: BiomarkerEndpointContextEnum
  regulatory_endpoint_refs:
    name: regulatory_endpoint_refs
    description: Source-table regulatory endpoint row IDs linked to this readout.
      Keep regulatory details in the source table; use this field only as a local
      bridge from disease biology to regulatory context.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: regulatory_endpoint_refs
    owner: BiomarkerReadout
    domain_of:
    - BiomarkerReadout
    range: string
    multivalued: true
  interpretation:
    name: interpretation
    description: Human-readable interpretation of the link for display and curation
      review.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: interpretation
    owner: BiomarkerReadout
    domain_of:
    - ExperimentalReadout
    - BiomarkerReadout
    range: string
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: BiomarkerReadout
    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
  evidence:
    name: evidence
    description: Evidence supporting this biomarker-to-pathograph-node readout link
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: BiomarkerReadout
    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