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Class: ModuleCollection

A curated navigation or framework record that organizes mechanism modules. A ModuleCollection is not itself a mechanism and does not assert disease membership. It points down to module filename stems, may nest more specific collections, and may cite the publication that defines the framework.

URI: dismech:class/ModuleCollection

 classDiagram
    class ModuleCollection
    click ModuleCollection href "../../classes/ModuleCollection/"
      ModuleCollection : child_collections

      ModuleCollection : collection_type





        ModuleCollection --> "1" ModuleCollectionTypeEnum : collection_type
        click ModuleCollectionTypeEnum href "../../enums/ModuleCollectionTypeEnum/"



      ModuleCollection : creation_date

      ModuleCollection : description

      ModuleCollection : display_name

      ModuleCollection : evidence





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



      ModuleCollection : module_members





        ModuleCollection --> "1..*" ModuleCollectionMember : module_members
        click ModuleCollectionMember href "../../classes/ModuleCollectionMember/"



      ModuleCollection : name

      ModuleCollection : notes

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 Preferred collection name (unique; serves as an FK target) direct
display_name 0..1
String		 Human-readable display name for a subtype, used when the name (which serves a... direct
creation_date 0..1 recommended
String		 Timestamp for initial creation of this module collection direct
description 0..1
String		 direct
collection_type 1
ModuleCollectionTypeEnum		 The organizing principle represented by a ModuleCollection direct
module_members 1..*
ModuleCollectionMember		 The mechanism modules explicitly included in this collection direct
child_collections *
String		 Names of more specific ModuleCollection records nested under this collection direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ModuleCollection
description: A curated navigation or framework record that organizes mechanism modules.
  A ModuleCollection is not itself a mechanism and does not assert disease membership.
  It points down to module filename stems, may nest more specific collections, and
  may cite the publication that defines the framework.
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- display_name
- creation_date
- description
- collection_type
- module_members
- child_collections
- evidence
- notes
slot_usage:
  name:
    name: name
    description: Preferred collection name (unique; serves as an FK target).
    required: true
  creation_date:
    name: creation_date
    description: Timestamp for initial creation of this module collection. Keep this
      stable after first set.
    recommended: true
  collection_type:
    name: collection_type
    required: true
  module_members:
    name: module_members
    required: true

Induced

name: ModuleCollection
description: A curated navigation or framework record that organizes mechanism modules.
  A ModuleCollection is not itself a mechanism and does not assert disease membership.
  It points down to module filename stems, may nest more specific collections, and
  may cite the publication that defines the framework.
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  name:
    name: name
    description: Preferred collection name (unique; serves as an FK target).
    required: true
  creation_date:
    name: creation_date
    description: Timestamp for initial creation of this module collection. Keep this
      stable after first set.
    recommended: true
  collection_type:
    name: collection_type
    required: true
  module_members:
    name: module_members
    required: true
attributes:
  name:
    name: name
    description: Preferred collection name (unique; serves as an FK target).
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: ModuleCollection
    domain_of:
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ReferenceRangeBand
    - SurrogateEndpointCollection
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ComorbidityAssociation
    - Grouping
    - ModuleCollection
    range: string
    required: true
  display_name:
    name: display_name
    description: Human-readable display name for a subtype, used when the name (which
      serves as the FK target) is too terse for comfortable display. Optional; when
      absent, renderers should fall back to name.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: display_name
    owner: ModuleCollection
    domain_of:
    - Subtype
    - Grouping
    - GroupingMember
    - ModuleCollection
    range: string
  creation_date:
    name: creation_date
    description: Timestamp for initial creation of this module collection. Keep this
      stable after first set.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: creation_date
    owner: ModuleCollection
    domain_of:
    - Disease
    - ComorbidityAssociation
    - Grouping
    - ModuleCollection
    range: string
    recommended: true
    pattern: ^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}(?:\.\d+)?(?:Z|[+\-]\d{2}:\d{2})$
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: ModuleCollection
    domain_of:
    - Descriptor
    - DietaryModification
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - SurrogateEndpointCollection
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - ImagingFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Grouping
    - GroupingCriteria
    - LogicalCriterion
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string
  collection_type:
    name: collection_type
    description: The organizing principle represented by a ModuleCollection.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: collection_type
    owner: ModuleCollection
    domain_of:
    - ModuleCollection
    range: ModuleCollectionTypeEnum
    required: true
  module_members:
    name: module_members
    description: The mechanism modules explicitly included in this collection. Module
      filename stems are used as foreign keys.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: module_members
    owner: ModuleCollection
    domain_of:
    - ModuleCollection
    range: ModuleCollectionMember
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  child_collections:
    name: child_collections
    description: Names of more specific ModuleCollection records nested under this
      collection.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: child_collections
    owner: ModuleCollection
    domain_of:
    - ModuleCollection
    range: string
    multivalued: true
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: ModuleCollection
    domain_of:
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - ReferenceRange
    - SurrogateEndpoint
    - ExternalAssertion
    - Finding
    - Prevalence
    - GeneCaseFraction
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - AlgorithmValidationStatus
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Discussion
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    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: ModuleCollection
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - ReferenceRange
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - ExternalAssertion
    - TrackedIssue
    - Prevalence
    - GeneCaseFraction
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - Transmission
    - Diagnosis
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    - Discussion
    - Grouping
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string