Class: GeneClassificationCollection

A source-level transcription of one gene-classification system: which genes the source lists, and which of its categories each gene falls in.

This is a lookup table, deliberately not a Disease-like entity. It carries no pathophysiology, no per-row evidence, and no disease links; provenance is recorded once at the file level. It is a transcription of a source, not an inference engine — include only genes the source itself lists, and do not derive memberships.

Distinct from gene_sets, which reference flat, typically experimentally-derived gene sets (signatures, perturbation results) used as enrichment inputs. A gene classification is instead a curated, authoritative assertion about which genes cause disease in a domain, and usually carries its own category structure.

URI: dismech:class/GeneClassificationCollection

 classDiagram
    class GeneClassificationCollection
    click GeneClassificationCollection href "../../classes/GeneClassificationCollection/"
      GeneClassificationCollection : classification_system

      GeneClassificationCollection : description

      GeneClassificationCollection : genes





        GeneClassificationCollection --> "1..*" GeneClassification : genes
        click GeneClassification href "../../classes/GeneClassification/"



      GeneClassificationCollection : name

      GeneClassificationCollection : notes

      GeneClassificationCollection : retrieved_date

      GeneClassificationCollection : source_content_current_as_of

      GeneClassificationCollection : source_url

      GeneClassificationCollection : source_version

      GeneClassificationCollection : tracked_issues





        GeneClassificationCollection --> "*" TrackedIssue : tracked_issues
        click TrackedIssue href "../../classes/TrackedIssue/"

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 String		direct
description	0..1 String		direct
source_url	0..1 Uri	URL of the source page for a curated assertion or source collection	direct
source_content_current_as_of	0..1 Date	Date shown by the source as the content-current-as-of date	direct
retrieved_date	0..1 Date	Date on which the source was retrieved for curation	direct
tracked_issues	* TrackedIssue	Structured pointers to external tracker issues (e	direct
notes	0..1 String		direct
classification_system	1 String	Identifier for the classification system this collection transcribes, naming ...	direct
source_version	0..1 String	The source's own version string for this snapshot, where it publishes one (e	direct
genes	1..* GeneClassification	One row per gene listed by the source	direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GeneClassificationCollection
description: 'A source-level transcription of one gene-classification system: which
  genes the source lists, and which of its categories each gene falls in.

  This is a lookup table, deliberately not a `Disease`-like entity. It carries no
  pathophysiology, no per-row evidence, and no disease links; provenance is recorded
  once at the file level. It is a transcription of a source, not an inference engine
  — include only genes the source itself lists, and do not derive memberships.

  Distinct from `gene_sets`, which reference flat, typically experimentally-derived
  gene sets (signatures, perturbation results) used as enrichment inputs. A gene classification
  is instead a curated, authoritative assertion about which genes cause disease in
  a domain, and usually carries its own category structure.'
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- description
- source_url
- source_content_current_as_of
- retrieved_date
- tracked_issues
- notes
slot_usage:
  name:
    name: name
    required: true
attributes:
  classification_system:
    name: classification_system
    description: Identifier for the classification system this collection transcribes,
      naming the enum its `values` are drawn from (e.g. GENE_TABLE_NMD -> GeneTableNMDGroupEnum).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    domain_of:
    - GeneClassificationCollection
    range: string
    required: true
  source_version:
    name: source_version
    description: The source's own version string for this snapshot, where it publishes
      one (e.g. "GT_NMD 2026").
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    domain_of:
    - GeneClassificationCollection
    range: string
  genes:
    name: genes
    description: One row per gene listed by the source.
    from_schema: https://w3id.org/monarch-initiative/dismech
    domain_of:
    - GeneticContext
    - Dataset
    - ExperimentalPerturbation
    - Subtype
    - GeneClassificationCollection
    - Pathophysiology
    - AnimalModel
    range: GeneClassification
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: GeneClassificationCollection
description: 'A source-level transcription of one gene-classification system: which
  genes the source lists, and which of its categories each gene falls in.

  This is a lookup table, deliberately not a `Disease`-like entity. It carries no
  pathophysiology, no per-row evidence, and no disease links; provenance is recorded
  once at the file level. It is a transcription of a source, not an inference engine
  — include only genes the source itself lists, and do not derive memberships.

  Distinct from `gene_sets`, which reference flat, typically experimentally-derived
  gene sets (signatures, perturbation results) used as enrichment inputs. A gene classification
  is instead a curated, authoritative assertion about which genes cause disease in
  a domain, and usually carries its own category structure.'
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  name:
    name: name
    required: true
attributes:
  classification_system:
    name: classification_system
    description: Identifier for the classification system this collection transcribes,
      naming the enum its `values` are drawn from (e.g. GENE_TABLE_NMD -> GeneTableNMDGroupEnum).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: classification_system
    owner: GeneClassificationCollection
    domain_of:
    - GeneClassificationCollection
    range: string
    required: true
  source_version:
    name: source_version
    description: The source's own version string for this snapshot, where it publishes
      one (e.g. "GT_NMD 2026").
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: source_version
    owner: GeneClassificationCollection
    domain_of:
    - GeneClassificationCollection
    range: string
  genes:
    name: genes
    description: One row per gene listed by the source.
    from_schema: https://w3id.org/monarch-initiative/dismech
    alias: genes
    owner: GeneClassificationCollection
    domain_of:
    - GeneticContext
    - Dataset
    - ExperimentalPerturbation
    - Subtype
    - GeneClassificationCollection
    - Pathophysiology
    - AnimalModel
    range: GeneClassification
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: GeneClassificationCollection
    domain_of:
    - GenomicRegion
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ReferenceRangeBand
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - 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
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: GeneClassificationCollection
    domain_of:
    - Descriptor
    - DietaryModification
    - GenomicRegion
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - ImagingFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - VariantPopulationEffect
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Grouping
    - GroupingCriteria
    - LogicalCriterion
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string
  source_url:
    name: source_url
    description: URL of the source page for a curated assertion or source collection
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: source_url
    owner: GeneClassificationCollection
    domain_of:
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    range: uri
  source_content_current_as_of:
    name: source_content_current_as_of
    description: Date shown by the source as the content-current-as-of date
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: source_content_current_as_of
    owner: GeneClassificationCollection
    domain_of:
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    range: date
  retrieved_date:
    name: retrieved_date
    description: Date on which the source was retrieved for curation
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: retrieved_date
    owner: GeneClassificationCollection
    domain_of:
    - ExecutableProtocol
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    range: date
  tracked_issues:
    name: tracked_issues
    description: Structured pointers to external tracker issues (e.g., GitHub ontology
      term requests, schema follow-ups) that provide curation provenance for this
      entry or nested object. Use this in preference to stashing issue URLs inside
      free-text `notes` fields so they can be validated, rendered, and queried consistently.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: tracked_issues
    owner: GeneClassificationCollection
    domain_of:
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - Disease
    - TermMapping
    range: TrackedIssue
    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: GeneClassificationCollection
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - ReferenceRange
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - GeneClassification
    - GeneClassificationCollection
    - ExternalAssertion
    - TrackedIssue
    - Prevalence
    - GeneCaseFraction
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - Transmission
    - Diagnosis
    - VariantPopulationEffect
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    - Discussion
    - Grouping
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string