Class: GeneClassification

One gene's membership in a gene-classification system, as asserted by that system's source. A row in a GeneClassificationCollection.

values is multivalued because gene classifications are genuinely set-valued: a gene appears in as many groups as it has clinically distinct disease associations. Its range is left open here because each collection draws from its own enum (GeneTableNMDGroupEnum for the neuromuscular gene table, and others as further sources are added); the per-collection test asserts membership of the right enum.

URI: dismech:class/GeneClassification

 classDiagram
    class GeneClassification
    click GeneClassification href "../../classes/GeneClassification/"
      GeneClassification : gene





        GeneClassification --> "1" GeneDescriptor : gene
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      GeneClassification : notes

      GeneClassification : source_label

      GeneClassification : values

Slots

Name	Cardinality and Range	Description	Inheritance
gene	1 GeneDescriptor		direct
notes	0..1 String		direct
values	1..* String	Classification values this gene carries in the collection's system, drawn fro...	direct
source_label	0..1 String	The gene symbol as written by the source, recorded when it differs from the H...	direct

Usages

used by	used in	type	used
GeneClassificationCollection	genes	range	GeneClassification

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GeneClassification
description: 'One gene''s membership in a gene-classification system, as asserted
  by that system''s source. A row in a `GeneClassificationCollection`.

  `values` is multivalued because gene classifications are genuinely set-valued: a
  gene appears in as many groups as it has clinically distinct disease associations.
  Its range is left open here because each collection draws from its own enum (`GeneTableNMDGroupEnum`
  for the neuromuscular gene table, and others as further sources are added); the
  per-collection test asserts membership of the right enum.'
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- gene
- notes
slot_usage:
  gene:
    name: gene
    required: true
attributes:
  values:
    name: values
    description: Classification values this gene carries in the collection's system,
      drawn from the enum named by the collection's `classification_system`. Transcribed
      from the source, never inferred.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    domain_of:
    - GeneClassification
    range: string
    required: true
    multivalued: true
  source_label:
    name: source_label
    description: The gene symbol as written by the source, recorded when it differs
      from the HGNC-approved symbol in `gene` (for example when the source still uses
      a previous symbol). Lets a reader confirm the mapping.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    domain_of:
    - GeneClassification
    range: string

Induced

name: GeneClassification
description: 'One gene''s membership in a gene-classification system, as asserted
  by that system''s source. A row in a `GeneClassificationCollection`.

  `values` is multivalued because gene classifications are genuinely set-valued: a
  gene appears in as many groups as it has clinically distinct disease associations.
  Its range is left open here because each collection draws from its own enum (`GeneTableNMDGroupEnum`
  for the neuromuscular gene table, and others as further sources are added); the
  per-collection test asserts membership of the right enum.'
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  gene:
    name: gene
    required: true
attributes:
  values:
    name: values
    description: Classification values this gene carries in the collection's system,
      drawn from the enum named by the collection's `classification_system`. Transcribed
      from the source, never inferred.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: values
    owner: GeneClassification
    domain_of:
    - GeneClassification
    range: string
    required: true
    multivalued: true
  source_label:
    name: source_label
    description: The gene symbol as written by the source, recorded when it differs
      from the HGNC-approved symbol in `gene` (for example when the source still uses
      a previous symbol). Lets a reader confirm the mapping.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: source_label
    owner: GeneClassification
    domain_of:
    - GeneClassification
    range: string
  gene:
    name: gene
    examples:
    - value: '{preferred_term: MEFV}'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: gene
    owner: GeneClassification
    domain_of:
    - GeneticContext
    - ExperimentalPerturbation
    - GeneClassification
    - Pathophysiology
    - Variant
    - LogicalCriterion
    - DifferentiatingMechanism
    range: GeneDescriptor
    required: true
    inlined: 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: GeneClassification
    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