Class: GeneticContext

A structured description of a genetic context that modifies phenotype frequency, severity, or presentation. Flexible enough to capture single genes, multiple genes, mutation types, zygosity, complementation groups, and complex genotypes. The description slot accommodates contexts that don't fit neatly into the structured fields (e.g., structural variants, complex rearrangements).

URI: dismech:GeneticContext

 classDiagram
    class GeneticContext
    click GeneticContext href "../GeneticContext/"
      GeneticContext : allele_type

      GeneticContext : complementation_group

      GeneticContext : description

      GeneticContext : functional_impact

      GeneticContext : gene





        GeneticContext --> "0..1" GeneDescriptor : gene
        click GeneDescriptor href "../GeneDescriptor/"



      GeneticContext : genes





        GeneticContext --> "*" GeneDescriptor : genes
        click GeneDescriptor href "../GeneDescriptor/"



      GeneticContext : notes

      GeneticContext : zygosity





        GeneticContext --> "0..1" ZygosityEnum : zygosity
        click ZygosityEnum href "../ZygosityEnum/"

Slots

Name	Cardinality and Range	Description	Inheritance
gene	0..1 GeneDescriptor		direct
genes	* GeneDescriptor		direct
allele_type	0..1 String	Type of allele or mutation (e	direct
zygosity	0..1 ZygosityEnum	Zygosity context	direct
functional_impact	0..1 String	Functional consequence of the genetic variant (e	direct
complementation_group	0..1 String	Complementation group designation (e	direct
description	0..1 String		direct
notes	0..1 String		direct

Usages

used by	used in	type	used
PhenotypeContext	genetic_context	range	GeneticContext

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GeneticContext
description: A structured description of a genetic context that modifies phenotype
  frequency, severity, or presentation. Flexible enough to capture single genes, multiple
  genes, mutation types, zygosity, complementation groups, and complex genotypes.
  The description slot accommodates contexts that don't fit neatly into the structured
  fields (e.g., structural variants, complex rearrangements).
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- gene
- genes
- allele_type
- zygosity
- functional_impact
- complementation_group
- description
- notes

Induced

name: GeneticContext
description: A structured description of a genetic context that modifies phenotype
  frequency, severity, or presentation. Flexible enough to capture single genes, multiple
  genes, mutation types, zygosity, complementation groups, and complex genotypes.
  The description slot accommodates contexts that don't fit neatly into the structured
  fields (e.g., structural variants, complex rearrangements).
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  gene:
    name: gene
    examples:
    - value: '{preferred_term: MEFV}'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: gene
    owner: GeneticContext
    domain_of:
    - GeneticContext
    - Pathophysiology
    - Variant
    range: GeneDescriptor
    inlined: true
  genes:
    name: genes
    examples:
    - value: '[{preferred_term: HLA-DQ2}, {preferred_term: INS}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: genes
    owner: GeneticContext
    domain_of:
    - GeneticContext
    - Dataset
    - Subtype
    - Pathophysiology
    - AnimalModel
    range: GeneDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  allele_type:
    name: allele_type
    description: Type of allele or mutation (e.g., null, missense, splice_site, deletion,
      frameshift, nonsense, hypomorphic, structural_variant). Free text to accommodate
      the diversity of mutation nomenclature.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: allele_type
    owner: GeneticContext
    domain_of:
    - GeneticContext
    range: string
  zygosity:
    name: zygosity
    description: Zygosity context
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: zygosity
    owner: GeneticContext
    domain_of:
    - GeneticContext
    range: ZygosityEnum
  functional_impact:
    name: functional_impact
    description: Functional consequence of the genetic variant (e.g., loss_of_function,
      gain_of_function, dominant_negative).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: functional_impact
    owner: GeneticContext
    domain_of:
    - GeneticContext
    range: string
  complementation_group:
    name: complementation_group
    description: Complementation group designation (e.g., FA-A, FA-D1, BBS1). Used
      for genetically heterogeneous diseases where subtypes are historically named
      by complementation analysis.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: complementation_group
    owner: GeneticContext
    domain_of:
    - GeneticContext
    range: string
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: GeneticContext
    domain_of:
    - Descriptor
    - GeneticContext
    - Dataset
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - 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
  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: GeneticContext
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - 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
    range: string