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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). Physical variant class and sequence overlap use the same controlled fields as Variant. Separate alternative initiating alterations into distinct pathophysiology nodes when their classes or overlaps differ.

URI: dismech:class/GeneticContext

 classDiagram
    class GeneticContext
    click GeneticContext href "../../classes/GeneticContext/"
      GeneticContext : affected_regions





        GeneticContext --> "*" GenomicRegion : affected_regions
        click GenomicRegion href "../../classes/GenomicRegion/"



      GeneticContext : allele_type

      GeneticContext : allelic_events





        GeneticContext --> "*" AllelicEventEnum : allelic_events
        click AllelicEventEnum href "../../enums/AllelicEventEnum/"



      GeneticContext : allelic_hit_role





        GeneticContext --> "0..1" AllelicHitRoleEnum : allelic_hit_role
        click AllelicHitRoleEnum href "../../enums/AllelicHitRoleEnum/"



      GeneticContext : complementation_group

      GeneticContext : description

      GeneticContext : functional_impact

      GeneticContext : functional_impact_category





        GeneticContext --> "0..1" FunctionalImpactEnum : functional_impact_category
        click FunctionalImpactEnum href "../../enums/FunctionalImpactEnum/"



      GeneticContext : gene





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



      GeneticContext : genes





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



      GeneticContext : genomic_contexts





        GeneticContext --> "*" GenomicContextEnum : genomic_contexts
        click GenomicContextEnum href "../../enums/GenomicContextEnum/"



      GeneticContext : notes

      GeneticContext : variant_origin





        GeneticContext --> "0..1" VariantOriginEnum : variant_origin
        click VariantOriginEnum href "../../enums/VariantOriginEnum/"



      GeneticContext : variant_type





        GeneticContext --> "0..1" VariantTypeEnum : variant_type
        click VariantTypeEnum href "../../enums/VariantTypeEnum/"



      GeneticContext : zygosity





        GeneticContext --> "0..1" ZygosityEnum : zygosity
        click ZygosityEnum href "../../enums/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
variant_type 0..1
VariantTypeEnum		 Optional controlled physical variant class direct
genomic_contexts *
GenomicContextEnum		 Sequence features overlapped by the variant direct
affected_regions *
GenomicRegion		 Named genomic regions affected by the physical alteration, including regulato... direct
variant_origin 0..1
VariantOriginEnum		 The origin of disease-associated variation in this gene (germline, somatic, d... direct
allelic_hit_role 0..1
AllelicHitRoleEnum		 Role of the alteration in a multi-hit mechanism, such as first hit, second hi... direct
allelic_events *
AllelicEventEnum		 Event types affecting the allele or locus direct
zygosity 0..1
ZygosityEnum		 Zygosity context direct
functional_impact 0..1
String		 Functional consequence of the genetic variant (e direct
functional_impact_category 0..1
FunctionalImpactEnum		 Controlled functional impact category for a genetic context 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
Pathophysiology 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). Physical variant class
  and sequence overlap use the same controlled fields as Variant. Separate alternative
  initiating alterations into distinct pathophysiology nodes when their classes or
  overlaps differ.
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- gene
- genes
- allele_type
- variant_type
- genomic_contexts
- affected_regions
- variant_origin
- allelic_hit_role
- allelic_events
- zygosity
- functional_impact
- functional_impact_category
- 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). Physical variant class
  and sequence overlap use the same controlled fields as Variant. Separate alternative
  initiating alterations into distinct pathophysiology nodes when their classes or
  overlaps differ.
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
    - ExperimentalPerturbation
    - GeneClassification
    - Pathophysiology
    - Variant
    - LogicalCriterion
    - DifferentiatingMechanism
    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
    - ExperimentalPerturbation
    - Subtype
    - GeneClassificationCollection
    - 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 retained for
      legacy or unusually complex contexts. Prefer the structured `variant_type`,
      `genomic_contexts`, `allelic_events`, `allelic_hit_role`, `variant_origin`,
      and `functional_impact_category` slots when possible.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: allele_type
    owner: GeneticContext
    domain_of:
    - GeneticContext
    range: string
  variant_type:
    name: variant_type
    description: Optional controlled physical variant class. Complements the legacy
      free-text type without requiring it or replacing its narrative detail. Does
      not imply a coding or regulatory functional effect.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: variant_type
    owner: GeneticContext
    domain_of:
    - GeneticContext
    - Variant
    range: VariantTypeEnum
  genomic_contexts:
    name: genomic_contexts
    description: Sequence features overlapped by the variant. Multiple values are
      allowed because an SV may span several features, or transcripts may differ.
      Specify relevant genes, transcripts, and overlap details in description; an
      intronic host gene need not be the regulatory target. Omit when unknown.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: genomic_contexts
    owner: GeneticContext
    domain_of:
    - GeneticContext
    - Variant
    range: GenomicContextEnum
    multivalued: true
  affected_regions:
    name: affected_regions
    description: Named genomic regions affected by the physical alteration, including
      regulatory elements or chromosome intervals. Each item describes the named feature,
      which need not span the entire variant. Record only source-supported locations;
      disease-level regions need not have exact patient-specific breakpoints. Evidence
      belongs on the enclosing record. Location landmarks do not assert regulatory
      targeting or causal gene involvement. Existing free-text descriptions remain
      valid.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: affected_regions
    owner: GeneticContext
    domain_of:
    - GeneticContext
    - Genetic
    - Variant
    range: GenomicRegion
    multivalued: true
    inlined: true
    inlined_as_list: true
  variant_origin:
    name: variant_origin
    description: The origin of disease-associated variation in this gene (germline,
      somatic, de novo, or both). Bound to GENO allele origin terms.
    examples:
    - value: SOMATIC
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: variant_origin
    owner: GeneticContext
    domain_of:
    - GeneticContext
    - Genetic
    range: VariantOriginEnum
  allelic_hit_role:
    name: allelic_hit_role
    description: Role of the alteration in a multi-hit mechanism, such as first hit,
      second hit, or biallelic inactivation.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: allelic_hit_role
    owner: GeneticContext
    domain_of:
    - GeneticContext
    range: AllelicHitRoleEnum
  allelic_events:
    name: allelic_events
    description: Event types affecting the allele or locus. Multivalued so events
      such as deletion plus loss of heterozygosity can be composed without cross-product
      enum values.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: allelic_events
    owner: GeneticContext
    domain_of:
    - GeneticContext
    range: AllelicEventEnum
    multivalued: true
  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). Free text retained for legacy values;
      prefer `functional_impact_category` when a controlled value applies.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: functional_impact
    owner: GeneticContext
    domain_of:
    - GeneticContext
    range: string
  functional_impact_category:
    name: functional_impact_category
    description: Controlled functional impact category for a genetic context.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: functional_impact_category
    owner: GeneticContext
    domain_of:
    - GeneticContext
    range: FunctionalImpactEnum
  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
    - 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
  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
    - 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