Skip to content

Class: GenomicRegion

A named genomic feature or interval affected by an alteration. Supports qualitative reference-genome location without requiring an ontology identifier, assembly, or patient-specific coordinates. Use a specific name and description to distinguish an affected subfeature (such as a regulatory boundary) from the full altered interval. Gene relations describe linear reference-genome placement only; keep regulatory targets, expression consequences, and mechanistic confidence on the enclosing variant or pathophysiology record.

URI: dismech:class/GenomicRegion

 classDiagram
    class GenomicRegion
    click GenomicRegion href "../../classes/GenomicRegion/"
      GenomicRegion : adjacent_to_genes





        GenomicRegion --> "*" GeneDescriptor : adjacent_to_genes
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      GenomicRegion : between_genes





        GenomicRegion --> "2..*" GeneDescriptor : between_genes
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      GenomicRegion : chromosomal_region

      GenomicRegion : description

      GenomicRegion : name

      GenomicRegion : overlaps_genes





        GenomicRegion --> "*" GeneDescriptor : overlaps_genes
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      GenomicRegion : regulatory_element_type





        GenomicRegion --> "0..1" RegulatoryElementTypeEnum : regulatory_element_type
        click RegulatoryElementTypeEnum href "../../enums/RegulatoryElementTypeEnum/"



      GenomicRegion : within_gene





        GenomicRegion --> "0..1" GeneDescriptor : within_gene
        click GeneDescriptor href "../../classes/GeneDescriptor/"

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
description 0..1
String		 direct
chromosomal_region 0..1
String		 Qualitative human cytogenetic location: a chromosome, arm, band, or band rang... direct
regulatory_element_type 0..1
RegulatoryElementTypeEnum		 Type of gene regulatory element affected by a variant (e direct
between_genes 2..*
GeneDescriptor		 Exactly two distinct genes on opposite sides of the named region in the linea... direct
within_gene 0..1
GeneDescriptor		 Gene whose genomic span contains the entire named region in the linear refere... direct
overlaps_genes *
GeneDescriptor		 Genes sharing reference-genome sequence with the named region direct
adjacent_to_genes *
GeneDescriptor		 Genes whose sequence boundary directly meets the named region in the linear r... direct

Usages

used by used in type used
GeneticContext affected_regions range GenomicRegion
Genetic affected_regions range GenomicRegion
Variant affected_regions range GenomicRegion

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GenomicRegion
description: A named genomic feature or interval affected by an alteration. Supports
  qualitative reference-genome location without requiring an ontology identifier,
  assembly, or patient-specific coordinates. Use a specific name and description to
  distinguish an affected subfeature (such as a regulatory boundary) from the full
  altered interval. Gene relations describe linear reference-genome placement only;
  keep regulatory targets, expression consequences, and mechanistic confidence on
  the enclosing variant or pathophysiology record.
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- description
- chromosomal_region
- regulatory_element_type
- between_genes
- within_gene
- overlaps_genes
- adjacent_to_genes
slot_usage:
  name:
    name: name
    required: true

Induced

name: GenomicRegion
description: A named genomic feature or interval affected by an alteration. Supports
  qualitative reference-genome location without requiring an ontology identifier,
  assembly, or patient-specific coordinates. Use a specific name and description to
  distinguish an affected subfeature (such as a regulatory boundary) from the full
  altered interval. Gene relations describe linear reference-genome placement only;
  keep regulatory targets, expression consequences, and mechanistic confidence on
  the enclosing variant or pathophysiology record.
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  name:
    name: name
    required: true
attributes:
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: GenomicRegion
    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: GenomicRegion
    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
  chromosomal_region:
    name: chromosomal_region
    description: 'Qualitative human cytogenetic location: a chromosome, arm, band,
      or band range on one chromosome (e.g., 21, 7q, 17p13.3, or 16p12.2-p11.2). Use
      a single chromosome prefix and no chr prefix. This syntax does not validate
      band existence or imply exact coordinates, common breakpoints, or a genome assembly.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: chromosomal_region
    owner: GenomicRegion
    domain_of:
    - GenomicRegion
    range: string
    pattern: ^([1-9]|1[0-9]|2[0-2]|X|Y)([pq]([1-9][0-9]*(\.[0-9]+)?)?(-[pq]([1-9][0-9]*(\.[0-9]+)?)?)?)?$
  regulatory_element_type:
    name: regulatory_element_type
    description: Type of gene regulatory element affected by a variant (e.g., promoter,
      enhancer, silencer, insulator, TAD boundary).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: regulatory_element_type
    owner: GenomicRegion
    domain_of:
    - GenomicRegion
    - FunctionalEffect
    range: RegulatoryElementTypeEnum
  between_genes:
    name: between_genes
    description: Exactly two distinct genes on opposite sides of the named region
      in the linear reference genome, with no overlap between the region and either
      gene. The pair is unordered. Neither nearest-gene status nor direct adjacency
      is implied; intervening sequence may be present. Apply this to the named feature,
      not automatically to the entire altered interval. Do not use it for chromatin
      contacts or newly juxtaposed genes on a rearranged allele.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: between_genes
    owner: GenomicRegion
    domain_of:
    - GenomicRegion
    range: GeneDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
    minimum_cardinality: 2
    maximum_cardinality: 2
  within_gene:
    name: within_gene
    description: Gene whose genomic span contains the entire named region in the linear
      reference genome (e.g., an intronic enhancer). Does not imply that this gene
      is the regulatory target or a disease-causal gene.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: within_gene
    owner: GenomicRegion
    domain_of:
    - GenomicRegion
    range: GeneDescriptor
    inlined: true
  overlaps_genes:
    name: overlaps_genes
    description: Genes sharing reference-genome sequence with the named region. The
      list need not be exhaustive and does not assert complete deletion, dosage effects,
      regulatory targeting, or disease causality.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: overlaps_genes
    owner: GenomicRegion
    domain_of:
    - GenomicRegion
    range: GeneDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  adjacent_to_genes:
    name: adjacent_to_genes
    description: Genes whose sequence boundary directly meets the named region in
      the linear reference genome, without overlap or intervening sequence. This is
      strict adjacency, not approximate proximity. Omit when the source establishes
      only that a gene is nearby. Does not describe chromatin contacts or adjacency
      created by a rearrangement.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: adjacent_to_genes
    owner: GenomicRegion
    domain_of:
    - GenomicRegion
    range: GeneDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true