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GeneGeneticMapAssociation

The mapping of a gene along a chromosome using recombination frequency relative to other visible markers to calculate the genetic distance in centiMorgan (cM) units.

classDiagram SingleReferenceAssociation <|-- GeneGeneticMapAssociation GeneGeneticMapAssociation : created_by GeneGeneticMapAssociation : date_created GeneGeneticMapAssociation : date_updated GeneGeneticMapAssociation : db_date_created GeneGeneticMapAssociation : db_date_updated GeneGeneticMapAssociation : gene_association_subject GeneGeneticMapAssociation : gene_genetic_map_association_object GeneGeneticMapAssociation : genetic_map_position_centimorgan GeneGeneticMapAssociation : genetic_map_position_centimorgan_error GeneGeneticMapAssociation : internal GeneGeneticMapAssociation : obsolete GeneGeneticMapAssociation : relation GeneGeneticMapAssociation : single_reference GeneGeneticMapAssociation : updated_by

URI: alliance:GeneGeneticMapAssociation

Parent Classes

Slots

Name Description
created_by The individual that created the entity.
date_created The date on which an entity was created. This can be applied to nodes or edges.
date_updated Date on which an entity was last modified.
db_date_created The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).
db_date_updated Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.
gene_association_subject Subject slot to be used for gene associations
gene_genetic_map_association_object None
genetic_map_position_centimorgan Genetic map distance calculated along a chromosome in centiMorgans: e.g., 22.3366 cM.
genetic_map_position_centimorgan_error Error in calculated genetic map distance in centiMorgans: e.g., 0.045 cM.
internal Classifies the entity as private (for internal use) or not (for public use).
obsolete Entity is no longer current.
relation A high-level grouping for the relationship type. This is analogous to category for nodes. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type.
single_reference holds between an object and a single reference
updated_by The individual that last modified the entity.

Mappings

Mapping Type Mapped Value
self ['alliance:GeneGeneticMapAssociation']
native ['alliance:GeneGeneticMapAssociation']

LinkML Specification

Direct

name: GeneGeneticMapAssociation
description: The mapping of a gene along a chromosome using recombination frequency
  relative to other visible markers to calculate the genetic distance in centiMorgan
  (cM) units.
notes:
- Should this be limited to reports of specific cM on a given chromosome, or should
  it include genetic segregation studies that link gene to a chromosome?
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SingleReferenceAssociation
slots:
- gene_association_subject
- genetic_map_position_centimorgan
- genetic_map_position_centimorgan_error
slot_usage:
  relation:
    name: relation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    any_of:
    - equals_string: has_location
attributes:
  gene_genetic_map_association_object:
    name: gene_genetic_map_association_object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/gene.yaml
    range: Chromosome
    required: true

Induced

name: GeneGeneticMapAssociation
description: The mapping of a gene along a chromosome using recombination frequency
  relative to other visible markers to calculate the genetic distance in centiMorgan
  (cM) units.
notes:
- Should this be limited to reports of specific cM on a given chromosome, or should
  it include genetic segregation studies that link gene to a chromosome?
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SingleReferenceAssociation
slot_usage:
  relation:
    name: relation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    any_of:
    - equals_string: has_location
attributes:
  gene_genetic_map_association_object:
    name: gene_genetic_map_association_object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/gene.yaml
    alias: gene_genetic_map_association_object
    owner: GeneGeneticMapAssociation
    domain_of:
    - GeneGeneticMapAssociation
    range: Chromosome
    required: true
  gene_association_subject:
    name: gene_association_subject
    description: Subject slot to be used for gene associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: gene_association_subject
    owner: GeneGeneticMapAssociation
    domain_of:
    - GeneGenomicLocationAssociation
    - GeneChromosomalLocationAssociation
    - GeneGeneticMapAssociation
    - GeneGeneAssociation
    - GenePathwayAssociation
    range: Gene
    required: true
  genetic_map_position_centimorgan:
    name: genetic_map_position_centimorgan
    description: 'Genetic map distance calculated along a chromosome in centiMorgans:
      e.g., 22.3366 cM.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneGeneticMapAssociation
    multivalued: false
    alias: genetic_map_position_centimorgan
    owner: GeneGeneticMapAssociation
    domain_of:
    - GeneGeneticMapAssociation
    range: float
    required: false
  genetic_map_position_centimorgan_error:
    name: genetic_map_position_centimorgan_error
    description: 'Error in calculated genetic map distance in centiMorgans: e.g.,
      0.045 cM.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneGeneticMapAssociation
    multivalued: false
    alias: genetic_map_position_centimorgan_error
    owner: GeneGeneticMapAssociation
    domain_of:
    - GeneGeneticMapAssociation
    range: float
    required: false
  single_reference:
    name: single_reference
    description: holds between an object and a single reference
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: single_reference
    owner: GeneGeneticMapAssociation
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    range: Reference
  relation:
    name: relation
    description: A high-level grouping for the relationship type. This is analogous
      to category for nodes. In RDF, this corresponds to rdf:predicate and in Neo4j
      this corresponds to the relationship type.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: association_slot
    alias: relation
    owner: GeneGeneticMapAssociation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    range: string
    required: true
    any_of:
    - equals_string: has_location
  created_by:
    name: created_by
    description: The individual that created the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: created_by
    owner: GeneGeneticMapAssociation
    domain_of:
    - AuditedObject
    range: Person
  date_created:
    name: date_created
    description: The date on which an entity was created. This can be applied to nodes
      or edges.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - creation_date
    exact_mappings:
    - dct:createdOn
    - WIKIDATA_PROPERTY:P577
    alias: date_created
    owner: GeneGeneticMapAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by:
    name: updated_by
    description: The individual that last modified the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: updated_by
    owner: GeneGeneticMapAssociation
    domain_of:
    - AuditedObject
    range: Person
  date_updated:
    name: date_updated
    description: Date on which an entity was last modified.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - date_last_modified
    alias: date_updated
    owner: GeneGeneticMapAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_created:
    name: db_date_created
    description: The date on which an entity was created in the Alliance database.  This
      is distinct from date_created, which represents the date when the entity was
      originally created (i.e. at the MOD for imported data).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_created
    owner: GeneGeneticMapAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_updated:
    name: db_date_updated
    description: Date on which an entity was last modified in the Alliance database.  This
      is distinct from date_updated, which represents the date when the entity was
      last modified and may predate import into the Alliance database.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_updated
    owner: GeneGeneticMapAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  internal:
    name: internal
    description: Classifies the entity as private (for internal use) or not (for public
      use).
    notes:
    - Default value is true.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: internal
    owner: GeneGeneticMapAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
    required: true
  obsolete:
    name: obsolete
    description: Entity is no longer current.
    notes:
    - Obsolete entities are preserved in the database for posterity but should not
      be publicly displayed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: obsolete
    owner: GeneGeneticMapAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean