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GeneChromosomalLocationAssociation

Localization of the gene to a chromosome, in some cases in reference to specific markers.

classDiagram SingleReferenceAssociation <|-- GeneChromosomalLocationAssociation GeneChromosomalLocationAssociation : created_by GeneChromosomalLocationAssociation : date_created GeneChromosomalLocationAssociation : date_updated GeneChromosomalLocationAssociation : db_date_created GeneChromosomalLocationAssociation : db_date_updated GeneChromosomalLocationAssociation : gene_association_subject GeneChromosomalLocationAssociation : gene_chromosomal_location_association_object GeneChromosomalLocationAssociation : internal GeneChromosomalLocationAssociation : left_boundary_marker GeneChromosomalLocationAssociation : obsolete GeneChromosomalLocationAssociation : relation GeneChromosomalLocationAssociation : right_boundary_marker GeneChromosomalLocationAssociation : single_reference GeneChromosomalLocationAssociation : updated_by

URI: alliance:GeneChromosomalLocationAssociation

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_chromosomal_location_association_object None
internal Classifies the entity as private (for internal use) or not (for public use).
left_boundary_marker The left boundary of a feature location relative to the landmark's inherent orientation.
obsolete Entity is no longer current.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.
right_boundary_marker The right boundary of a feature location relative to the landmark's inherent orientation.
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:GeneChromosomalLocationAssociation']
native ['alliance:GeneChromosomalLocationAssociation']

LinkML Specification

Direct

name: GeneChromosomalLocationAssociation
description: Localization of the gene to a chromosome, in some cases in reference
  to specific markers.
notes:
- Should we implement an even more generic LocationAssociaton object where start and
  end are not constrained to integer, but can be markers like genes or chromosome
  bands? Is this limited to cytological studies (e.g., chromosome in situs), or does
  this include genetic segregation studies? How do we handle location to specific
  chromosome arms? Different asso'n, or different slot here, etc?
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SingleReferenceAssociation
slots:
- gene_association_subject
- left_boundary_marker
- right_boundary_marker
slot_usage:
  relation:
    name: relation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    any_of:
    - equals_string: has_location
attributes:
  gene_chromosomal_location_association_object:
    name: gene_chromosomal_location_association_object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/gene.yaml
    range: Chromosome
    required: true

Induced

name: GeneChromosomalLocationAssociation
description: Localization of the gene to a chromosome, in some cases in reference
  to specific markers.
notes:
- Should we implement an even more generic LocationAssociaton object where start and
  end are not constrained to integer, but can be markers like genes or chromosome
  bands? Is this limited to cytological studies (e.g., chromosome in situs), or does
  this include genetic segregation studies? How do we handle location to specific
  chromosome arms? Different asso'n, or different slot here, etc?
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_chromosomal_location_association_object:
    name: gene_chromosomal_location_association_object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/gene.yaml
    alias: gene_chromosomal_location_association_object
    owner: GeneChromosomalLocationAssociation
    domain_of:
    - GeneChromosomalLocationAssociation
    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: GeneChromosomalLocationAssociation
    domain_of:
    - GeneGenomicLocationAssociation
    - GeneChromosomalLocationAssociation
    - GeneGeneticMapAssociation
    - GeneGeneAssociation
    - GenePathwayAssociation
    range: Gene
    required: true
  left_boundary_marker:
    name: left_boundary_marker
    description: The left boundary of a feature location relative to the landmark's
      inherent orientation.
    notes:
    - This marker could be a chromosomal band, gene, or some other marker.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneChromosomalLocationAssociation
    multivalued: false
    alias: left_boundary_marker
    owner: GeneChromosomalLocationAssociation
    domain_of:
    - GeneChromosomalLocationAssociation
    range: BiologicalEntity
    required: false
  right_boundary_marker:
    name: right_boundary_marker
    description: The right boundary of a feature location relative to the landmark's
      inherent orientation.
    notes:
    - This marker could be a chromosomal band, gene, or some other marker.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneChromosomalLocationAssociation
    multivalued: false
    alias: right_boundary_marker
    owner: GeneChromosomalLocationAssociation
    domain_of:
    - GeneChromosomalLocationAssociation
    range: BiologicalEntity
    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: GeneChromosomalLocationAssociation
    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: GeneChromosomalLocationAssociation
    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: GeneChromosomalLocationAssociation
    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: GeneChromosomalLocationAssociation
    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: GeneChromosomalLocationAssociation
    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: GeneChromosomalLocationAssociation
    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: GeneChromosomalLocationAssociation
    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: GeneChromosomalLocationAssociation
    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: GeneChromosomalLocationAssociation
    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: GeneChromosomalLocationAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean