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GeneGenomicLocationAssociation

Location(s) of the gene on the genome.

classDiagram LocationAssociation <|-- GeneGenomicLocationAssociation GeneGenomicLocationAssociation : created_by GeneGenomicLocationAssociation : date_created GeneGenomicLocationAssociation : date_updated GeneGenomicLocationAssociation : db_date_created GeneGenomicLocationAssociation : db_date_updated GeneGenomicLocationAssociation : end GeneGenomicLocationAssociation : evidence GeneGenomicLocationAssociation : gene_association_subject GeneGenomicLocationAssociation : gene_genomic_location_association_object GeneGenomicLocationAssociation : internal GeneGenomicLocationAssociation : obsolete GeneGenomicLocationAssociation : relation GeneGenomicLocationAssociation : start GeneGenomicLocationAssociation : strand GeneGenomicLocationAssociation : updated_by

URI: alliance:GeneGenomicLocationAssociation

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.
end The end of the feature in positive 1-based integer coordinates relative to the reference landmark.
evidence The evidence that supports some assertion.
gene_association_subject Subject slot to be used for gene associations
gene_genomic_location_association_object None
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obsolete Entity is no longer current.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.
start The start of the feature in positive 1-based integer coordinates relative to the reference landmark.
strand The strand of a DNA reference object to which an entity maps.
updated_by The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: GeneGenomicLocationAssociation
description: Location(s) of the gene on the genome.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: LocationAssociation
slots:
- gene_association_subject
- strand
slot_usage:
  evidence:
    name: evidence
    notes:
    - List all references that support a given location association.
    domain_of:
    - Note
    - SlotAnnotation
    - EvidenceAssociation
  start:
    name: start
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    required: true
  end:
    name: end
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    required: true
  strand:
    name: strand
    domain_of:
    - TranscriptGenomicLocationAssociation
    - ExonGenomicLocationAssociation
    - CodingSequenceGenomicLocationAssociation
    - GeneGenomicLocationAssociation
    required: true
attributes:
  gene_genomic_location_association_object:
    name: gene_genomic_location_association_object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/gene.yaml
    range: AssemblyComponent
    required: true

Induced

name: GeneGenomicLocationAssociation
description: Location(s) of the gene on the genome.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: LocationAssociation
slot_usage:
  evidence:
    name: evidence
    notes:
    - List all references that support a given location association.
    domain_of:
    - Note
    - SlotAnnotation
    - EvidenceAssociation
  start:
    name: start
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    required: true
  end:
    name: end
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    required: true
  strand:
    name: strand
    domain_of:
    - TranscriptGenomicLocationAssociation
    - ExonGenomicLocationAssociation
    - CodingSequenceGenomicLocationAssociation
    - GeneGenomicLocationAssociation
    required: true
attributes:
  gene_genomic_location_association_object:
    name: gene_genomic_location_association_object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/gene.yaml
    alias: gene_genomic_location_association_object
    owner: GeneGenomicLocationAssociation
    domain_of:
    - GeneGenomicLocationAssociation
    range: AssemblyComponent
    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: GeneGenomicLocationAssociation
    domain_of:
    - GeneGenomicLocationAssociation
    - GeneChromosomalLocationAssociation
    - GeneGeneticMapAssociation
    - GeneGeneAssociation
    - GenePathwayAssociation
    range: Gene
    required: true
  strand:
    name: strand
    description: The strand of a DNA reference object to which an entity maps.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: strand
    owner: GeneGenomicLocationAssociation
    domain_of:
    - TranscriptGenomicLocationAssociation
    - ExonGenomicLocationAssociation
    - CodingSequenceGenomicLocationAssociation
    - GeneGenomicLocationAssociation
    range: strand_enum
    required: true
  start:
    name: start
    description: The start of the feature in positive 1-based integer coordinates
      relative to the reference landmark.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: LocationAssociation
    alias: start
    owner: GeneGenomicLocationAssociation
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    range: integer
    required: true
  end:
    name: end
    description: The end of the feature in positive 1-based integer coordinates relative
      to the reference landmark.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: LocationAssociation
    alias: end
    owner: GeneGenomicLocationAssociation
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    range: integer
    required: true
  evidence:
    name: evidence
    description: The evidence that supports some assertion.
    notes:
    - List all references that support a given location association.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: evidence
    owner: GeneGenomicLocationAssociation
    domain_of:
    - Note
    - SlotAnnotation
    - EvidenceAssociation
    range: InformationContentEntity
  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: GeneGenomicLocationAssociation
    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: GeneGenomicLocationAssociation
    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: GeneGenomicLocationAssociation
    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: GeneGenomicLocationAssociation
    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: GeneGenomicLocationAssociation
    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: GeneGenomicLocationAssociation
    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: GeneGenomicLocationAssociation
    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: GeneGenomicLocationAssociation
    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: GeneGenomicLocationAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean