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GeneToGeneOrthologyCurated

Class that holds the properties necessary to store a curated orthology record.

classDiagram GeneToGeneOrthology <|-- GeneToGeneOrthologyCurated GeneToGeneOrthologyCurated : created_by GeneToGeneOrthologyCurated : date_created GeneToGeneOrthologyCurated : date_updated GeneToGeneOrthologyCurated : db_date_created GeneToGeneOrthologyCurated : db_date_updated GeneToGeneOrthologyCurated : evidence_code GeneToGeneOrthologyCurated : internal GeneToGeneOrthologyCurated : object_gene GeneToGeneOrthologyCurated : obsolete GeneToGeneOrthologyCurated : single_reference GeneToGeneOrthologyCurated : subject_gene GeneToGeneOrthologyCurated : updated_by

URI: alliance:GeneToGeneOrthologyCurated

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.
evidence_code None
internal Classifies the entity as private (for internal use) or not (for public use).
object_gene The second gene in the homology match pair
obsolete Entity is no longer current.
single_reference holds between an object and a single reference
subject_gene The first gene in the homology match pair
updated_by The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: GeneToGeneOrthologyCurated
description: Class that holds the properties necessary to store a curated orthology
  record.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GeneToGeneOrthology
slots:
- single_reference
- evidence_code

Induced

name: GeneToGeneOrthologyCurated
description: Class that holds the properties necessary to store a curated orthology
  record.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GeneToGeneOrthology
attributes:
  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: GeneToGeneOrthologyCurated
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    range: Reference
  evidence_code:
    name: evidence_code
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: evidence_code
    owner: GeneToGeneOrthologyCurated
    domain_of:
    - AlleleGenomicEntityAssociation
    - GeneToGeneOrthologyCurated
    range: ECOTerm
  subject_gene:
    name: subject_gene
    description: The first gene in the homology match pair
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: subject_gene
    owner: GeneToGeneOrthologyCurated
    domain_of:
    - GeneToGeneOrthology
    - GeneToGeneParalogy
    range: Gene
    required: true
  object_gene:
    name: object_gene
    description: The second gene in the homology match pair
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: object_gene
    owner: GeneToGeneOrthologyCurated
    domain_of:
    - GeneToGeneOrthology
    - GeneToGeneParalogy
    range: Gene
    required: true
  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: GeneToGeneOrthologyCurated
    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: GeneToGeneOrthologyCurated
    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: GeneToGeneOrthologyCurated
    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: GeneToGeneOrthologyCurated
    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: GeneToGeneOrthologyCurated
    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: GeneToGeneOrthologyCurated
    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: GeneToGeneOrthologyCurated
    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: GeneToGeneOrthologyCurated
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean