GeneToGeneOrthologyGenerated

Class that holds the properties necessary to record an orthology record from DIOPT

classDiagram GeneToGeneOrthology <|-- GeneToGeneOrthologyGenerated GeneToGeneOrthologyGenerated : created_by GeneToGeneOrthologyGenerated : date_created GeneToGeneOrthologyGenerated : date_updated GeneToGeneOrthologyGenerated : db_date_created GeneToGeneOrthologyGenerated : db_date_updated GeneToGeneOrthologyGenerated : homology_confidence GeneToGeneOrthologyGenerated : internal GeneToGeneOrthologyGenerated : is_best_reverse_score GeneToGeneOrthologyGenerated : is_best_score GeneToGeneOrthologyGenerated : moderate_filter GeneToGeneOrthologyGenerated : object_gene GeneToGeneOrthologyGenerated : obsolete GeneToGeneOrthologyGenerated : prediction_methods_matched GeneToGeneOrthologyGenerated : prediction_methods_not_called GeneToGeneOrthologyGenerated : prediction_methods_not_matched GeneToGeneOrthologyGenerated : strict_filter GeneToGeneOrthologyGenerated : subject_gene GeneToGeneOrthologyGenerated : updated_by

URI: alliance:GeneToGeneOrthologyGenerated

Parent Classes

AuditedObject
- GeneToGeneOrthology
  - GeneToGeneOrthologyGenerated

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.
homology_confidence	Confidence of homology match Permissible values: moderate / high / low
internal	Classifies the entity as private (for internal use) or not (for public use).
is_best_reverse_score	DIOPT schema highlights the best pair Permissible values: Yes / No
is_best_score	DIOPT schema highlights the best pair Permissible values: Yes / No / Yes_Adjusted
moderate_filter	Indicates whether this homology match is displayed when the moderate filter is selected
object_gene	The second gene in the homology match pair
obsolete	Entity is no longer current.
prediction_methods_matched	Source of the homology match
prediction_methods_not_called	Prediction methods that were not called
prediction_methods_not_matched	Prediction methods not matched
strict_filter	Indicates whether this homology match is displayed when the strict filter is selected
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:GeneToGeneOrthologyGenerated']
native	['alliance:GeneToGeneOrthologyGenerated']

LinkML Specification

Direct

name: GeneToGeneOrthologyGenerated
description: Class that holds the properties necessary to record an orthology record
  from DIOPT
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GeneToGeneOrthology
slots:
- is_best_score
- is_best_reverse_score
- homology_confidence
- strict_filter
- moderate_filter
- prediction_methods_matched
- prediction_methods_not_matched
- prediction_methods_not_called

Induced

name: GeneToGeneOrthologyGenerated
description: Class that holds the properties necessary to record an orthology record
  from DIOPT
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GeneToGeneOrthology
attributes:
  is_best_score:
    name: is_best_score
    description: 'DIOPT schema highlights the best pair Permissible values: Yes /
      No / Yes_Adjusted'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: is_best_score
    owner: GeneToGeneOrthologyGenerated
    domain_of:
    - GeneToGeneOrthologyGenerated
    range: VocabularyTerm
    required: true
  is_best_reverse_score:
    name: is_best_reverse_score
    description: 'DIOPT schema highlights the best pair Permissible values: Yes /
      No'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: is_best_reverse_score
    owner: GeneToGeneOrthologyGenerated
    domain_of:
    - GeneToGeneOrthologyGenerated
    range: VocabularyTerm
    required: true
  homology_confidence:
    name: homology_confidence
    description: 'Confidence of homology match Permissible values: moderate / high
      / low'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: homology_confidence
    owner: GeneToGeneOrthologyGenerated
    domain_of:
    - GeneToGeneOrthologyGenerated
    - GeneToGeneParalogy
    range: VocabularyTerm
    required: true
  strict_filter:
    name: strict_filter
    description: Indicates whether this homology match is displayed when the strict
      filter is selected
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: strict_filter
    owner: GeneToGeneOrthologyGenerated
    domain_of:
    - GeneToGeneOrthologyGenerated
    range: boolean
  moderate_filter:
    name: moderate_filter
    description: Indicates whether this homology match is displayed when the moderate
      filter is selected
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: moderate_filter
    owner: GeneToGeneOrthologyGenerated
    domain_of:
    - GeneToGeneOrthologyGenerated
    range: boolean
  prediction_methods_matched:
    name: prediction_methods_matched
    description: Source of the homology match
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: prediction_methods_matched
    owner: GeneToGeneOrthologyGenerated
    domain_of:
    - GeneToGeneOrthologyGenerated
    - GeneToGeneParalogy
    range: VocabularyTerm
  prediction_methods_not_matched:
    name: prediction_methods_not_matched
    description: Prediction methods not matched
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: prediction_methods_not_matched
    owner: GeneToGeneOrthologyGenerated
    domain_of:
    - GeneToGeneOrthologyGenerated
    - GeneToGeneParalogy
    range: VocabularyTerm
  prediction_methods_not_called:
    name: prediction_methods_not_called
    description: Prediction methods that were not called
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: prediction_methods_not_called
    owner: GeneToGeneOrthologyGenerated
    domain_of:
    - GeneToGeneOrthologyGenerated
    - GeneToGeneParalogy
    range: VocabularyTerm
  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: GeneToGeneOrthologyGenerated
    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: GeneToGeneOrthologyGenerated
    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: GeneToGeneOrthologyGenerated
    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: GeneToGeneOrthologyGenerated
    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: GeneToGeneOrthologyGenerated
    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: GeneToGeneOrthologyGenerated
    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: GeneToGeneOrthologyGenerated
    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: GeneToGeneOrthologyGenerated
    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: GeneToGeneOrthologyGenerated
    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: GeneToGeneOrthologyGenerated
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean