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GeneToGeneParalogy

None

classDiagram AuditedObject <|-- GeneToGeneParalogy GeneToGeneParalogy : created_by GeneToGeneParalogy : date_created GeneToGeneParalogy : date_updated GeneToGeneParalogy : db_date_created GeneToGeneParalogy : db_date_updated GeneToGeneParalogy : homology_confidence GeneToGeneParalogy : identity GeneToGeneParalogy : internal GeneToGeneParalogy : length GeneToGeneParalogy : object_gene GeneToGeneParalogy : obsolete GeneToGeneParalogy : prediction_methods_matched GeneToGeneParalogy : prediction_methods_not_called GeneToGeneParalogy : prediction_methods_not_matched GeneToGeneParalogy : rank GeneToGeneParalogy : similarity GeneToGeneParalogy : subject_gene GeneToGeneParalogy : updated_by

URI: alliance:GeneToGeneParalogy

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.
homology_confidence Confidence of homology match Permissible values: moderate / high / low
identity Identity score between the two genes
internal Classifies the entity as private (for internal use) or not (for public use).
length The length of the aligned regions between two genes
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obsolete Entity is no longer current.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
rank The rank (order) of the paralog result
similarity Similarity score between the two genes
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:GeneToGeneParalogy']
native ['alliance:GeneToGeneParalogy']

LinkML Specification

Direct

name: GeneToGeneParalogy
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
slots:
- subject_gene
- object_gene
- rank
- homology_confidence
- length
- similarity
- prediction_methods_matched
- prediction_methods_not_matched
- prediction_methods_not_called
- identity

Induced

name: GeneToGeneParalogy
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
attributes:
  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: GeneToGeneParalogy
    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: GeneToGeneParalogy
    domain_of:
    - GeneToGeneOrthology
    - GeneToGeneParalogy
    range: Gene
    required: true
  rank:
    name: rank
    description: The rank (order) of the paralog result
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: rank
    owner: GeneToGeneParalogy
    domain_of:
    - GeneToGeneParalogy
    range: integer
    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: GeneToGeneParalogy
    domain_of:
    - GeneToGeneOrthologyGenerated
    - GeneToGeneParalogy
    range: VocabularyTerm
    required: true
  length:
    name: length
    description: The length of the aligned regions between two genes
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: length
    owner: GeneToGeneParalogy
    domain_of:
    - GeneToGeneParalogy
    range: integer
    required: false
  similarity:
    name: similarity
    description: Similarity score between the two genes
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: similarity
    owner: GeneToGeneParalogy
    domain_of:
    - GeneToGeneParalogy
    range: integer
    required: false
  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: GeneToGeneParalogy
    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: GeneToGeneParalogy
    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: GeneToGeneParalogy
    domain_of:
    - GeneToGeneOrthologyGenerated
    - GeneToGeneParalogy
    range: VocabularyTerm
  identity:
    name: identity
    description: Identity score between the two genes
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: identity
    owner: GeneToGeneParalogy
    domain_of:
    - GeneToGeneParalogy
    range: integer
    required: false
  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: GeneToGeneParalogy
    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: GeneToGeneParalogy
    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: GeneToGeneParalogy
    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: GeneToGeneParalogy
    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: GeneToGeneParalogy
    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: GeneToGeneParalogy
    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: GeneToGeneParalogy
    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: GeneToGeneParalogy
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean