AnnotationDTO

Ingest class for an annotation

classDiagram SingleReferenceAssociationDTO <|-- AnnotationDTO AnnotationDTO : condition_relation_dtos AnnotationDTO : created_by_curie AnnotationDTO : data_provider_dto AnnotationDTO : date_created AnnotationDTO : date_updated AnnotationDTO : db_date_created AnnotationDTO : db_date_updated AnnotationDTO : evidence_curie AnnotationDTO : internal AnnotationDTO : mod_internal_id AnnotationDTO : note_dtos AnnotationDTO : obsolete AnnotationDTO : primary_external_id AnnotationDTO : updated_by_curie

URI: alliance:AnnotationDTO

Parent Classes

AuditedObjectDTO
- SingleReferenceAssociationDTO
  - AnnotationDTO
    - PhenotypeAnnotationDTO
    - DiseaseAnnotationDTO

Children

AuditedObjectDTO
- SingleReferenceAssociationDTO
  - AnnotationDTO
    - PhenotypeAnnotationDTO
    - DiseaseAnnotationDTO

Slots

Name	Description
condition_relation_dtos	None
created_by_curie	Curie of the Person object representing the individual that created the entity
data_provider_dto	Ingest object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site
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_curie	Curie of InformationContentEntity object given as evidence
internal	Classifies the entity as private (for internal use) or not (for public use).
mod_internal_id	The model organism database (MOD) internal identifier for the object
note_dtos	None
obsolete	Entity is no longer current.
primary_external_id	The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.
updated_by_curie	Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: AnnotationDTO
description: Ingest class for an annotation
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SingleReferenceAssociationDTO
abstract: true
slots:
- mod_internal_id
- primary_external_id
- note_dtos
- data_provider_dto
- condition_relation_dtos
slot_usage:
  reference_curie:
    name: reference_curie
    required: true

Induced

name: AnnotationDTO
description: Ingest class for an annotation
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SingleReferenceAssociationDTO
abstract: true
slot_usage:
  reference_curie:
    name: reference_curie
    required: true
attributes:
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database (MOD) internal identifier for the object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: AnnotationDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-Alliance) database identifier/curie for
      the object. Note that this may be an external (non-Alliance member) identifier
      for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance
      member's primary key for the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: primary_external_id
    owner: AnnotationDTO
    domain_of:
    - Person
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  note_dtos:
    name: note_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: note_dtos
    owner: AnnotationDTO
    domain_of:
    - AlleleDTO
    - GeneDTO
    - ReagentDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - ConstructCassetteAssociationDTO
    - CassetteComponentSlotAnnotationDTO
    - CassetteGenomicEntityAssociationDTO
    - CassetteTransgenicToolAssociationDTO
    - CassetteStrAssociationDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    - VariantDTO
    range: NoteDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  data_provider_dto:
    name: data_provider_dto
    description: Ingest object representing the organization (e.g. MOD) from which
      the data was sourced and a CrossReference to that organisation's site
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: data_provider_dto
    owner: AnnotationDTO
    domain_of:
    - SubmittedObjectDTO
    - ChromosomeDTO
    - AssemblyComponentDTO
    - AnnotationDTO
    range: DataProviderDTO
    required: true
    multivalued: false
    inlined: true
  condition_relation_dtos:
    name: condition_relation_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: condition_relation_dtos
    owner: AnnotationDTO
    domain_of:
    - AnnotationDTO
    range: ConditionRelationDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  evidence_curie:
    name: evidence_curie
    description: Curie of InformationContentEntity object given as evidence
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: evidence_curie
    owner: AnnotationDTO
    domain_of:
    - SingleReferenceAssociationDTO
    range: string
  created_by_curie:
    name: created_by_curie
    description: Curie of the Person object representing the individual that created
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: created_by_curie
    owner: AnnotationDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: AnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by_curie:
    name: updated_by_curie
    description: Curie of the Person object representing the individual that updated
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: updated_by_curie
    owner: AnnotationDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: AnnotationDTO
    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: AnnotationDTO
    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: AnnotationDTO
    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: AnnotationDTO
    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: AnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean