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ExternalDataBaseEntityDTO

DTO entity for a local database entry representing an external database entry; used currently for datasets or dataset samples; htpId.json in agr_schemas json

classDiagram AuditedObjectDTO <|-- ExternalDataBaseEntityDTO ExternalDataBaseEntityDTO : created_by_curie ExternalDataBaseEntityDTO : cross_reference_dtos ExternalDataBaseEntityDTO : curie ExternalDataBaseEntityDTO : date_created ExternalDataBaseEntityDTO : date_updated ExternalDataBaseEntityDTO : db_date_created ExternalDataBaseEntityDTO : db_date_updated ExternalDataBaseEntityDTO : internal ExternalDataBaseEntityDTO : obsolete ExternalDataBaseEntityDTO : preferred_cross_reference_dto ExternalDataBaseEntityDTO : secondary_identifiers ExternalDataBaseEntityDTO : updated_by_curie

URI: alliance:ExternalDataBaseEntityDTO

Parent Classes

Slots

Name Description
created_by_curie Curie of the Person object representing the individual that created the entity
cross_reference_dtos Optional cross references to the MOD sample or dataset page.
curie The ID from the data provider for the dataset. When available, this is the GEO ID. When no GEO ID is available, it will be the ArrayExpress ID. When these both are unavailable, it will be the MOD ID.
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.
internal Classifies the entity as private (for internal use) or not (for public use).
obsolete Entity is no longer current.
preferred_cross_reference_dto The cross reference to the preferred page to link to in search
secondary_identifiers list of optional cross reference ids to the primary dataset id.
updated_by_curie Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: ExternalDataBaseEntityDTO
description: DTO entity for a local database entry representing an external database
  entry; used currently for datasets or dataset samples; htpId.json in agr_schemas
  json
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObjectDTO
slots:
- curie
- secondary_identifiers
- preferred_cross_reference_dto
- cross_reference_dtos
slot_usage:
  curie:
    name: curie
    description: The ID from the data provider for the dataset. When available, this
      is the GEO ID. When no GEO ID is available, it will be the ArrayExpress ID.
      When these both are unavailable, it will be the MOD ID.
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
  secondary_identifiers:
    name: secondary_identifiers
    description: list of optional cross reference ids to the primary dataset id.
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Reagent
    - ReagentDTO
    - OntologyTerm
    - Figure
    - Image
    - ExternalDataBaseEntity
    - ExternalDataBaseEntityDTO
  preferred_cross_reference_dto:
    name: preferred_cross_reference_dto
    description: The cross reference to the preferred page to link to in search
    domain_of:
    - ExternalDataBaseEntityDTO
  cross_reference_dtos:
    name: cross_reference_dtos
    description: Optional cross references to the MOD sample or dataset page.
    domain_of:
    - AntibodyDTO
    - GenomicEntityDTO
    - GenomeAssemblyDTO
    - ExternalDataBaseEntityDTO
    - GeneInteractionDTO

Induced

name: ExternalDataBaseEntityDTO
description: DTO entity for a local database entry representing an external database
  entry; used currently for datasets or dataset samples; htpId.json in agr_schemas
  json
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObjectDTO
slot_usage:
  curie:
    name: curie
    description: The ID from the data provider for the dataset. When available, this
      is the GEO ID. When no GEO ID is available, it will be the ArrayExpress ID.
      When these both are unavailable, it will be the MOD ID.
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
  secondary_identifiers:
    name: secondary_identifiers
    description: list of optional cross reference ids to the primary dataset id.
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Reagent
    - ReagentDTO
    - OntologyTerm
    - Figure
    - Image
    - ExternalDataBaseEntity
    - ExternalDataBaseEntityDTO
  preferred_cross_reference_dto:
    name: preferred_cross_reference_dto
    description: The cross reference to the preferred page to link to in search
    domain_of:
    - ExternalDataBaseEntityDTO
  cross_reference_dtos:
    name: cross_reference_dtos
    description: Optional cross references to the MOD sample or dataset page.
    domain_of:
    - AntibodyDTO
    - GenomicEntityDTO
    - GenomeAssemblyDTO
    - ExternalDataBaseEntityDTO
    - GeneInteractionDTO
attributes:
  curie:
    name: curie
    description: The ID from the data provider for the dataset. When available, this
      is the GEO ID. When no GEO ID is available, it will be the ArrayExpress ID.
      When these both are unavailable, it will be the MOD ID.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    alias: curie
    owner: ExternalDataBaseEntityDTO
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  secondary_identifiers:
    name: secondary_identifiers
    description: list of optional cross reference ids to the primary dataset id.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: secondary_identifiers
    owner: ExternalDataBaseEntityDTO
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Reagent
    - ReagentDTO
    - OntologyTerm
    - Figure
    - Image
    - ExternalDataBaseEntity
    - ExternalDataBaseEntityDTO
    range: uriorcurie
  preferred_cross_reference_dto:
    name: preferred_cross_reference_dto
    description: The cross reference to the preferred page to link to in search
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ExternalDataBaseEntityDTO
    multivalued: false
    alias: preferred_cross_reference_dto
    owner: ExternalDataBaseEntityDTO
    domain_of:
    - ExternalDataBaseEntityDTO
    range: CrossReferenceDTO
    required: false
    inlined: true
  cross_reference_dtos:
    name: cross_reference_dtos
    description: Optional cross references to the MOD sample or dataset page.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: cross_reference_dtos
    owner: ExternalDataBaseEntityDTO
    domain_of:
    - AntibodyDTO
    - GenomicEntityDTO
    - GenomeAssemblyDTO
    - ExternalDataBaseEntityDTO
    - GeneInteractionDTO
    range: CrossReferenceDTO
    inlined: true
    inlined_as_list: true
  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: ExternalDataBaseEntityDTO
    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: ExternalDataBaseEntityDTO
    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: ExternalDataBaseEntityDTO
    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: ExternalDataBaseEntityDTO
    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: ExternalDataBaseEntityDTO
    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: ExternalDataBaseEntityDTO
    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: ExternalDataBaseEntityDTO
    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: ExternalDataBaseEntityDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean