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ExternalDataBaseEntity

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

classDiagram CurieObject <|-- ExternalDataBaseEntity ExternalDataBaseEntity : created_by ExternalDataBaseEntity : cross_references ExternalDataBaseEntity : curie ExternalDataBaseEntity : date_created ExternalDataBaseEntity : date_updated ExternalDataBaseEntity : db_date_created ExternalDataBaseEntity : db_date_updated ExternalDataBaseEntity : internal ExternalDataBaseEntity : obsolete ExternalDataBaseEntity : preferred_cross_reference ExternalDataBaseEntity : secondary_identifiers ExternalDataBaseEntity : updated_by

URI: alliance:ExternalDataBaseEntity

Parent Classes

Slots

Name Description
created_by The individual that created the entity.
cross_references 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obsolete Entity is no longer current.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 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 The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: ExternalDataBaseEntity
description: 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: CurieObject
slots:
- secondary_identifiers
- preferred_cross_reference
- cross_references
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:
    name: preferred_cross_reference
    description: The cross reference to the preferred page to link to in search
    domain_of:
    - ExternalDataBaseEntity
  cross_references:
    name: cross_references
    description: Optional cross references to the MOD sample or dataset page.
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction

Induced

name: ExternalDataBaseEntity
description: 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: CurieObject
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:
    name: preferred_cross_reference
    description: The cross reference to the preferred page to link to in search
    domain_of:
    - ExternalDataBaseEntity
  cross_references:
    name: cross_references
    description: Optional cross references to the MOD sample or dataset page.
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction
attributes:
  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: ExternalDataBaseEntity
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Reagent
    - ReagentDTO
    - OntologyTerm
    - Figure
    - Image
    - ExternalDataBaseEntity
    - ExternalDataBaseEntityDTO
    range: uriorcurie
  preferred_cross_reference:
    name: preferred_cross_reference
    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: ExternalDataBaseEntity
    multivalued: false
    alias: preferred_cross_reference
    owner: ExternalDataBaseEntity
    domain_of:
    - ExternalDataBaseEntity
    range: CrossReference
    required: false
  cross_references:
    name: cross_references
    description: Optional cross references to the MOD sample or dataset page.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    singular_name: cross_reference
    multivalued: true
    alias: cross_references
    owner: ExternalDataBaseEntity
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction
    range: CrossReference
  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: ExternalDataBaseEntity
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  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: ExternalDataBaseEntity
    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: ExternalDataBaseEntity
    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: ExternalDataBaseEntity
    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: ExternalDataBaseEntity
    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: ExternalDataBaseEntity
    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: ExternalDataBaseEntity
    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: ExternalDataBaseEntity
    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: ExternalDataBaseEntity
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean