TransgenicToolDTO

An ingest class for a Transgenic Tool; a Transgenic Tool is defined as a commonly used sequence that forms part of a Construct or Transgene, and which has useful properties that are exploited to study the biological function of another gene product or a biological process.

classDiagram ReagentDTO <|-- TransgenicToolDTO TransgenicToolDTO : created_by_curie TransgenicToolDTO : cross_reference_dtos TransgenicToolDTO : data_provider_dto TransgenicToolDTO : date_created TransgenicToolDTO : date_updated TransgenicToolDTO : db_date_created TransgenicToolDTO : db_date_updated TransgenicToolDTO : internal TransgenicToolDTO : mod_internal_id TransgenicToolDTO : note_dtos TransgenicToolDTO : obsolete TransgenicToolDTO : placeholder TransgenicToolDTO : primary_external_id TransgenicToolDTO : reference_curies TransgenicToolDTO : secondary_identifiers TransgenicToolDTO : transgenic_tool_full_name_dto TransgenicToolDTO : transgenic_tool_symbol_dto TransgenicToolDTO : transgenic_tool_synonym_dtos TransgenicToolDTO : updated_by_curie TransgenicToolDTO : use_curies

URI: alliance:TransgenicToolDTO

Parent Classes

AuditedObjectDTO
- SubmittedObjectDTO
  - ReagentDTO
    - TransgenicToolDTO

Slots

Name	Description
created_by_curie	Curie of the Person object representing the individual that created the entity
cross_reference_dtos	None
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.
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obsolete	Entity is no longer current.
placeholder	A boolean property to indicate whether a data record/object/entity is intended to be a placeholder data object rather than a publicly displayed object with a proper ID, name and/or symbol, for example. For example, the Cassette class has been introduced to support FlyBase Cassette objects with IDs and names, but not every Alliance member has data tables/classes for these objects and any IDs or names/symbols would likely be derived and not helpful to end users. Data records/entities where the placeholder value is set to true would have various visible properties suppressed, so as not to confuse end users with private, internal or otherwise contrived representations.
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.
reference_curies	External reference curies used for ingest
secondary_identifiers	None
transgenic_tool_full_name_dto	Holds between a TransgenicTool and a full name.
transgenic_tool_symbol_dto	Holds between a TransgenicTool and the one current accepted symbol
transgenic_tool_synonym_dtos	Holds between a TransgenicTool and a list of synonyms.
updated_by_curie	Curie of the Person object representing the individual that updated the entity
use_curies	Holds between a TransgenicTool and a list of curies of FBcv terms with namespace 'experimental_tool_descriptor'

Mappings

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

LinkML Specification

Direct

name: TransgenicToolDTO
description: An ingest class for a Transgenic Tool; a Transgenic Tool is defined as
  a commonly used sequence that forms part of a Construct or Transgene, and which
  has useful properties that are exploited to study the biological function of another
  gene product or a biological process.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: ReagentDTO
slots:
- cross_reference_dtos
- transgenic_tool_symbol_dto
- transgenic_tool_full_name_dto
- transgenic_tool_synonym_dtos
- use_curies
- reference_curies

Induced

name: TransgenicToolDTO
description: An ingest class for a Transgenic Tool; a Transgenic Tool is defined as
  a commonly used sequence that forms part of a Construct or Transgene, and which
  has useful properties that are exploited to study the biological function of another
  gene product or a biological process.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: ReagentDTO
attributes:
  cross_reference_dtos:
    name: cross_reference_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: cross_reference_dtos
    owner: TransgenicToolDTO
    domain_of:
    - GenomicEntityDTO
    - GenomeAssemblyDTO
    - GeneInteractionDTO
    - AntibodyDTO
    - TransgenicToolDTO
    - ExternalDataBaseEntityDTO
    range: CrossReferenceDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  transgenic_tool_symbol_dto:
    name: transgenic_tool_symbol_dto
    description: Holds between a TransgenicTool and the one current accepted symbol
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: TransgenicToolDTO
    alias: transgenic_tool_symbol_dto
    owner: TransgenicToolDTO
    domain_of:
    - TransgenicToolDTO
    range: TransgenicToolSlotAnnotationDTO
    required: true
    multivalued: false
    inlined: true
  transgenic_tool_full_name_dto:
    name: transgenic_tool_full_name_dto
    description: Holds between a TransgenicTool and a full name.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: TransgenicToolDTO
    alias: transgenic_tool_full_name_dto
    owner: TransgenicToolDTO
    domain_of:
    - TransgenicToolDTO
    range: NameSlotAnnotationDTO
    required: false
    multivalued: false
    inlined: true
  transgenic_tool_synonym_dtos:
    name: transgenic_tool_synonym_dtos
    description: Holds between a TransgenicTool and a list of synonyms.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: TransgenicToolDTO
    alias: transgenic_tool_synonym_dtos
    owner: TransgenicToolDTO
    domain_of:
    - TransgenicToolDTO
    range: NameSlotAnnotationDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  use_curies:
    name: use_curies
    description: Holds between a TransgenicTool and a list of curies of FBcv terms
      with namespace 'experimental_tool_descriptor'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: use_curies
    owner: TransgenicToolDTO
    domain_of:
    - TransgenicToolDTO
    range: string
    multivalued: true
  reference_curies:
    name: reference_curies
    description: External reference curies used for ingest
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: reference_curies
    owner: TransgenicToolDTO
    domain_of:
    - AffectedGenomicModelDTO
    - AlleleDTO
    - SequenceTargetingReagentDTO
    - AntibodyDTO
    - ConstructDTO
    - CassetteDTO
    - TransgenicToolDTO
    - HTPExpressionDatasetAnnotationDTO
    - VariantDTO
    range: string
    multivalued: true
  secondary_identifiers:
    name: secondary_identifiers
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - secondary_ids
    alias: secondary_identifiers
    owner: TransgenicToolDTO
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Reagent
    - ReagentDTO
    - Figure
    - Image
    - OntologyTerm
    - ExternalDataBaseEntity
    - ExternalDataBaseEntityDTO
    range: uriorcurie
    multivalued: true
  note_dtos:
    name: note_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: note_dtos
    owner: TransgenicToolDTO
    domain_of:
    - AlleleDTO
    - GeneDTO
    - ReagentDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - ConstructCassetteAssociationDTO
    - CassetteComponentSlotAnnotationDTO
    - CassetteGenomicEntityAssociationDTO
    - CassetteTransgenicToolAssociationDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    - VariantDTO
    range: NoteDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  placeholder:
    name: placeholder
    description: A boolean property to indicate whether a data record/object/entity
      is intended to be a placeholder data object rather than a publicly displayed
      object with a proper ID, name and/or symbol, for example. For example, the Cassette
      class has been introduced to support FlyBase Cassette objects with IDs and names,
      but not every Alliance member has data tables/classes for these objects and
      any IDs or names/symbols would likely be derived and not helpful to end users.
      Data records/entities where the placeholder value is set to true would have
      various visible properties suppressed, so as not to confuse end users with private,
      internal or otherwise contrived representations.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: placeholder
    owner: TransgenicToolDTO
    domain_of:
    - Reagent
    - ReagentDTO
    range: boolean
  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: TransgenicToolDTO
    domain_of:
    - Person
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database (MOD) internal identifier for the object
    notes:
    - This is required if primary_external_id is not submitted
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: TransgenicToolDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  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: TransgenicToolDTO
    domain_of:
    - SubmittedObjectDTO
    - ChromosomeDTO
    - AssemblyComponentDTO
    - AnnotationDTO
    range: DataProviderDTO
    required: true
    multivalued: false
    inlined: 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: TransgenicToolDTO
    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: TransgenicToolDTO
    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: TransgenicToolDTO
    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: TransgenicToolDTO
    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: TransgenicToolDTO
    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: TransgenicToolDTO
    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: TransgenicToolDTO
    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: TransgenicToolDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean