GeneDTO

Ingest class for genes

classDiagram GenomicEntityDTO <|-- GeneDTO GeneDTO : created_by_curie GeneDTO : cross_reference_dtos GeneDTO : data_provider_dto GeneDTO : date_created GeneDTO : date_updated GeneDTO : db_date_created GeneDTO : db_date_updated GeneDTO : gene_full_name_dto GeneDTO : gene_secondary_id_dtos GeneDTO : gene_symbol_dto GeneDTO : gene_synonym_dtos GeneDTO : gene_systematic_name_dto GeneDTO : gene_type_curie GeneDTO : internal GeneDTO : mod_internal_id GeneDTO : note_dtos GeneDTO : obsolete GeneDTO : primary_external_id GeneDTO : taxon_curie GeneDTO : updated_by_curie

URI: alliance:GeneDTO

Parent Classes

AuditedObjectDTO
- SubmittedObjectDTO
  - BiologicalEntityDTO
    - GenomicEntityDTO
      - GeneDTO

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.
gene_full_name_dto	The one current full name for a gene: e.g., wingless, paired box 2a.
gene_secondary_id_dtos	None
gene_symbol_dto	The one current accepted symbol for a gene: e.g., wg, pax2a.
gene_synonym_dtos	None
gene_systematic_name_dto	The one current systematic name for a gene: e.g., YHR084W, R09F10.2.
gene_type_curie	Curie of SOTerm describing gene type
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obsolete	Entity is no longer current.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.
taxon_curie	Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives
updated_by_curie	Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: GeneDTO
description: Ingest class for genes
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntityDTO
slots:
- gene_symbol_dto
- gene_full_name_dto
- gene_systematic_name_dto
- gene_synonym_dtos
- gene_secondary_id_dtos
- gene_type_curie
- note_dtos
slot_usage:
  primary_external_id:
    name: primary_external_id
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    required: true

Induced

name: GeneDTO
description: Ingest class for genes
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntityDTO
slot_usage:
  primary_external_id:
    name: primary_external_id
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    required: true
attributes:
  gene_symbol_dto:
    name: gene_symbol_dto
    description: 'The one current accepted symbol for a gene: e.g., wg, pax2a.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneDTO
    multivalued: false
    alias: gene_symbol_dto
    owner: GeneDTO
    domain_of:
    - GeneDTO
    range: SymbolSlotAnnotationDTO
    required: true
    inlined: true
  gene_full_name_dto:
    name: gene_full_name_dto
    description: 'The one current full name for a gene: e.g., wingless, paired box
      2a.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneDTO
    multivalued: false
    alias: gene_full_name_dto
    owner: GeneDTO
    domain_of:
    - GeneDTO
    range: FullNameSlotAnnotationDTO
    required: false
    inlined: true
  gene_systematic_name_dto:
    name: gene_systematic_name_dto
    description: 'The one current systematic name for a gene: e.g., YHR084W, R09F10.2.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneDTO
    multivalued: false
    alias: gene_systematic_name_dto
    owner: GeneDTO
    domain_of:
    - GeneDTO
    range: SystematicNameSlotAnnotationDTO
    required: false
    inlined: true
  gene_synonym_dtos:
    name: gene_synonym_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneDTO
    multivalued: true
    alias: gene_synonym_dtos
    owner: GeneDTO
    domain_of:
    - GeneDTO
    range: NameSlotAnnotationDTO
    inlined: true
    inlined_as_list: true
  gene_secondary_id_dtos:
    name: gene_secondary_id_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneDTO
    multivalued: true
    alias: gene_secondary_id_dtos
    owner: GeneDTO
    domain_of:
    - GeneDTO
    range: SecondaryIdSlotAnnotationDTO
    inlined: true
    inlined_as_list: true
  gene_type_curie:
    name: gene_type_curie
    description: Curie of SOTerm describing gene type
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: genomic_entity_type_curie
    domain: GeneDTO
    alias: gene_type_curie
    owner: GeneDTO
    domain_of:
    - GeneDTO
    range: string
    required: true
  note_dtos:
    name: note_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: note_dtos
    owner: GeneDTO
    domain_of:
    - VariantDTO
    - AlleleDTO
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - GeneDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NoteDTO
    inlined: true
    inlined_as_list: true
  cross_reference_dtos:
    name: cross_reference_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: cross_reference_dtos
    owner: GeneDTO
    domain_of:
    - AntibodyDTO
    - GenomicEntityDTO
    - GenomeAssemblyDTO
    - ExternalDataBaseEntityDTO
    - GeneInteractionDTO
    range: CrossReferenceDTO
    inlined: true
    inlined_as_list: true
  taxon_curie:
    name: taxon_curie
    description: Curie of the NCBITaxonTerm representing the taxon from which the
      biological entity derives
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: taxon_curie
    owner: GeneDTO
    domain_of:
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - BiologicalEntityDTO
    - ChromosomeDTO
    range: string
    required: true
  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: GeneDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
    required: true
  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: GeneDTO
    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
    multivalued: false
    alias: data_provider_dto
    owner: GeneDTO
    domain_of:
    - SubmittedObjectDTO
    - ChromosomeDTO
    - AssemblyComponentDTO
    - AnnotationDTO
    range: DataProviderDTO
    required: true
    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: GeneDTO
    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: GeneDTO
    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: GeneDTO
    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: GeneDTO
    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: GeneDTO
    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: GeneDTO
    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: GeneDTO
    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: GeneDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean