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AlleleDTO

Ingest class for an Allele object

classDiagram GenomicEntityDTO <|-- AlleleDTO AlleleDTO : allele_database_status_dto AlleleDTO : allele_full_name_dto AlleleDTO : allele_functional_impact_dtos AlleleDTO : allele_germline_transmission_status_dto AlleleDTO : allele_inheritance_mode_dtos AlleleDTO : allele_mutation_type_dtos AlleleDTO : allele_nomenclature_event_dtos AlleleDTO : allele_secondary_id_dtos AlleleDTO : allele_symbol_dto AlleleDTO : allele_synonym_dtos AlleleDTO : created_by_curie AlleleDTO : cross_reference_dtos AlleleDTO : data_provider_dto AlleleDTO : date_created AlleleDTO : date_updated AlleleDTO : db_date_created AlleleDTO : db_date_updated AlleleDTO : in_collection_name AlleleDTO : internal AlleleDTO : is_extinct AlleleDTO : is_extrachromosomal AlleleDTO : is_integrated AlleleDTO : laboratory_of_origin_curie AlleleDTO : mod_internal_id AlleleDTO : note_dtos AlleleDTO : obsolete AlleleDTO : primary_external_id AlleleDTO : reference_curies AlleleDTO : taxon_curie AlleleDTO : transgene_chromosome_location_name AlleleDTO : updated_by_curie

URI: alliance:AlleleDTO

Parent Classes

Slots

Name Description
allele_database_status_dto None
allele_full_name_dto The one current full name for an allele: e.g., wg1.
allele_functional_impact_dtos None
allele_germline_transmission_status_dto None
allele_inheritance_mode_dtos One or more allele inheritance mode DTO objects to be submitted
allele_mutation_type_dtos None
allele_nomenclature_event_dtos None
allele_secondary_id_dtos None
allele_symbol_dto The one current accepted symbol for the allele: e.g., wg1.
allele_synonym_dtos None
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.
in_collection_name Name of VocabularyTerm describing the collection from the 'Allele collection vocabulary' Vocabulary
internal Classifies the entity as private (for internal use) or not (for public use).
is_extinct Does the allele still exist in a population somewhere?
is_extrachromosomal Used by WormBase to indicate whether a transgenic allele is known to be extrachromosomal.
is_integrated Used by WormBase to indicate whether a transgenic allele is known to be integrated into the genome.
laboratory_of_origin_curie The curie of the laboratory of origin for the entity.
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.
reference_curies External reference curies used for ingest
taxon_curie Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives
transgene_chromosome_location_name The name of the chromosome to which a transgene has been mapped. Used for WormBase transgenes that have been integrated into the genome and mapped to a chromosome.
updated_by_curie Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: AlleleDTO
description: Ingest class for an Allele object
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntityDTO
slots:
- allele_symbol_dto
- allele_full_name_dto
- reference_curies
- in_collection_name
- laboratory_of_origin_curie
- is_extinct
- is_extrachromosomal
- is_integrated
- transgene_chromosome_location_name
- note_dtos
- allele_mutation_type_dtos
- allele_inheritance_mode_dtos
- allele_germline_transmission_status_dto
- allele_functional_impact_dtos
- allele_database_status_dto
- allele_secondary_id_dtos
- allele_nomenclature_event_dtos
- allele_synonym_dtos
slot_usage:
  note_dtos:
    name: note_dtos
    notes:
    - note_type CV 'Allele Note Type'
    domain_of:
    - VariantDTO
    - AlleleDTO
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - GeneDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
  primary_external_id:
    name: primary_external_id
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    required: true

Induced

name: AlleleDTO
description: Ingest class for an Allele object
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntityDTO
slot_usage:
  note_dtos:
    name: note_dtos
    notes:
    - note_type CV 'Allele Note Type'
    domain_of:
    - VariantDTO
    - AlleleDTO
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - GeneDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
  primary_external_id:
    name: primary_external_id
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    required: true
attributes:
  allele_symbol_dto:
    name: allele_symbol_dto
    description: 'The one current accepted symbol for the allele: e.g., wg<sup>1</sup>.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    multivalued: false
    alias: allele_symbol_dto
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: SymbolSlotAnnotationDTO
    required: true
    inlined: true
  allele_full_name_dto:
    name: allele_full_name_dto
    description: 'The one current full name for an allele: e.g., wg<sup>1</sup>.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    multivalued: false
    alias: allele_full_name_dto
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: FullNameSlotAnnotationDTO
    inlined: 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
    multivalued: true
    alias: reference_curies
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    - SequenceTargetingReagentDTO
    - AntibodyDTO
    - ConstructDTO
    - AffectedGenomicModelDTO
    - HTPExpressionDatasetAnnotationDTO
    range: string
  in_collection_name:
    name: in_collection_name
    description: Name of VocabularyTerm describing the collection from the 'Allele
      collection vocabulary' Vocabulary
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    alias: in_collection_name
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: string
  laboratory_of_origin_curie:
    name: laboratory_of_origin_curie
    description: The curie of the laboratory of origin for the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    alias: laboratory_of_origin_curie
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: string
  is_extinct:
    name: is_extinct
    description: Does the allele still exist in a population somewhere?
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: is_extinct
    owner: AlleleDTO
    domain_of:
    - Allele
    - AlleleDTO
    range: boolean
  is_extrachromosomal:
    name: is_extrachromosomal
    description: Used by WormBase to indicate whether a transgenic allele is known
      to be extrachromosomal.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: is_extrachromosomal
    owner: AlleleDTO
    domain_of:
    - Allele
    - AlleleDTO
    range: boolean
  is_integrated:
    name: is_integrated
    description: Used by WormBase to indicate whether a transgenic allele is known
      to be integrated into the genome.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: is_integrated
    owner: AlleleDTO
    domain_of:
    - Allele
    - AlleleDTO
    range: boolean
  transgene_chromosome_location_name:
    name: transgene_chromosome_location_name
    description: The name of the chromosome to which a transgene has been mapped.
      Used for WormBase transgenes that have been integrated into the genome and mapped
      to a chromosome.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    multivalued: false
    alias: transgene_chromosome_location_name
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: string
  note_dtos:
    name: note_dtos
    notes:
    - note_type CV 'Allele Note Type'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: note_dtos
    owner: AlleleDTO
    domain_of:
    - VariantDTO
    - AlleleDTO
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - GeneDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NoteDTO
    inlined: true
    inlined_as_list: true
  allele_mutation_type_dtos:
    name: allele_mutation_type_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    multivalued: true
    alias: allele_mutation_type_dtos
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: AlleleMutationTypeSlotAnnotationDTO
    inlined: true
    inlined_as_list: true
  allele_inheritance_mode_dtos:
    name: allele_inheritance_mode_dtos
    description: One or more allele inheritance mode DTO objects to be submitted
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    multivalued: true
    alias: allele_inheritance_mode_dtos
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: AlleleInheritanceModeSlotAnnotationDTO
    inlined: true
    inlined_as_list: true
  allele_germline_transmission_status_dto:
    name: allele_germline_transmission_status_dto
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    multivalued: false
    alias: allele_germline_transmission_status_dto
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: AlleleGermlineTransmissionStatusSlotAnnotationDTO
    inlined: true
  allele_functional_impact_dtos:
    name: allele_functional_impact_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    multivalued: true
    alias: allele_functional_impact_dtos
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: AlleleFunctionalImpactSlotAnnotationDTO
    inlined: true
    inlined_as_list: true
  allele_database_status_dto:
    name: allele_database_status_dto
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    alias: allele_database_status_dto
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: AlleleDatabaseStatusSlotAnnotationDTO
    inlined: true
  allele_secondary_id_dtos:
    name: allele_secondary_id_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    multivalued: true
    alias: allele_secondary_id_dtos
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: SecondaryIdSlotAnnotationDTO
    inlined: true
    inlined_as_list: true
  allele_nomenclature_event_dtos:
    name: allele_nomenclature_event_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    multivalued: true
    alias: allele_nomenclature_event_dtos
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: AlleleNomenclatureEventSlotAnnotationDTO
    inlined: true
    inlined_as_list: true
  allele_synonym_dtos:
    name: allele_synonym_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleDTO
    multivalued: true
    alias: allele_synonym_dtos
    owner: AlleleDTO
    domain_of:
    - AlleleDTO
    range: NameSlotAnnotationDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    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: AlleleDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean