VariantDTO

Ingest class for a Variant object

classDiagram GenomicEntityDTO <|-- VariantDTO VariantDTO : created_by_curie VariantDTO : cross_reference_dtos VariantDTO : data_provider_dto VariantDTO : date_created VariantDTO : date_updated VariantDTO : db_date_created VariantDTO : db_date_updated VariantDTO : internal VariantDTO : mod_internal_id VariantDTO : note_dtos VariantDTO : obsolete VariantDTO : primary_external_id VariantDTO : source_general_consequence_dtos VariantDTO : taxon_curie VariantDTO : updated_by_curie VariantDTO : variant_status_name VariantDTO : variant_type_curie

URI: alliance:VariantDTO

Parent Classes

AuditedObjectDTO
- SubmittedObjectDTO
  - BiologicalEntityDTO
    - GenomicEntityDTO
      - VariantDTO

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obsolete	Entity is no longer current.
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.
source_general_consequence_dtos	None
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
variant_status_name	Name of the VocabularyTerm describing the status of the variant. From the Variant Status CV
variant_type_curie	Curie of the SOTerm describing the type of variant. In practice, variant type will be limited to a subset of the SO specified in an Alliance controlled vocabulary in order to maintain consistency.

Mappings

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

LinkML Specification

Direct

name: VariantDTO
description: Ingest class for a Variant object
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntityDTO
slots:
- variant_type_curie
- note_dtos
- source_general_consequence_dtos
- variant_status_name

Induced

name: VariantDTO
description: Ingest class for a Variant object
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntityDTO
attributes:
  variant_type_curie:
    name: variant_type_curie
    description: Curie of the SOTerm describing the type of variant. In practice,
      variant type will be limited to a subset of the SO specified in an Alliance
      controlled vocabulary in order to maintain consistency.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: genomic_entity_type_curie
    domain: VariantDTO
    alias: variant_type_curie
    owner: VariantDTO
    domain_of:
    - VariantDTO
    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: VariantDTO
    domain_of:
    - VariantDTO
    - AlleleDTO
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - GeneDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NoteDTO
    inlined: true
    inlined_as_list: true
  source_general_consequence_dtos:
    name: source_general_consequence_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantDTO
    multivalued: true
    alias: source_general_consequence_dtos
    owner: VariantDTO
    domain_of:
    - VariantDTO
    range: VariantSourceGeneralConsequenceSlotAnnotationDTO
    required: false
    inlined: true
    inlined_as_list: true
  variant_status_name:
    name: variant_status_name
    description: Name of the VocabularyTerm describing the status of the variant.  From
      the Variant Status CV
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: variant_status_name
    owner: VariantDTO
    domain_of:
    - VariantDTO
    range: string
  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: VariantDTO
    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: VariantDTO
    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: VariantDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
  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: VariantDTO
    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: VariantDTO
    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: VariantDTO
    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: VariantDTO
    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: VariantDTO
    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: VariantDTO
    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: VariantDTO
    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: VariantDTO
    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: VariantDTO
    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: VariantDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean