GenomeAssemblyDTO

Ingest class for genome assemblies

classDiagram BiologicalEntityDTO <|-- GenomeAssemblyDTO GenomeAssemblyDTO : created_by_curie GenomeAssemblyDTO : cross_reference_dtos GenomeAssemblyDTO : data_provider_dto GenomeAssemblyDTO : date_created GenomeAssemblyDTO : date_updated GenomeAssemblyDTO : db_date_created GenomeAssemblyDTO : db_date_updated GenomeAssemblyDTO : internal GenomeAssemblyDTO : mod_internal_id GenomeAssemblyDTO : obsolete GenomeAssemblyDTO : primary_external_id GenomeAssemblyDTO : specimen_genomic_model_identifier GenomeAssemblyDTO : taxon_curie GenomeAssemblyDTO : updated_by_curie

URI: alliance:GenomeAssemblyDTO

Parent Classes

AuditedObjectDTO
- SubmittedObjectDTO
  - BiologicalEntityDTO
    - GenomeAssemblyDTO

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
obsolete	Entity is no longer current.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.
specimen_genomic_model_identifier	The identifier of the AffectedGenomicModel of the specimen. This can be a MOD curie, a MOD internal ID or an external (3rd party) identifier.
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:GenomeAssemblyDTO']
native	['alliance:GenomeAssemblyDTO']

LinkML Specification

Direct

name: GenomeAssemblyDTO
description: Ingest class for genome assemblies
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: BiologicalEntityDTO
slots:
- specimen_genomic_model_identifier
- cross_reference_dtos

Induced

name: GenomeAssemblyDTO
description: Ingest class for genome assemblies
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: BiologicalEntityDTO
attributes:
  specimen_genomic_model_identifier:
    name: specimen_genomic_model_identifier
    description: The identifier of the AffectedGenomicModel of the specimen. This
      can be a MOD curie, a MOD internal ID or an external (3rd party) identifier.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: specimen_genomic_model_identifier
    owner: GenomeAssemblyDTO
    domain_of:
    - GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    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: GenomeAssemblyDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean