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VariantSourceGeneralConsequenceSlotAnnotationDTO

The consequence of the variant, as stated in the source reference when no transcript ID is provided.

classDiagram SlotAnnotationDTO <|-- VariantSourceGeneralConsequenceSlotAnnotationDTO VariantSourceGeneralConsequenceSlotAnnotationDTO : created_by_curie VariantSourceGeneralConsequenceSlotAnnotationDTO : date_created VariantSourceGeneralConsequenceSlotAnnotationDTO : date_updated VariantSourceGeneralConsequenceSlotAnnotationDTO : db_date_created VariantSourceGeneralConsequenceSlotAnnotationDTO : db_date_updated VariantSourceGeneralConsequenceSlotAnnotationDTO : evidence_curies VariantSourceGeneralConsequenceSlotAnnotationDTO : internal VariantSourceGeneralConsequenceSlotAnnotationDTO : obsolete VariantSourceGeneralConsequenceSlotAnnotationDTO : source_general_consequence_curie VariantSourceGeneralConsequenceSlotAnnotationDTO : updated_by_curie

URI: alliance:VariantSourceGeneralConsequenceSlotAnnotationDTO

Parent Classes

Slots

Name Description
created_by_curie Curie of the Person object representing the individual that created the entity
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.
evidence_curies Curies of InformationContentEntity objects given as evidence
internal Classifies the entity as private (for internal use) or not (for public use).
obsolete Entity is no longer current.
source_general_consequence_curie Curie of the SOTerm (child of SO:0001576 - transcript_variant) that describes the consequence of the variant, as stated in the source reference when no transcript ID is provided. Since a curator would determine variant location and consequences relative to at least one specific genome assembly, transcript and/or polypeptide, no slot for curated general consequence is provided.
updated_by_curie Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: VariantSourceGeneralConsequenceSlotAnnotationDTO
description: The consequence of the variant, as stated in the source reference when
  no transcript ID is provided.
notes:
- Since a curator would determine variant location and consequences relative to at
  least one specific genome assembly, transcript and/or polypeptide, no slot for curated
  general consequence is provided.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
aliases:
- transcript_consequence
is_a: SlotAnnotationDTO
slots:
- source_general_consequence_curie

Induced

name: VariantSourceGeneralConsequenceSlotAnnotationDTO
description: The consequence of the variant, as stated in the source reference when
  no transcript ID is provided.
notes:
- Since a curator would determine variant location and consequences relative to at
  least one specific genome assembly, transcript and/or polypeptide, no slot for curated
  general consequence is provided.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
aliases:
- transcript_consequence
is_a: SlotAnnotationDTO
attributes:
  source_general_consequence_curie:
    name: source_general_consequence_curie
    description: Curie of the SOTerm (child of SO:0001576 - transcript_variant) that
      describes the consequence of the variant, as stated in the source reference
      when no transcript ID is provided. Since a curator would determine variant location
      and consequences relative to at least one specific genome assembly, transcript
      and/or polypeptide, no slot for curated general consequence is provided.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantSourceGeneralConsequenceSlotAnnotationDTO
    multivalued: false
    alias: source_general_consequence_curie
    owner: VariantSourceGeneralConsequenceSlotAnnotationDTO
    domain_of:
    - VariantSourceGeneralConsequenceSlotAnnotationDTO
    range: string
    required: true
  evidence_curies:
    name: evidence_curies
    description: Curies of InformationContentEntity objects given as evidence
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: evidence_curies
    owner: VariantSourceGeneralConsequenceSlotAnnotationDTO
    domain_of:
    - NoteDTO
    - SlotAnnotationDTO
    - EvidenceAssociationDTO
    - GeneGeneAssociationDTO
    range: string
  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: VariantSourceGeneralConsequenceSlotAnnotationDTO
    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: VariantSourceGeneralConsequenceSlotAnnotationDTO
    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: VariantSourceGeneralConsequenceSlotAnnotationDTO
    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: VariantSourceGeneralConsequenceSlotAnnotationDTO
    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: VariantSourceGeneralConsequenceSlotAnnotationDTO
    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: VariantSourceGeneralConsequenceSlotAnnotationDTO
    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: VariantSourceGeneralConsequenceSlotAnnotationDTO
    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: VariantSourceGeneralConsequenceSlotAnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean