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VariantSourceGeneralConsequenceSlotAnnotation

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

classDiagram SlotAnnotation <|-- VariantSourceGeneralConsequenceSlotAnnotation VariantSourceGeneralConsequenceSlotAnnotation : created_by VariantSourceGeneralConsequenceSlotAnnotation : date_created VariantSourceGeneralConsequenceSlotAnnotation : date_updated VariantSourceGeneralConsequenceSlotAnnotation : db_date_created VariantSourceGeneralConsequenceSlotAnnotation : db_date_updated VariantSourceGeneralConsequenceSlotAnnotation : evidence VariantSourceGeneralConsequenceSlotAnnotation : internal VariantSourceGeneralConsequenceSlotAnnotation : obsolete VariantSourceGeneralConsequenceSlotAnnotation : single_variant VariantSourceGeneralConsequenceSlotAnnotation : updated_by VariantSourceGeneralConsequenceSlotAnnotation : variant_source_general_consequence

URI: alliance:VariantSourceGeneralConsequenceSlotAnnotation

Parent Classes

Slots

Name Description
created_by 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 The evidence that supports some assertion.
internal Classifies the entity as private (for internal use) or not (for public use).
obsolete Entity is no longer current.
single_variant The variant that is the subject of a SlotAnnotation.
updated_by The individual that last modified the entity.
variant_source_general_consequence The general consequence of the variant on the transcript.

Mappings

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

LinkML Specification

Direct

name: VariantSourceGeneralConsequenceSlotAnnotation
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: SlotAnnotation
slots:
- single_variant
- variant_source_general_consequence

Induced

name: VariantSourceGeneralConsequenceSlotAnnotation
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: SlotAnnotation
attributes:
  single_variant:
    name: single_variant
    description: The variant that is the subject of a SlotAnnotation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: single_variant
    owner: VariantSourceGeneralConsequenceSlotAnnotation
    domain_of:
    - VariantSourceGeneralConsequenceSlotAnnotation
    range: Variant
    required: true
  variant_source_general_consequence:
    name: variant_source_general_consequence
    description: The general consequence of the variant on the transcript.
    notes:
    - The SOTerm should be a child of SO:0001576 - transcript_variant.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantSourceGeneralConsequenceSlotAnnotation
    multivalued: false
    alias: variant_source_general_consequence
    owner: VariantSourceGeneralConsequenceSlotAnnotation
    domain_of:
    - VariantSourceGeneralConsequenceSlotAnnotation
    range: SOTerm
    required: true
  evidence:
    name: evidence
    description: The evidence that supports some assertion.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: evidence
    owner: VariantSourceGeneralConsequenceSlotAnnotation
    domain_of:
    - Note
    - SlotAnnotation
    - EvidenceAssociation
    range: InformationContentEntity
  created_by:
    name: created_by
    description: The individual that created the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: created_by
    owner: VariantSourceGeneralConsequenceSlotAnnotation
    domain_of:
    - AuditedObject
    range: Person
  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: VariantSourceGeneralConsequenceSlotAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by:
    name: updated_by
    description: The individual that last modified the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: updated_by
    owner: VariantSourceGeneralConsequenceSlotAnnotation
    domain_of:
    - AuditedObject
    range: Person
  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: VariantSourceGeneralConsequenceSlotAnnotation
    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: VariantSourceGeneralConsequenceSlotAnnotation
    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: VariantSourceGeneralConsequenceSlotAnnotation
    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: VariantSourceGeneralConsequenceSlotAnnotation
    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: VariantSourceGeneralConsequenceSlotAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean