GeneSynonymSlotAnnotation

All aliases (non-preferred names) for the gene. Any type of synonym is acceptable.

classDiagram NameSlotAnnotation <|-- GeneSynonymSlotAnnotation GeneSynonymSlotAnnotation : created_by GeneSynonymSlotAnnotation : date_created GeneSynonymSlotAnnotation : date_updated GeneSynonymSlotAnnotation : db_date_created GeneSynonymSlotAnnotation : db_date_updated GeneSynonymSlotAnnotation : display_text GeneSynonymSlotAnnotation : evidence GeneSynonymSlotAnnotation : format_text GeneSynonymSlotAnnotation : internal GeneSynonymSlotAnnotation : name_type GeneSynonymSlotAnnotation : obsolete GeneSynonymSlotAnnotation : single_gene GeneSynonymSlotAnnotation : synonym_scope GeneSynonymSlotAnnotation : synonym_url GeneSynonymSlotAnnotation : updated_by

URI: alliance:GeneSynonymSlotAnnotation

Parent Classes

AuditedObject
- SlotAnnotation
  - NameSlotAnnotation
    - GeneSynonymSlotAnnotation

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.
display_text	A version of a synonym string for display. Any UTF8 character is permitted.
evidence	The evidence that supports some assertion.
format_text	A version of a synonym string using only ASCII characters, which is easier to type (for searches), print and parse. For example, Greek characters are transliterated.
internal	Classifies the entity as private (for internal use) or not (for public use).
name_type	The type of name: e.g., symbol, full_name, systematic_name, etc.
obsolete	Entity is no longer current.
single_gene	None
synonym_scope	the scope of the synonym - permissible values are narrow / broad / related / exact
synonym_url	URL for a synonym: e.g., NCBI URL for the NCBI synonym of an object.
updated_by	The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: GeneSynonymSlotAnnotation
description: All aliases (non-preferred names) for the gene. Any type of synonym is
  acceptable.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: NameSlotAnnotation
slots:
- single_gene
slot_usage:
  single_gene:
    name: single_gene
    domain_of:
    - GeneSymbolSlotAnnotation
    - GeneFullNameSlotAnnotation
    - GeneSecondaryIdSlotAnnotation
    - GeneSystematicNameSlotAnnotation
    - GeneSynonymSlotAnnotation
    - GeneChangeEventSlotAnnotation
    - GeneOntologyAnnotation
    required: true

Induced

name: GeneSynonymSlotAnnotation
description: All aliases (non-preferred names) for the gene. Any type of synonym is
  acceptable.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: NameSlotAnnotation
slot_usage:
  single_gene:
    name: single_gene
    domain_of:
    - GeneSymbolSlotAnnotation
    - GeneFullNameSlotAnnotation
    - GeneSecondaryIdSlotAnnotation
    - GeneSystematicNameSlotAnnotation
    - GeneSynonymSlotAnnotation
    - GeneChangeEventSlotAnnotation
    - GeneOntologyAnnotation
    required: true
attributes:
  single_gene:
    name: single_gene
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: single_gene
    owner: GeneSynonymSlotAnnotation
    domain_of:
    - GeneSymbolSlotAnnotation
    - GeneFullNameSlotAnnotation
    - GeneSecondaryIdSlotAnnotation
    - GeneSystematicNameSlotAnnotation
    - GeneSynonymSlotAnnotation
    - GeneChangeEventSlotAnnotation
    - GeneOntologyAnnotation
    range: Gene
    required: true
  name_type:
    name: name_type
    description: 'The type of name: e.g., symbol, full_name, systematic_name, etc.'
    notes:
    - "Proposed vocabulary terms for name_type.\n  nomenclature_symbol: A symbol for\
      \ an object: e.g., pax6a, lin-12.\n  full_name: The full length name of an entity:\
      \ e.g., paired box 6a.\n  systematic_name: A systematic name: e.g., YHR084W,\
      \ R09F10.2, CG4889.\n  ncbi_protein_name: Synonyms developed by SGD and NCBI\
      \ curators.\n  uniform: SGD-specific.\n  non_uniform: SGD-specific.\n  retired_name:\
      \ SGD-specific.\n  unspecified: unclassified names."
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: NameSlotAnnotation
    multivalued: false
    alias: name_type
    owner: GeneSynonymSlotAnnotation
    domain_of:
    - NameSlotAnnotation
    range: VocabularyTerm
    required: true
  format_text:
    name: format_text
    description: A version of a synonym string using only ASCII characters, which
      is easier to type (for searches), print and parse. For example, Greek characters
      are transliterated.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - synonym_text
    multivalued: false
    alias: format_text
    owner: GeneSynonymSlotAnnotation
    domain_of:
    - NameSlotAnnotation
    - NameSlotAnnotationDTO
    range: string
    required: true
  display_text:
    name: display_text
    description: A version of a synonym string for display. Any UTF8 character is
      permitted.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - synonym_sgml
    multivalued: false
    alias: display_text
    owner: GeneSynonymSlotAnnotation
    domain_of:
    - NameSlotAnnotation
    - NameSlotAnnotationDTO
    range: string
    required: true
  synonym_url:
    name: synonym_url
    description: 'URL for a synonym: e.g., NCBI URL for the NCBI synonym of an object.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: synonym_url
    owner: GeneSynonymSlotAnnotation
    domain_of:
    - NameSlotAnnotation
    - NameSlotAnnotationDTO
    range: uri
  synonym_scope:
    name: synonym_scope
    description: the scope of the synonym - permissible values are narrow / broad
      / related / exact
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: NameSlotAnnotation
    alias: synonym_scope
    owner: GeneSynonymSlotAnnotation
    domain_of:
    - NameSlotAnnotation
    range: VocabularyTerm
  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: GeneSynonymSlotAnnotation
    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: GeneSynonymSlotAnnotation
    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: GeneSynonymSlotAnnotation
    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: GeneSynonymSlotAnnotation
    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: GeneSynonymSlotAnnotation
    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: GeneSynonymSlotAnnotation
    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: GeneSynonymSlotAnnotation
    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: GeneSynonymSlotAnnotation
    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: GeneSynonymSlotAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean