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Reference

None

classDiagram InformationContentEntity <|-- Reference Reference : abstract Reference : authors Reference : category Reference : created_by Reference : curie Reference : date_arrived_in_pubmed Reference : date_created Reference : date_last_modified_in_pubmed Reference : date_published Reference : date_updated Reference : db_date_created Reference : db_date_updated Reference : internal Reference : issue_name Reference : keywords Reference : language Reference : merged_into_id Reference : obsolete Reference : open_access Reference : page_range Reference : plain_language_abstract Reference : publisher Reference : pubmed_abstract_languages Reference : pubmed_publication_status Reference : pubmed_type Reference : reference_id Reference : resource_id Reference : title Reference : updated_by Reference : volume

URI: alliance:Reference

Parent Classes

Slots

Name Description
abstract The author summary of the publication. From PubMed otherwise from Mod or manual reference creation.
authors Ordered author entities for this publication. An Author is associated with only one publication. A Person can be associated with multiple publications.
category The alliance category type. Only relevant at Alliance.
created_by The individual that created the entity.
curie A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
date_arrived_in_pubmed Day in which a reference or resource was created in PubMed. Only relevant for PubMed references.
date_created The date on which an entity was created. This can be applied to nodes or edges.
date_last_modified_in_pubmed Date on which entity was last updated at PubMed. Only relevant for PubMed references.
date_published Date on which an entity was published. From PubMed otherwise from Mod or manual reference creation.
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).
issue_name The number of the journal issue in which the article was published. From PubMed otherwise from Mod or manual reference creation.
keywords Keywords tagging a publication. Aggregation of PubMed and ZFIN, editable at Alliance.
language Language of the reference. Aggregation of PubMed and FlyBase, editable at Alliance.
merged_into_id ID that used to refer to this reference
obsolete Entity is no longer current.
open_access Indicates if the reference is freely available for use by anyone, usually with fewer copyright and licensing barriers.
page_range Page numbers of source referenced for statement or publication. From PubMed otherwise from Mod or manual reference creation.
plain_language_abstract Lay person, readable version of the abstract. Only relevant for PubMed references.
publisher Publisher associated with a reference or resource. From PubMed otherwise from Mod or manual reference creation.
pubmed_abstract_languages Languages for the abstract. Only relevant for PubMed references.
pubmed_publication_status Status of the publication at PubMed. Only relevant for PubMed references.
pubmed_type Type of Reference as described by PubMed. Only relevant for PubMed references.
reference_id The primary key for the Reference object in the references table.
resource_id None
title A human readable title for a reference. From PubMed otherwise from Mod or manual reference creation.
updated_by The individual that last modified the entity.
volume Volume associated with a reference. From PubMed otherwise from Mod or manual reference creation.

Mappings

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

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • PMID

  • NLMID

  • DOI

  • SGD

  • FB

  • WB

  • ZFIN

  • MGI

  • RGD

  • PMC

  • DOI

LinkML Specification

Direct

name: Reference
id_prefixes:
- PMID
- NLMID
- DOI
- SGD
- FB
- WB
- ZFIN
- MGI
- RGD
- PMC
- DOI
notes:
- In the ABC literature database, the table holding Reference objects is named references.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
aliases:
- references
- publication
is_a: InformationContentEntity
slots:
- abstract
- authors
- category
- date_arrived_in_pubmed
- date_last_modified_in_pubmed
- date_published
- issue_name
- keywords
- language
- merged_into_id
- open_access
- page_range
- plain_language_abstract
- publisher
- pubmed_abstract_languages
- pubmed_publication_status
- pubmed_type
- reference_id
- resource_id
- title
- volume
slot_usage:
  reference_id:
    name: reference_id
    description: The primary key for the Reference object in the references table.
    domain_of:
    - Reference
    - MeshDetail
    - ModCorpusAssociation

Induced

name: Reference
id_prefixes:
- PMID
- NLMID
- DOI
- SGD
- FB
- WB
- ZFIN
- MGI
- RGD
- PMC
- DOI
notes:
- In the ABC literature database, the table holding Reference objects is named references.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
aliases:
- references
- publication
is_a: InformationContentEntity
slot_usage:
  reference_id:
    name: reference_id
    description: The primary key for the Reference object in the references table.
    domain_of:
    - Reference
    - MeshDetail
    - ModCorpusAssociation
attributes:
  abstract:
    name: abstract
    description: The author summary of the publication. From PubMed otherwise from
      Mod or manual reference creation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: abstract
    owner: Reference
    domain_of:
    - Reference
    range: string
  authors:
    name: authors
    description: Ordered author entities for this publication.  An Author is associated
      with only one publication.  A Person can be associated with multiple publications.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: true
    alias: authors
    owner: Reference
    domain_of:
    - Reference
    - Resource
    range: AuthorReference
  category:
    name: category
    description: The alliance category type.  Only relevant at Alliance.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: category
    owner: Reference
    domain_of:
    - Reference
    range: reference_category_enum
  date_arrived_in_pubmed:
    name: date_arrived_in_pubmed
    description: Day in which a reference or resource was created in PubMed. Only
      relevant for PubMed references.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: true
    alias: date_arrived_in_pubmed
    owner: Reference
    domain_of:
    - Reference
    range: string
  date_last_modified_in_pubmed:
    name: date_last_modified_in_pubmed
    description: Date on which entity was last updated at PubMed. Only relevant for
      PubMed references.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: date_last_modified_in_pubmed
    owner: Reference
    domain_of:
    - Reference
    range: string
  date_published:
    name: date_published
    description: Date on which an entity was published.  From PubMed otherwise from
      Mod or manual reference creation.
    notes:
    - 'Values here can be quite variable: e.g., just a year, or a year-season, etc.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: date_published
    owner: Reference
    domain_of:
    - Reference
    range: string
  issue_name:
    name: issue_name
    description: The number of the journal issue in which the article was published.
      From PubMed otherwise from Mod or manual reference creation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: issue_name
    owner: Reference
    domain_of:
    - Reference
    range: string
  keywords:
    name: keywords
    description: Keywords tagging a publication.  Aggregation of PubMed and ZFIN,
      editable at Alliance.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: keywords
    owner: Reference
    domain_of:
    - Reference
    range: string
  language:
    name: language
    description: Language of the reference.  Aggregation of PubMed and FlyBase, editable
      at Alliance.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: language
    owner: Reference
    domain_of:
    - Reference
    range: string
  merged_into_id:
    name: merged_into_id
    description: ID that used to refer to this reference
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: merged_into_id
    owner: Reference
    domain_of:
    - Reference
    range: uriorcurie
  open_access:
    name: open_access
    description: Indicates if the reference is freely available for use by anyone,
      usually with fewer copyright and licensing barriers.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: open_access
    owner: Reference
    domain_of:
    - Reference
    range: boolean
  page_range:
    name: page_range
    description: Page numbers of source referenced for statement or publication. From
      PubMed otherwise from Mod or manual reference creation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    close_mappings:
    - WIKIDATA_PROPERTY:P304
    multivalued: false
    alias: page_range
    owner: Reference
    domain_of:
    - Reference
    range: string
  plain_language_abstract:
    name: plain_language_abstract
    description: Lay person, readable version of the abstract. Only relevant for PubMed
      references.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: plain_language_abstract
    owner: Reference
    domain_of:
    - Reference
    range: string
  publisher:
    name: publisher
    description: Publisher associated with a reference or resource. From PubMed otherwise
      from Mod or manual reference creation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: publisher
    owner: Reference
    domain_of:
    - Reference
    - Resource
    range: string
  pubmed_abstract_languages:
    name: pubmed_abstract_languages
    description: Languages for the abstract. Only relevant for PubMed references.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: true
    alias: pubmed_abstract_languages
    owner: Reference
    domain_of:
    - Reference
    range: string
  pubmed_publication_status:
    name: pubmed_publication_status
    description: Status of the publication at PubMed. Only relevant for PubMed references.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: pubmed_publication_status
    owner: Reference
    domain_of:
    - Reference
    range: pubmed_publication_status_enum
  pubmed_type:
    name: pubmed_type
    description: Type of Reference as described by PubMed. Only relevant for PubMed
      references.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: true
    alias: pubmed_type
    owner: Reference
    domain_of:
    - Reference
    range: pubmed_type_enum
  reference_id:
    name: reference_id
    description: The primary key for the Reference object in the references table.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: table_key
    multivalued: false
    alias: reference_id
    owner: Reference
    domain_of:
    - Reference
    - MeshDetail
    - ModCorpusAssociation
    range: integer
    required: true
  resource_id:
    name: resource_id
    notes:
    - The value is the primary key for the resources table (an integer).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    alias: resource_id
    owner: Reference
    domain_of:
    - Reference
    range: integer
  title:
    name: title
    description: A human readable title for a reference. From PubMed otherwise from
      Mod or manual reference creation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: title
    owner: Reference
    domain_of:
    - Reference
    - Resource
    range: string
  volume:
    name: volume
    description: Volume associated with a reference. From PubMed otherwise from Mod
      or manual reference creation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Reference
    multivalued: false
    alias: volume
    owner: Reference
    domain_of:
    - Reference
    - Resource
    range: string
  curie:
    name: curie
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    alias: curie
    owner: Reference
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  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: Reference
    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: Reference
    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: Reference
    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: Reference
    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: Reference
    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: Reference
    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: Reference
    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: Reference
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean