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Class: Publication

Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP).

URI: biolink:Publication

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Identifier prefixes

  • PMID
  • PMC
  • doi
  • NLMID

Parents

  • is_a: InformationContentEntity - a piece of information that typically describes some topic of discourse or is used as support.

Children

  • Article - a piece of writing on a particular topic presented as a stand-alone section of a larger publication
  • Book - This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.
  • BookChapter
  • DrugLabel - a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc.
  • Patent - a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time.
  • PreprintPublication - a document reresenting an early version of an author’s original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal.
  • Serial - This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.
  • WebPage - a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features.

Referenced by class

Attributes

Own

  • authors 0..*
    • Description: connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author’s name be formatted as “surname, firstname initial.”. Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.
    • Range: Agent
  • keywords 0..*
    • Description: keywords tagging a publication
    • Range: String
  • mesh terms 0..*
    • Description: mesh terms tagging a publication
    • Range: Uriorcurie
  • id 1..1
    • Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
    • Range: String
    • in subsets: (translator_minimal)
  • name 0..1
    • Description: A human-readable name for an attribute or entity.
    • Range: LabelType
    • in subsets: (translator_minimal,samples)
  • pages 0..*
    • Description: page number of source referenced for statement or publication
    • Range: String
  • publication type 0..*
    • Description: Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.
    • Range: String
  • summary 0..1
    • Description: executive summary of a publication
    • Range: String

Inherited from entity:

  • id 1..1
    • Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
    • Range: String
    • in subsets: (translator_minimal)
  • iri 0..1
    • Description: An IRI for an entity. This is determined by the id using expansion rules.
    • Range: IriType
    • in subsets: (translator_minimal,samples)
  • category 0..*
    • Description: Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.
  • In a neo4j database this MAY correspond to the neo4j label tag.
  • In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values biolink:Protein, biolink:GeneProduct, biolink:MolecularEntity, … In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}
  • type 0..*
  • description 0..1
    • Description: a human-readable description of an entity
    • Range: NarrativeText
    • in subsets: (translator_minimal)
  • has attribute 0..*
    • Description: connects any entity to an attribute
    • Range: Attribute
    • in subsets: (samples)

Inherited from gene product mixin:

  • xref 0..*
    • Description: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
    • Range: Uriorcurie
    • in subsets: (translator_minimal)

Inherited from information content entity:

Inherited from named thing:

  • provided by 0..*
    • Description: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
    • Range: String
  • category 0..*
    • Description: Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.
  • In a neo4j database this MAY correspond to the neo4j label tag.
  • In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values biolink:Protein, biolink:GeneProduct, biolink:MolecularEntity, … In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}

Domain for slot:

  • authors 0..*
    • Description: connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author’s name be formatted as “surname, firstname initial.”. Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.
    • Range: Agent
  • keywords 0..*
    • Description: keywords tagging a publication
    • Range: String
  • mesh terms 0..*
    • Description: mesh terms tagging a publication
    • Range: Uriorcurie
  • id 1..1
    • Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
    • Range: String
    • in subsets: (translator_minimal)
  • name 0..1
    • Description: A human-readable name for an attribute or entity.
    • Range: LabelType
    • in subsets: (translator_minimal,samples)
  • pages 0..*
    • Description: page number of source referenced for statement or publication
    • Range: String
  • publication type 0..*
    • Description: Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.
    • Range: String
  • summary 0..1
    • Description: executive summary of a publication
    • Range: String

Other properties

     
In Subsets:   model_organism_database
Exact Mappings:   IAO:0000311
Narrow Mappings:   IAO:0000013
    STY:T170