biolink-model

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

---

---

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

• Agent author _0..* Publication
• Agent editor _0..* Publication
• Association publications _0..* Publication
• Agent publisher _0..* Publication

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}
  • Range: CategoryType
  • in subsets: (translator_minimal)
• type _0..*
  • Range: String
• 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:

• synonym _0..*
  • Description: Alternate human-readable names for a thing
  • Range: LabelType
  • in subsets: (translator_minimal)
• 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:

• license _0..1
  • Range: String
• rights _0..1
  • Range: String
• format _0..1
  • Range: String
• creation date _0..1
  • Description: date on which an entity was created. This can be applied to nodes or edges
  • Range: Date

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
• full name _0..1
  • Description: a long-form human readable name for a thing
  • Range: LabelType
• 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}
  • Range: CategoryType
  • in subsets: (translator_minimal)

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

This site is open source. Improve this page.