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Publication

Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses.

classDiagram InformationContentEntity <|-- Publication Publication : authors Publication : category Publication : creation_date Publication : description Publication : format Publication : has_attribute Publication : id Publication : iri Publication : keywords Publication : license Publication : mesh_terms Publication : name Publication : pages Publication : provided_by Publication : rights Publication : source Publication : summary Publication : type Publication : xref

Parent Classes

Children

Slots

Name Description
authors 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.
category 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, etc. 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}
creation_date date on which an entity was created. This can be applied to nodes or edges
description a human-readable description of an entity
format None
has_attribute connects any entity to an attribute
id Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.
iri An IRI for an entity. This is determined by the id using expansion rules.
keywords keywords tagging a publication
license None
mesh_terms mesh terms tagging a publication
name the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).
pages When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.
provided_by 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.
rights None
source None
summary executive summary of a publication
type 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.
xref Alternate CURIEs for a thing

Mappings

Mapping Type Mapped Value
self ['biolink:Publication']
native ['biolink:Publication']
exact ['IAO:0000311']
narrow ['IAO:0000013', 'STY:T170']