Class: Publication
Description: 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).
classDiagram
class Publication
InformationContentEntity <|-- Publication
Publication <|-- Book
Publication <|-- BookChapter
Publication <|-- Serial
Publication <|-- Article
Publication <|-- Patent
Publication <|-- WebPage
Publication <|-- PreprintPublication
Publication <|-- DrugLabel
Publication : authors
Publication --|> Agent : authors
Publication : category
Publication : creation_date
Publication : deprecated
Publication : description
Publication : format
Publication : full_name
Publication : has_attribute
Publication --|> Attribute : has_attribute
Publication : id
Publication : iri
Publication : keywords
Publication : license
Publication : mesh_terms
Publication : name
Publication : pages
Publication : provided_by
Publication : publication_type
Publication : rights
Publication : summary
Publication : synonym
Publication : type
Publication : xref
Inheritance
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| 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. |
0..* Agent |
direct | |
| 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. |
0..* String |
direct | |
| summary: executive summary of a publication |
0..1 String |
direct | |
| keywords: keywords tagging a publication |
0..* String |
direct | |
| mesh_terms: mesh terms tagging a publication |
0..* Uriorcurie |
direct | |
| xref: 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. |
0..* Uriorcurie |
direct | |
| 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. |
1..* String |
direct | |
| license: None |
0..1 String |
InformationContentEntity | |
| rights: None |
0..1 String |
InformationContentEntity | |
| format: None |
0..1 String |
InformationContentEntity | |
| creation_date: date on which an entity was created. This can be applied to nodes or edges |
0..1 Date |
InformationContentEntity | |
| 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. |
0..* String |
NamedThing | |
| full_name: a long-form human readable name for a thing |
0..1 LabelType |
NamedThing | |
| synonym: Alternate human-readable names for a thing |
0..* LabelType |
NamedThing | |
| 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. |
1..1 String |
Entity | |
| iri: An IRI for an entity. This is determined by the id using expansion rules. |
0..1 IriType |
Entity | |
| 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. 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} |
1..* Uriorcurie |
Entity | |
| type: None |
0..* String |
Entity | |
| 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). |
0..1 LabelType |
Entity | |
| description: a human-readable description of an entity |
0..1 NarrativeText |
Entity | |
| has_attribute: connects any entity to an attribute |
0..* Attribute |
Entity | |
| deprecated: A boolean flag indicating that an entity is no longer considered current or valid. |
0..1 Boolean |
Entity |
Usages
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:
| ID Prefix | Usage |
|---|---|
| PMID | Publication Article JournalArticle |
| PMC | Publication |
| doi | InformationContentEntity Publication JournalArticle |
| NLMID | Publication Book Serial |
LinkML Source
name: publication
id_prefixes:
- PMID
- PMC
- doi
- NLMID
description: 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).
in_subset:
- model_organism_database
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- IAO:0000311
narrow_mappings:
- IAO:0000013
- STY:T170
is_a: information content entity
slots:
- authors
- pages
- summary
- keywords
- mesh terms
- xref
- publication type
slot_usage:
id:
name: id
description: '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.'
domain_of:
- ontology class
- entity
name:
name: name
description: 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).
domain_of:
- attribute
- entity
- macromolecular machine mixin
publication type:
name: publication type
domain_of:
- publication
required: true
pages:
name: pages
description: 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.
multivalued: true
domain_of:
- publication