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Class: Article

Description: a piece of writing on a particular topic presented as a stand-alone section of a larger publication
classDiagram class Article Publication <|-- Article Article <|-- JournalArticle Article : authors Article --|> Agent : authors Article : category Article : creation_date Article : deprecated Article : description Article : format Article : full_name Article : has_attribute Article --|> Attribute : has_attribute Article : id Article : iri Article : iso_abbreviation Article : issue Article : keywords Article : license Article : mesh_terms Article : name Article : pages Article : provided_by Article : publication_type Article : published_in Article : rights Article : summary Article : synonym Article : type Article : volume Article : xref

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
published_in:
The enclosing parent serial containing the article should have industry-standard identifier from ISSN.
1
Uriorcurie		 direct
iso_abbreviation:
Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent. 		0..1
String		 direct
volume:
volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication 		0..1
String		 direct
issue:
issue of a newspaper, a scientific journal or magazine for reference purpose 		0..1
String		 direct
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. 		*
Agent		 Publication
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. 		*
String		 Publication
summary:
executive summary of a publication 		0..1
String		 Publication
keywords:
keywords tagging a publication 		*
String		 Publication
mesh_terms:
mesh terms tagging a publication 		*
Uriorcurie		 Publication
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. 		*
Uriorcurie		 Publication, NamedThing
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		 Publication
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. 		*
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 		*
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
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 		*
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 		*
Attribute		 Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid. 		0..1
Boolean		 Entity

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

LinkML Source

name: article
id_prefixes:
- PMID
description: a piece of writing on a particular topic presented as a stand-alone section
  of a larger publication
in_subset:
- model_organism_database
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- SIO:000154
- fabio:article
is_a: publication
slots:
- published in
- iso abbreviation
- volume
- issue
slot_usage:
  published in:
    name: published in
    description: The enclosing parent serial containing the article should have industry-standard
      identifier from ISSN.
    required: true
  iso abbreviation:
    name: iso abbreviation
    description: Optional value, if used locally as a convenience, is set to the iso
      abbreviation of the 'published in' parent.