title: A controlled vocabulary for pathway entities and events.
abstract: Entities involved in pathways and the events they participate in require descriptive and unambiguous names that are often not available in the literature or elsewhere. Reactome is a manually curated open-source resource of human pathways. It is accessible via a website, available as downloads in standard reusable formats and via Representational State Transfer (REST)-ful and Simple Object Access Protocol (SOAP) application programming interfaces (APIs). We have devised a controlled vocabulary (CV) that creates concise, unambiguous and unique names for reactions (pathway events) and all the molecular entities they involve. The CV could be reapplied in any situation where names are used for pathway entities and events. Adoption of this CV would significantly improve naming consistency and readability, with consequent benefits for searching and data mining within and between databases. Database URL: http://www.reactome.org.
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK sjupe@ebi.ac.uk.
authors.forename: Steve
authors.initials: S
authors.lastname: Jupe
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Bijay
authors.initials: B
authors.lastname: Jassal
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Mark
authors.initials: M
authors.lastname: Williams
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Guanming
authors.initials: G
authors.lastname: Wu
mesh_terms: D006801:Humans; D010455:Peptides / Q000737:chemistry; D015398:Signal Transduction; D054852:Small Molecule Libraries / Q000737:chemistry; D018875:Vocabulary, Controlled
chemical_list: D010455:Peptides; D054852:Small Molecule Libraries