A controlled vocabulary for pathway entities and events

Steve Jupe, Bijay Jassal, Mark Williams, Guanming Wu

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

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.

Original languageEnglish (US)
JournalDatabase
Volume2014
DOIs
StatePublished - 2014
Externally publishedYes

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

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