A controlled vocabulary for pathway entities and events by Steve Jupe, et al.
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
There is no doubt that “unambiguous and unique names for reactions (pathway events) and all the molecular entities they involve” would have all the benefits listed by the authors.
Unfortunately, the experience of the HUGO Gene Nomenclature Committee, for example, has been that “other” names for genes are used and then the HUGO designation is created. Making the HUGO designation only one of several names a gene may have.
Another phrase for “universal name” is “an additional name.”
It is an impressive effort and should be useful in disambiguating the additional names for pathway entities and events.
FYI, from the homepage of the database:
Reactome is a free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education.