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. 2014 Jun 20:2014:bau060.
doi: 10.1093/database/bau060. Print 2014.

A controlled vocabulary for pathway entities and events

Steve Jupe  1 , Bijay Jassal  2 , Mark Williams  3 , Guanming Wu  2
Affiliations

A controlled vocabulary for pathway entities and events

Steve Jupe et al. Database (Oxford). .

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.

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Figures

Figure 1.
Figure 1.
Pathway diagram segment using abbreviated small molecule names.
Figure 2.
Figure 2.
Pathway diagram segment using full small molecule names.
See this image and copyright information in PMC

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