Apellicon: a web-based tool for constructing and curating Textpresso databases.

Abstract

As more research literature in the biological sciences is made available in electronic format, text mining systems are increasingly being used to improve the ability of investigators to retrieve relevant information. Through the use of advanced indexing techniques that utilize biological ontologies, semantic databases, and other formal representations of biological concepts text mining systems have been able to effectively parse biological literature. While text mining systems are increasingly effective at creating the linkages required to provide context-specific search results, the systems themselves are difficult to set up and use by novice computer users due to the highly technical nature of the applications. Because most researchers in the biological sciences do not have a strong computer science background we have focused on improving the quality of existing, proven text mining systems by implementing a web-based GUI that greatly improves the workflow of these systems. Textpresso in particular has an excellent web-based interface for searching literature but does not have an easy to use administrative interface. We developed the Apellicon interface to enable a wide range of users to build and manage a Textpresso database. An important feature of Apellicon is that it can enable groups to collaborate in building a Textpresso database.