To the rescue!

07 Nov 2011

Good news for those of you working on the family of G protein-coupled receptors (GPCR).  Keeping up with the massive amount of literature and data has become a lot easier thanks to work by Bas Vroling (CMBI, Nijmegen) and colleagues. In a paper in BMC Bioinformatics, they describe the GPCR-specific PDF reader, a new tool that is now part of the GPCR database (GPCRDB, www.gpcr.org/7tm/). When using the tool to read a paper, annotated concepts are immediately visible, which provides the researchers with quick access to related publications and relevant data sources.

"Our main goal was to develop a reader that allows researchers to easily review, find and analyse data and relevant literature. When a user opens a paper, the system immediately provides feedback by highlighting the annotated concepts, such as proteins, residues and mutations. Importantly, this information is also stored by the system to keep the information flow up to date", Vroling explains. According to him, what makes their tool stand out from other tools that target the same problems is that they can validate their tools using the GPCRDB. "This validation step makes our work unique. It is essential to have access to a reliable data source. That is what we hope to show with our work as well. Developing text mining tools is only worthwhile when you can check your results against a well-maintained, curated database."

A particularly sympathetic feature of GPCR-specific PDF reader is that it can help to rescue old data from oblivion. Vroling: "Because past interpretations have turned out to be wrong, the raw data can still be very useful. Our tool can track this data down so it can be interpreted again using current insights."

Bas Vroling, David Thorne, Philip McDermott, Teresa K Attwood, Gert Vriend and Steve Pettifer
Integrating GPCR-specific information with full text articles
BMC Bioinformatics 2011 12:362

By: Esther Thole

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