As a research biologist it is vital to know how to search and comprehend the literature effectively, and at BiteSize Bio there are now several illuminating articles describing how to use PubMed to its fullest capability. However, once you’ve got hold of an online paper, you may need to contend with unfamiliar molecule names and biological terms which hamper your understanding. In this short article I’ll describe a tool called Reflect, which provides a solution to this problem.

Reflect is a free, web-based tool that will process the text of any web-page (not only published articles) and mark up biological words and terms. Simply clicking on a highlighted  word opens a pop-up window in your browser which provides information on the molecule, such as its structure,  sub-cellular localization and interacting molecules, in a concise, unobtrusive format.  Furthermore, Wikipedia content is included, if available. This is a very handy way to quickly learn about the unfamiliar molecule without breaking your flow of reading the main text. So, its usage is not restricted to papers – blogs, online protocols and indeed any other resource can be annotated.

The screenshot below shows Reflect in action -  words or phrases with Wikipedia entries are highlighted in grey, and molecular terms in blue. In the pop-up, you can see an at-a-glance summary of  the protein RALA obtained by clicking on the word – it really is as simple as that!

Using Reflect

Accessing  Reflect couldn’t be easier either – simply paste a link to the web-page you want to examine into the Reflect website and that page  will be marked up for you.

For the minimal effort of installing a browser plugin ( for most common browsers) a Reflect button will appear on your browser toolbar, which will mark up pages directly.  Even for full length articles, Reflect is very fast, returning the annotated web page in a few seconds.  Finally, if you  installed the browser plugin, you can help improve Reflect’s accuracy by reporting any false positives or false negatives to its developers ( Reinhard Schneider’s group at EMBL ).

A sister project of Reflect, called On-the-fly extends Reflect’s capabilities by examining non-web based text, such as MS Word documents.

I hope you find Reflect useful, you can be using it in the time it takes to read this article, which can’t be said for a lot of bioinformatics software!  In future articles I’ll introduce some other text analysis tools to enhance your literature searches.

Resources

• Reflect: http://reflect.ws
• On the Fly: http://onthefly.embl.de
• Nature Biotech reference describing Reflect: Nature Biotechnology 27, 508 – 510 (2009)