Continuing with my current fascination with cool ways to enhance the experience of searching and engaging the literature online…

Deepak Singh at business|bytes|genes|molecules tells us about Reflect, a new tool for adding value to online articles:

Essentially, Reflect is an entity extraction engine with a specific purpose, recognizing molecular entities, both compounds and proteins. I have spoken at length about the value of entity extraction, and the availability of a service like Reflect just shows you how useful something like this can be. Using either the Reflect website where you can enter a URL, or the Firefox plugin, you can use extract molecular entities on a webpage quite easily. The service highlights recognized entities, and using your mouse you can get additional details as shown in the screenshot below.

Reflect identifies the names of proteins/genes or small molecules that appear in a body of text and generates a live link to a floating window containing informations (and further linkage) about that entity.

You can check it out at the Reflect website.

I had a lot of fun plugging in blog posts from Ouroboros and seeing what Reflect thought of them. It did a great job with genes and a fairly good job with small molecules, though the higher false positive rate in the latter case was a little disappointing (identifying words as small molecules that weren’t, and linking to things that aren’t small molecules at all, like the word “reset” that appears in a graph about something else).

(P.S.: By the way, Reflect was the winner of the Elsevier Grand Challenge, and its development may have been motivated by the incentive of the prize. In light of that, I just want to clarify that I still think Elsevier is the devil.)

Update: The developers of Reflect have a preprint up at Nature Precedings. Thanks to Hilary Spencer for the heads-up.