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New curation tool a boon for genetic biologists
Date:6/21/2011

e collection of articles on a topic and automatically partition it into subsets based on which words occur together, a function called clustering.

"The first thing you have to do if you have something that's simulating a curator is to decide what papers it's going to look at," Schatz said. "Then you have to decide what to extract from the text, and then what you're going to do with what you've extracted, what service you're going to provide. The system is designed to have easy ways of doing that."

The user-friendly interface allows biologists to build a unique space in a few simple steps, utilizing sub-searches and filters. For example, an entomologist interested in the genetic basis for foraging as a social behavior in bees would start with insect literature, then zero in on genes that are associated in literature with both foraging and social behavior a specific intersection of topics that typical search engines could not handle.

This type of directed data navigation has several advantages. It is much more directed than a simple search, but able to process much more data than a human curator. It can also be used in fields where there are no human curators, since only the most-studied animals like mice and flies have their own professional curators.

Schatz and his team equipped the navigator to perform several tasks that biologists often perform when trying to interpret gene function. Not only does the program summarize a gene, as a curator would, but it also can perform analysis to extrapolate functions from literature.

For example, a study will show that a gene controls a particular chemical, and another study will show that chemical plays a role in a certain behavior, so the software makes the link that the gene could, in part, control that behavior.

BeeSpace can also perform vocabulary switching, an automatic translation across species or behaviors. For example, if it is known that a specific gene in a hone
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Contact: Liz Ahlberg
eahlberg@illinois.edu
217-244-1073
University of Illinois at Urbana-Champaign
Source:Eurekalert  

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