With the BeeSpace Navigator, University of Illinois researchers have created both a curation tool for genetic biologists and a new approach to searching for information.
The project was a collaboration between researchers at the Institute for Genomic Biology and the department of computer science. Led by Bruce Schatz, professor and head of medical information science at the U. of I., the team described the software and its applications in the web server issue of the journal Nucleic Acids Research.
When biologists need information about a gene or its function, they turn to curators, who keep and organize vast quantities of information from academic papers and scientific studies. A curator will extract as much information as possible from the papers in his or her collection and provide the biologist with a detailed summary of what’s known about the gene – its location, function, sequence, regulation and more – by placing this information into an online database such as FlyBase.
“The question was, could you make an automatic version of that, which is accurate enough to be helpful?” Schatz said.
Schatz and his team developed BeeSpace Navigator, a free online software that draws upon databases of scholarly publications. The semantic indexing to support the automatic curation used the Cloud Computing Testbed, a national computing datacenter hosted at U. of I.
While BeeSpace originally was built around literature about the bee genome, it has since been expanded to the entire Medline database and has been used to study a number of insects as well as mice, pigs and fish.
The efficiency of BeeSpace Navigator is in its specific searches. A broad, general search of all known data would yield a chaotic myriad of results – the millions of hits generated by a Google search, for example. But with BeeSpace, users create “spaces,” or special collections of literature to search. It also can take a large collection of articles on a topic and automatically partition it into subsets based on which words occur together, a function called clustering.
BeeSpace Training materialp is at www.beespace.illinois.edu/bstwmaterials.php.