There's a lot of scientific data going to waste. Much of it has been painstakingly gathered through timely and costly experiments and is freely available in public databases. But researchers have been hard-pressed to use existing data to ask new questions, because they lack reliable descriptions and computational tools. Now, scientists at Harvard and Stanford have created a software application that overcomes some of these barriers. The program, called Genotext, trolled through publicly available data and came back with genes implicated in aging, leukemia and injury, as described this month in the journal Nature Biotechnology.
The program automatically analyzes text descriptions of different experiments. It then identifies which genes were turned on or off, up or down, in various diseases or environmental conditions.
That's no easy task, since a single experiment can collect millions of data points and descriptions of very similar experiments can vary widely.
"This is a real advance," said John Wilbanks, head of Science Commons, a nonprofit group dedicated to helping scientists find productive ways to share data. "The use of annotation and knowledge to understand functional relationships between genes is where the field has to go."...Scientific journals often require researchers to deposit their microarray data in publicly available databases. Though data formats to describe which genes are turned up to what level are fairly standard, the same can't be said for descriptions of the conditions and tissues in which the genes are measured. That makes it difficult to compare experiments that probe how the environment might change gene activity or how gene activity differs between sickness and health.
"We've all agreed on how to represent the genes, but we haven't agreed on how to represent what we actually did in the experiments," [Atul] Butte [Stanford bioinformatics specialist and the study's lead author] said. That's one of the problems that Butte, along with Isaac Kohane, a bioinformaticist at Harvard, set out to solve by creating Genotext....Though Genotext is available for free over the Web, researchers need some programming experience to use it. Plans to create a user-friendly query interface are underway.
Posted by
Peter Suber at 1/14/2006 01:05:00 PM.
The open access movement:
Putting peer-reviewed scientific and scholarly literature
on the internet. Making it available free of charge and
free of most copyright and licensing restrictions.
Removing the barriers to serious research.
