Catherine Varmazis, Web 2.0: Scientists Need to Mash It Up, Bio-IT World, April 6, 2006. Notes from the "Web 2.0" workshop at Bio-IT World’s Life Sciences Conference + Expo in Boston this week. Excerpt:
Declan Butler, Europe-based reporter for Nature magazine, said Web 2.0 can bring us back to original idea of the Web as a collaborative workspace. Just as developing nations bypassed copper-wire telephones and leapfrogged directly to cell phones, “the biggest revolution on the Web is passing science by,” he warned. Science has a collective intelligence that can be a drawback, Butler said, if scientists stay wedded only to traditional methods such as paper-based peer-reviewed journals. Very few scientists blog, he pointed out, for fear it could damage their careers. But many younger scientists see the current system as over-competitive and prefer to collaborate. And he believes scientists are enriched by blogging. In fact, a peer-reviewed blog such as scienceblogs.com, postgenomic.com, and realclimate.org, can serve as a journal by acting as a collaborative filtering and sorting service. Beyond the NCBI and other highly organized databases, Butler said, there is very little data sharing among scientists. He quoted UC Santa Cruz bioinformatician David Haussler, as saying: “Scientists are still in the Dark Ages when it comes to sharing data.” For example, Butler said, the World Health Organization has no usable data on avian flu. And a Swedish site on avian flu presents the data in PDF files. But there are signs of change. Mashups - user-generated applications that integrate new data into existing applications - are beginning to gain attention in the scientific world. For example, AntBase and AntWeb bring together data on 12,000 species, using Web services. And a mashup that Butler created single-handedly, mapping poultry density per nation and outbreaks of avian flu over Google Earth, resulted in six nations contacting him about a collaboration....
Jim Ostell, chief of information engineering at the National Center for Biotechnology Information (NCBI), explained the design principle behind the NCBI site that has resulted in ever-increasing amounts of traffic. The NCBI site, which includes PubMed, PubMed Central, GenBank, and other public databases, has become a content aggregator that allows users to make connections across various fields, said Ostell. When linking information, the “central dogma” is key. This means selecting elements that are things and then finding “computable values” between them....Ostell also pointed out that the NCBI is working on the Discovery Initiative to present users with deep links for their topic....Timo Hannay, director of Web publishing for Nature Publishing Group, presented Web 2.0 projects under development, including the Open Text Mining Interface (OTMI), and Connotea.org, which helps researchers organize and share their references.
Comment. I hope someone at the conference mentioned that the first step in optimizing scientific datasets for useful mashups is to make them open access. Or is everyone just taking for granted that OA is the future, both for research literature and research data, and planning how to take full advantage of it?
Posted by
Peter Suber at 4/06/2006 02:12:00 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.
I recommend the OA tracking project (OATP) as the best way to stay on top of new OA developments. You can read the OATP feed on a blog-like web page or subscribe to it by RSS, email, or Twitter. You can also help build the feed by tagging new developments you encounter.
