Blog archive for January, 2008

Speeding drug discovery through the Semantic Web

January 28th, 2008 by dwentworth

One of the most important reasons Science Commons exists is to help people find cures for disease faster. So we are delighted and honored to have made the FasterCures list of Ten to Watch in 2008 — recognizing “the top ten organizations, people, and ideas that are changing the face of biomedical research in 2008.”

FasterCures is a nonprofit organization dedicated to “saving lives by saving time.” FasterCures President Greg Simon, who oversaw a wide range of national scientific research initiatives as Chief Domestic Policy Advisor to former Vice President Al Gore, writes:

Collaborative science is the name of the game these days, as science gets bigger and more multi-disciplinary and the data available for research grows explosively. The technological opportunity presented by the Semantic Web for networking data and researchers will be transformative. Watch the Neurocommons Project, a demonstration of the power of the Semantic Web approach based on open access information.

What is a “Semantic Web” approach, and how can it help us meet the challenge of so-called network science?

In the simplest terms, it’s a way to mark research data so computers can help us make sense of it. The driving concept is that collaboration in science needs to make a shift from human-mediated to computer-mediated, from single-database access to data integration, from reading papers by people to reading papers with machines, and so on.

As part of the Neurocommons Project, we mark research that’s free to use — open access information — using the Semantic Web RDF language. This means that computers — not people — can sort through the data, giving researchers the ability to swiftly process much larger data sets. And that means that the research won’t simply be more accessible, it will also be easier to use — leading, we hope, to more (and faster) breakthroughs that benefit everyone.

Could the key to feeding the world be locked up in a company fridge somewhere?

January 10th, 2008 by dwentworth

That’s the question Australia’s Science Show asks to introduce a newly available podcast discussion featuring Science Commons’ own John Wilbanks and Brian Fitzgerald, who heads up Creative Commons Australia. The question isn’t nearly as tongue-in-cheek as it sounds; the discussion is about how to unlock the value of scientific research when so much of it is routinely balkanized — hidden away behind walls of secrecy, cost and technical obscurity.

At Science Commons, we work to make scientific research easier to find, share and use. This includes providing tools to “mark” research with usage rights, so scientists can work and collaborate within zones of legal certainty. But as Wilbanks explains in the lecture, “we need freedom to innovate, not simply freedom to operate” — something that requires more than developing licenses and contracts:

I think it’s clear that we face an exponential set of problems but we don’t have an exponential innovation capacity…we need to think about what we can do to enable that innovation to emerge.

If you’d like to learn more about what Science Commons is doing to spur innovation and discovery in science, follow the link above to the podcast (and podcast transcript) and browse our slides for the lecture.

Why we need to figure out what we already know

January 4th, 2008 by dwentworth

Over at Corante’s In the Pipeline , organic chemist Derek Lowe has a post that vividly demonstrates one of the unfortunate realities of the research environment: researchers can spend years “discovering” what’s already been discovered. In a recent case that Lowe cites, a group of researchers somehow managed to publish two papers documenting a chemical reaction that was discovered no less than a century ago:

Professor Manfred Cristl of Wurzburg, who apparently knows his pyridinium chemistry pretty well, recognized [the reaction] as an old way to make further pyridinium salts…. He recounts how over the last couple of months he exchanged awkward e-mails with the two sets of authors, pointing out that they seem to have rediscovered a 100-year-old reaction, and have they really looked at their spectral data closely, eh?

This kind of mistake is incredibly embarrassing; you can easily imagine a chemistry professor using it as a cautionary tale to help students understand the importance of a thorough literature search. But it also has deeper implications. One of the most common myths about the Web is that it makes mistakes like this impossible. If Google knows all, why not ask it to tell us everything there is to know about pyridinium chemistry?

Of course, it doesn’t work like that, for a number of reasons. One is that Google uses text-based matching to find web pages, and its method for determining whether a particular page is relevant relies in large part on the number of people who have linked to it. This is a useful for finding lots of things — especially consumer products. It doesn’t work nearly as well for scientific research.

At Science Commons, we want to enable scientists to use the Web to get precise answers to complex research questions — not 388,000+ search results that contain the word pyridinium. We hope to do much more than help researchers avoid embarrassing mistakes. We want to empower them to build on existing knowledge, so they can take the next steps toward discovery without having to repeatedly double-back.

John Wilbanks, who leads Science Commons, has a personal blog over on Nature Network, where he’s been sharing his ideas for realizing this vision. He writes: “[We] have to date published our knowledge in formats designed for a different world. One idea, one lab, one gene, one protein, one paper, one database. [If] we can mark up the knowledge better, we can do a lot better without a gee-whiz theoretical breakthrough, just by better using what we do indeed already know.”

If you’d like to learn about how Science Commons is “marking” knowledge, check out our Neurocommons project — an initiative aimed at demonstrating how a Semantic Web approach to making information useful can help us figure out what we already know.