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Sunday, May 25, 2008

Introduction to the Health Commons

John Wilbanks, Executive Director of Science Commons, has made a 6.5 minute video on his vision for a Health Commons.  I recommend it as a succinct overview of the obstacles slowing down the development of new cures and the solution he's proposing.

For more detail, see the just-released white paper he co-authored with Marty Tenenbaum, Health Commons:  Therapy Development in a Networked World, May 2008.  Tenenbaum is the founder of CommerceNet and CollabRx.  Excerpt:

The current path to drug discovery also perpetuates old traditions of information and intellectual property control. This deeply set inability to capture collective learning dooms everyone to revisit infinitely many blind alleys. The currency of scientific publication encourages individual scientists to hoard rather than share data that they will never have the time or resources to exhaustively mine. And, the wealth of “negative” information gleaned from clinical trial data is mostly lost to the need for companies to safeguard their commercial investments. Although computational and systems biology, aided by Moore’s law, make it feasible to systematically search the vast space of targets, leads, and interactions, this potential is limited in practice by lack of access to data, compound libraries, specimens, and shared services essential for economies of scale. As a result, many biological promising leads, and the knowledge surrounding them, are ultimately discarded.

Thankfully, we have a rare moment in time where we can change the entire system in one motion by establishing a collaborative ecosystem of knowledge and research services that can be rapidly assembled to develop new therapies with unprecedented efficiencies and economies of scale. We can create the same radical increase in efficiency for scientific research that commerce saw in the 1990s, as secure Internet transactions transformed many vertically integrated industries into horizontally integrated ecosystems of service providers and consumers. The explosion of contract vendors in biotechnology, covering the spectrum from gene to protein to drug discovery, development and trials, is one factor. The emergence of the Semantic Web for science is part of the story, as is the existence proof that common use licensing can create explosive value in software and culture. And the power of the network to bring these elements together into a unified system, a Health Commons, is the final piece of the puzzle....

Health Commons is a coalition of parties interested in changing the way basic science is translated into the understanding and improvement of human health. Coalition members agree to share data, knowledge, and services under standardized terms and conditions by committing to a set of common technologies, digital information standards, research materials, contracts, workflows, and software....

Scientific publishing is integral to the drug development process. But in the digital age, we must question whether the unit of a published paper is really the most efficient means of disseminating scientific knowledge. The elegance, clarity, and value of a carefully assembled, constructively peer-reviewed, professionally copy-edited and laid-out research article is clear. However, in this process, much information is delayed, or worse, lost. Interim data and results are typically discarded, especially the results of failed experiments, dooming others to waste time rediscovering them over again. Clinical trial data may never be published; a trial that fails because of an unknown toxicity, for which data has been captured previously, is both expensive –-- and tragic for the patients involved. Although journals and funding agencies are committed, in principle, to requiring data associated with publications be made available, in practice, this only succeeds in the few cases for which community endorsed repositories exist. And beyond access to data, there’s the deeper issue of making the conclusions conveyed in a scientific paper available in a structured form that can be understood and manipulated by computers as well as human scientists.

In Health Commons, all this will be different.  By integrating the TOPAZ publishing platform, which currently supports PLoS ONE, into Health Commons, publication of research results will be a visible and automatically staged process. Knowledge will simply be promoted from one’s personal repository in the Commons to be shared with one's laboratory, shared with one's collaborators, and ultimately to be made publically accessible. PLoS, along with other participating publishers, will provide vetting at many levels from community voting to review boards, as appropriate. Review by one's peers will occur at many stages: formal editorial boards could still provide traditional journal imprimaturs alongside more radical experiments in community voting....

Beyond ensuring timely access to knowledge by humans, semantic annotation is also the key to making that knowledge machine-understandable....

Because the range of potential applications is unlimited, computer access to published data and knowledge is likely one day to be at least as important as eyeball access....

The Health Commons is too complex for any one organization or company to create. It requires a coalition of partners across the spectrum....

Health Commons is a new and very practical project, not just a plan or vision.  The founding partners are Science Commons, CommerceNet, Public Library of Science, and CollabRx .