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Blog archive for July, 2008

WSJ: Putting Drug Development in Patients’ Hands

July 29th, 2008 by dwentworth

The Wall Street Journal has an article today featuring Marty Tenenbaum and CollabRx, one of our partners in the Health Commons project. The piece, Putting Drug Development in Patients’ Hands, explores how patients are using the Internet to take the reins in developing drugs for disease — especially rare and neglected diseases for which drug discovery has yet to prove commercially viable. Among the strategies patients are pursuing:  funding their own “virtual” pharmaceutical companies, tasked to specific diseases.

One patient profiled in the article, Bonnie J. Addario, is a lung-cancer survivor who turned to CollabRx for help. Addario began the search for a cure using the traditional approach. After raising $800, 000 and distributing it to researchers, she was struck by the realization that despite the hard work going into the research, lung-cancer survival rates hadn’t changed in 40 years. Addario and her husband convened a conference with researchers to uncover hidden roadblocks:

[The] group identified a number of problems that hinder progress toward a cure. Among them: Researchers didn’t know what others were doing, tissue and blood specimens needed for experiments weren’t centrally located or shared, and the findings of experiments weren’t integrated to help assess what the key priorities should be.

The Health Commons, also discussed in the article, was launched to help make it easier for anyone to pull together the resources necessary for advancing disease research, without the legal wrangling commonly associated with securing access to research, data and unique research materials like cell lines. This includes implementing standardized, machine-readable agreements to facilitate intra-academic and academic-industry transfer of biological materials.

“The Health Commons is creating the legal and technical foundation for a friction-free, point-and-click marketplace like Amazon or eBay, so disease research isn’t bogged down by needlessly complicated, costly legal negotiations,” explains John Wilbanks, who leads Science Commons. “Some resources may be freely available; others may be available for a fee. But if it’s in the Health Commons, it will be a swift, permissionless transaction, because permission will have already been granted.”

Our founding partners in the Health Commons are CommerceNet, CollabRx and the Public Library of Science.

To learn more about the Health Commons, visit the project page, where you’ll find a white paper co-authored by Wilbanks and Tenenbaum, plus a 6-minute video introduction to the project.

A public commitment to open science

July 28th, 2008 by dwentworth

Good design choices are the key to powerful network effects. And when the goal is accelerating scientific research, there may be no more powerful design element than institutional policy. By making the right policy choices, people at institutions can help usher in new norms for knowledge sharing — where research results are systematically “plugged into” the network, multiplying the opportunities for discovery.

Boston University’s Superfund Basic Research Program (BU SBRP) has embarked on just such an endeavor. The program, which works to uncover the effects of improperly managed hazardous waste on reproductive health, has published its own open science policy. The policy is a declaration of BU SBRP’s commitment to sharing research, and outlines the methods it uses to make the results freely available to anyone who can use them:

Our SBRP program holds the view that publicly supported scientific knowledge and tools produced by research programs like ours should be freely available and accessible. On this web site we have implemented our commitment to open science in different ways, including using new web-based technologies and alternative approaches to licensing work that make the vision of shared research possible. …

The use of open source wiki software encourages communication and collaboration on research, both externally with the public and internally within a research group. BU SBRP is developing an internal wiki for research collaborations.

RSS (Really Simple Syndication) allows subscribers to automatically see the latest products of research, including new publications, events, and research tools freely accessible through a web site.

Emerging permissionless licensing systems allow researchers to choose the terms under which they want to share their work; these include Creative Commons Licenses and the General Public License.

Finally, open access journals are those which make content available to everyone, without requiring a subscription. With the emergence of web-based publishing, this model can make research more easily available to more researchers in more locations. A list of open access journals can be found at DOAJ.

Acknowledging that the outputs of research “come in many forms,” the program uses these tools in many different ways:

Statistical techniques and computer code for modeling environmental exposures and health outcomes can be licensed through permissionless systems, written in open source languages and fully commented, and shared through a wiki. Laboratory methods and synthetic data created to test different techniques can also be shared, updated, modified by individual researchers or collaboratively, and discussed through wiki software. Published articles can be made accessible through Open Access on-line journals.

In publishing the policy, BU SBRP seeks not only to provide information about its approach, but also to develop a “compelling model” for other research programs dedicated to sharing “scientific findings, analytical tools, data, and research methods.”

It’s an extremely promising and worthwhile project. Kudos to BU SBRP for helping to define and propagate new norms for knowledge sharing that can foster the growth of open science.

Galapagos NV: drug discovery innovator

July 24th, 2008 by dwentworth

Not long ago, GlaxoSmithKline (GSK) made headlines with its “Massive Cancer Information Giveaway“: a gift of over 300 cell lines derived from a wide variety of tumors, including breast, prostate, lung and ovarian cancers. The cell lines were made freely available to cancer researchers via the National Cancer Institute’s caBIG, with the goal of “crowdsourcing” the search for predictive biomarkers, making clinical trials shorter and, ultimately, getting drugs more quickly to people suffering from disease.

Now Galapagos NV, a Belgium-based drug discovery company, is following in GSK’s footsteps. The company is making freely available several proprietary databases of information about small molecules and proteins through the EMBL‘s European Bioinformatics Institute (EMBL-EBI). With funding from the Wellcome Trust, EMBL-EBI is returning the data to the public domain — precisely what we recommend in the Science Commons Protocol for Implementing Open Access Data.

“This makes the scientific data that Galapagos has gathered an extraordinary gift — not just to science, but to open science,” says John Wilbanks, who leads Science Commons. “Returning the data to the public domain removes the legal barriers that prevent us from making full use of the latest technologies for data integration and analysis. The Galapagos data can now be used in ways no one can anticipate — the very definition of innovation.”

Building the foundation for open science

July 23rd, 2008 by dwentworth

The New York Times ran a much-discussed piece this week on open science and our colleague Karim Lakhani at the Harvard Business School: If You Have a Problem, Ask Everyone. John Wilbanks was with Lakhani at OSCON when the story broke, speaking at a forum on participatory cultures.

The piece gives a tantalizing glimpse of the potential for open science. With a foundation in a shared legal and technical framework, we could scale initiatives like the ones Lakhani has identified, with the Web itself functioning as an innovation engine for science.

That was the impetus behind the open science workshop we held last week in Barcelona in conjunction with ESOF 2008. We’ve now published our recommendations [PDF] for foundational principles to help foster the growth of open science across the globe — a way to connect and empower the people and organizations using open approaches to accelerating discovery. It provides definitions for four pillars of open science: open access to literature, access to research materials, open data and open cyberinfrastructure.

“We have to look hard at the foundations of science on the network and advocate ceaselessly for the necessary upgrades — to science as well as the network — that will allow us to get millions of new eyes on science, asking millions of new questions,” writes Wilbanks in a post on his blog at Nature Network. “Until that happens, we won’t really have a digital science culture. We’ll have simply made the old problems into digital problems.”

We’re grateful to all of the participants for joining us and helping to make the workshop a success. Special thanks go to Dr. Cameron Neylon, who not only participated but also blogged the event at Science in the open, sharing his insights with the community at large. Here are links to his notes, along with a few brief excerpts:

  • Policy and technology for e-science: a forum on open science policy: “James Boyle (Duke Law School, Chair of board of directors of Creative Commons, Founder of Science Commons) gave a wonderful talk (40 minutes, no slides, barely taking breath) where his central theme was the relationship between where we are today with open science and where international computer networks were in 1992. He likened making the case for open science today with that of people suggesting in 1992 that the networks would benefit from being made freely accessible, freely useable, and based on open standards.”
  • Policy for open science: the wrap-up session: “The benefits of the open web come from the explosion of people actually using a computer network. We must think of the users of an open-architected science [having] the same potential for explosion. “
  • Policy for open science — reflections on the workshop: “The workshop that I’ve reported on over the past few days was both positive and inspiring. There is a real sense that the ideas of Open Access and Open Data are becoming mainstream. As several speakers commented, within 12-18 months it will be very unusual for any leading institution not to have a policy on Open Access to its published literature. …Open Data remains further behind, both with respect to policy and awareness. … We need to look critically at different models [for building a commons], what they are good for, how they work.”

We’re hoping to continue the fruitful conversations started the Barcelona workshop. If you’re interested in joining us, send us an email to let us know.

How open is that data?

July 21st, 2008 by dwentworth

Last week we shared the news about research Melanie Dulong de Rosnay has been conducting on the complexities of opening access to scientific data. The research has now been published over at Nature Precedings, in the form of a paper entitled, Check Your Data Freedom: A Taxonomy to Assess Life Science Database Openness.

“Molecular biology data are subject to terms of use that vary widely between databases and curating institutions,” writes de Rosnay in the abstract. “[This paper] builds upon research led by Science Commons demonstrating why open data and the freedom to integrate facilitate innovation and how this openness can be achieved. … [Most terms of use for databases] are not harmonized, [are] difficult to understand and impose controls that prevent others from effectively reusing data.”

To address the problem, the paper proposes a “checklist for data openness…to assist database curators who wish to make their data more open to make sure they do so.”

That’s not all. Our outstanding research assistant, recent MIT graduate Shirley Fung (S.B. 2007 and M.Eng 2008), helped de Rosnay with the project and has published a website that lets anyone explore and evaluate the legal and technical openness of the sample set of scientific databases (and submit more databases). Here’s a look at the home page:

Find Open Data

Browse a list of databases compliant with the Science Commons Open Access Data Protocol

Browse Policies

View databases categorized by their technical and legal accessibility regimes

Classified Databases

Find all the databases classified by the project. You also may want to use the “Browse Policies” section for a specific kinds of databases

Submit Policy

Use the questionnaire to submit a database policy to our system

If you have questions about the project, let us know.

On the complexities of sharing scientific data

July 16th, 2008 by dwentworth

Ethan Zuckerman, the Berkman fellow who founded Geekcorps and co-leads Global Voices with Rebecca MacKinnon, has a nice piece today on our efforts to clear the legal hurdles blocking the integration of scientific databases, highlighting research by Melanie Dulong de Rosnay (see our post from earlier this week).

Writes Zuckerman at World Changing:

Creative Commons is a clever use of the copyright system intended to make it easier for people who want to, to share their work with others. Jonathan Coulton has used Creative Commons to enable an army of remixers and videomakers to produce promotional materials for his songs and albums. Authors like Dan Gillmor and Cory Doctorow have used Creative Commons to let people download, translate and make audio versions of their books. And Global Voices uses Creative Commons so that blogs and news sites can use our content without asking us for permission.

What about scientists?

[...]

Under US law, pretty much anything you write down is copyrighted. Scrawl an original note on a napkin and it’s protected until 70 years after your death. Facts, however, are another matter – they can’t be copyrighted. So while trivial but creative scribblings are copyrighted, unless you choose to release them into the public domain, the information painstakingly discovered about the human genome – DNA sequences, for instance – aren’t. But the containers they’re stored in – the databases they’re held in – can be copyrighted.

If I sound confused about this stuff, that’s because I am.

[...]

This question of complexity is what Melanie’s research has focused on. She looked at the terms of use for roughly 200 databases necessary for work in the life sciences. Evaluating the terms on all those databases, she discovered that only 7 met her stringent definitions of Open Access to data – these databases could be accessed without registration; they could be downloaded for local use; they could be incorporated into other works; they had clear, understandable terms of use. This last factor proved to be the most challenging. She spent hours reading these terms with other experts in the field and discovered that, a great deal of time, the experts disagreed on what was permitted under a specific agreement.

The reason this is important, Melanie explains, is that scientific research proceeds more quickly when researchers can share resources. But with databases encumbered by different, confusing legal protections, it can become a legal nightmare for researchers to do complex work building new tools that combine information from two databases in a novel way, for instance. And databases that are protected by access restrictions can be out of reach to scientists in developing nations who might not have the financial or technical resources to access them.

So how do you deal with the problem of conflicting terms of use for the “containers” of scientific data?

As Zuckerman points out, we initially offered advice aimed at helping database publishers figure out when it made sense to use Creative Commons licenses. But it was evident that this wouldn’t solve the problem.

After further research, Science Commons collaboratively developed and published the Protocol for Implementing Open Access Data, through which we recommend explicitly returning the data to the public domain, using legal tools like the CC0 waiver or the Open Data Commons Public Domain Dedication and License (ODC-PDDL).

If you’d like to learn more about the protocol, we encourage you to check out the FAQ or send us an email. We’re happy to answer any questions you may have.

Video: Timo Hannay on CC-based science publishing

July 14th, 2008 by dwentworth

In case you missed it over at Open Access News, there’s a new 3-part video documentary on publishing open content using Creative Commons licenses. Part two (below) is an interview with Nature’s Timo Hannay — an especially interesting bit in light of the recent discussions about business models for sustainable open access (OA) publishing.

If there’s anything that the interview makes clear, it’s that scientific publishing is undergoing a profound transformation, and people in OA are confronting its most difficult challenges head-on. They’re freeing science while providing us with valuable lessons about the kinds of publishing models that can work in the digital era — a boon on both counts.

Melanie Dulong de Rosnay on opening access to science

July 14th, 2008 by dwentworth

This spring, Harvard’s Berkman Center launched the Publius Project, which ccLearn‘s Jane Park aptly called a “Web 2.0 version of the Federalist papers.” The concept:  a diverse group of thinkers — scholars, technologists, activists and others — would publish essays about the “constitutional” moments shaping Internet governance. The essays, and responses to them, would serve to seed a broader discussion about the choices we’re making as we collectively build the future of the networked world.

Peter Suber penned an essay entitled The Opening of Science and Scholarship, asking who controls peer-reviewed research, and arguing for a future where scholars themselves ensure it is open access (OA). The latest response, written by Berkman Fellow Melanie Dulong de Rosnay, focuses on opening access to scientific research. De Rosnay is the legal lead of Creative Commons France, and works with us here at Science Commons on open data policy. She asks:

How can society take advantage of the opportunities offered by digital publishing and distributing to share scientific results more quickly and thus facilitate the discovery of new knowledge? … Should we simply ensure access to knowledge without paying a fee, or should we do even more to improve that access, such as enhancing legal and technical capabilities for finding, extracting, annotating and compiling information in order to make better use of it?

De Rosnay’s answer:  to take full advantage of OA’s benefits, we should lift all three barriers to access identified in the Budapest Open Access Initiative definition:  financial, legal and technical. That way,  she writes, “researchers and the public can not only access, but also redistribute and reuse materials in any way, including ways that initial creators had not considered.”

In other words, if we want more innovation and discovery to come from OA research, we should be designing for it — publishing research and data in open formats, with the legal rights “baked in” to make use of it.

If you’d like to hear more from de Rosnay, she’ll be giving a presentation on “Openness for Life Science Databases” tomorrow, Tuesday, July 15th, as part of the Berkman Center’s terrific luncheon series. There may still be spots open if you want to join in person, but if not, anyone is free to watch the live webcast or view the archived video when it is posted. You can find all the details here.

Where’s the CC in Science Commons?

July 10th, 2008 by dwentworth

When I joined Science Commons last year, that was the question at the core of the queries I got from curious friends. In most cases, they “got” Creative Commons — it was about freeing culture with licenses for the legal sharing and remixing of creative works. Science Commons, they reasoned, must be about freeing science by creating special licenses for sharing and remixing scientific research.

We do work to “free” science — that is, to make it easier to legally share, integrate and remix research and data, with the goal of accelerating discovery. But you won’t find any specialized licenses at Science Commons. Indeed, when the goal is integration of open scientific databases published under different jurisdictions, we advise against using licenses of any kind, including the CC-BY license.

So what exactly is Science Commons doing, and where’s the CC in it? Glad you asked. Last month, Creative Commons held its first TechSummit, which was graciously hosted by Google. John Wilbanks, who leads Science Commons, gave a short talk on our work, showing what the CC methodology “looks like” in the world of science rather than culture. You can watch the presentation by clicking on part 1, below, which begins with the keynote address by Creative Commons CEO Joi Ito (the Science Commons talk is at 1:05/1:21.53).

Of course, there were lots of other interesting presentations at the TechSummit, which brought together folks from every corner of CC. You can check out the details at the Creative Commons blog, and watch parts 2, 3 and 4 on YouTube.

If you watch the Science Commons presentation and have questions about our mission, methodology or any of our projects, feel free to send us an email. We’re happy to provide more detailed information.

Collaborating for breakthroughs

July 4th, 2008 by dwentworth

Over at the FasterCures blog, Margaret Anderson, the organization’s Chief Operating Officer, has a post on the recent Institute of Medicine forum: Breakthrough Business Models: Drug Development for Rare and Neglected Diseases and Individualized Therapies. Anderson, who moderated a panel at the forum, observes that while the Michael J. Fox Foundation is often cited as an example of what’s working well, surprisingly few research foundations embrace its innovative approaches. Key among them:  pursuing collaborations with for-profit companies.

The focus of the forum was on finding new models for drug development, and many speakers echoed Anderson in emphasizing the need for more public-private collaboration. Our own Kaitlin Thaney was there, and spoke with fellow participants about our newest project, the Health Commons. The project, launched in collaboration with CommerceNet, CollabRx and the Public Library of Science (PLoS), is designed specifically to lift barriers to collaborations among non-profit and for-profit entities.

“In the Health Commons, participants agree to share data, knowledge, materials and services under standard, pre-negotiated terms and conditions,” explains Thaney. “That way, resources can move smoothly among participants, without the legal wrangling and delays that can derail collaboration.”

One of the most troublesome areas, for foundations and companies alike, is materials transfer. On the panel that Anderson moderated, Michael Mowatt, who directs the Office of Technology Development at the National Institute of Allergy and Infectious Diseases, NIH, described how using standardized agreements and repositories can facilitate collaboration, and explained how our Biological Materials Transfer Agreement (MTA) project lays the groundwork for “virtual repositories” of biological materials.

You can find more information about the MTA project here. If you’d like to learn more about the Health Commons, you can check out the white paper or video introduction at the project site.  And if you’d like more details on the IOM forum, you can find the agenda and a collection of audio recordings and slides at the IOM forum website.

Update: Public Knowledge co-founder David Bollier has a post sharing his reflections on the Health Commons project:

For those of us who don’t venture into the laboratories of science, it’s difficult to appreciate how fragmented, proprietary and inefficient drug and disease research truly is. At a time when the Internet is making it easier than ever to share and collaborate, some of the most well-funded, high-tech scientific projects today still operate in their own isolated silos. They are effectively cut off from vast quantities of potentially useful research, scientific literature, emerging ideas and potential collaborators. [...]
Tenenbaum and Wilbanks are two of the champions behind an ambitious new project, Health Commons, which aspires to build a new ecosystem for scientific research.