Blog archive for the ‘weblog’ Category

NPR’s Science Friday program has now posted its interview with Harold Varmus on the landmark NIH open access mandate, which went into effect this past Monday. Varmus, the former NIH director who co-founded the Public Library of Science (PLoS), talks about what the mandate means for the future of biomedical research, fielding questions about everything from freeing dark data to expanding access to orphan disease research to reclaiming our scientific heritage in the literature.

Among the many other excellent points he makes, Varmus argues that more research funders should adopt open access policies — not only to magnify the impact of the research they fund, but also to open it to innovative uses:

You can imagine that if you were a funder of science anywhere in the world, you would want the results that you paid for to be out there for everyone — not just to see, but to work with. Indeed, the way in which one works with the information is extraordinarily important in this day in which we use the computer to mine research data for new ways to think about things.

Amen.

In case you missed it earlier this week, here’s Varmus’s PLoS editorial on the mandate: Progress Toward Public Access to Science. For more information about the NIH mandate going forward, including university-sponsored resources for authors, check out SPARC’s NIH implementation page.

The Scientist has a not-to-be-missed piece this month on the National Cancer Institute’s caBIG, the Cancer Biomedical Informatics Grid. The article, Heading for the BIG Time (free registration required), was written by caBIG founder Kenneth Buetow, and serves as an excellent introduction to the reasons why we need a collaborative infrastructure for knowledge sharing in science — one that works, to use Buetow’s phrase, as a “smart World Wide Web” for research.

“From my position as a senior cancer researcher at the NCI, groundbreaking observations and insights in biomedicine are accumulating at a dizzying rate. However, from the perspective of the approximately 1.4 million US patients who will hear their physicians say, ‘You have cancer,’ progress is unacceptably slow,” explains Buetow. “Something needed to be done to expedite the transformation of scientific findings into clinical solutions.”

That’s a daunting challenge, says Buetow, especially given the nature of the disease and the way research is currently done. “Cancer is an immensely complex disease, and in order to get a sense of the big picture, scientists need to combine observations from genomics, proteomics, pathology, imaging and clinical trials,” he says. “There was, however, no systematic way to do this.”

The caBIG solution: figuring out what kinds of data could be shared, and then connecting more than 60 NCI centers of cancer research using a strategy of “standards-based interoperability,” where information is shared and accessed using common standards and tools. The results so far are promising: the caBIG community is growing, and people are already adding new tools that increase the utility of the shared data.

We’re proud to have been a part of the NCI’s ongoing discussions about intellectual property and data sharing recently, as well. John Wilbanks was a closing panelist at the most recent Data Sharing and Intellectual Capital meeting of the Grid. We look forward to continuing - and deepening - our relationship with the Grid over the coming months.

James Boyle, the new Chairman of the Board at Creative Commons and a founder of Science Commons, is holding a contest to design a cover for his new book, The Public Domain: Enclosing the Commons of the Mind. In the book, Boyle argues that more and more of material that used to be free to use without having to pay a fee or ask permission is becoming private property — at the expense of innovation, science, culture and politics.

Details, including specs and a link to some great source material for imagery, are available at the Worth1000 website. Both the book and the cover will be distributed under a CC Attribution-NonCommercial license.

If you’re curious about the current state of play in efforts to make knowledge sharing easier so we can solve problems faster, look no further. Science Commons Advisory Board member Hal Abelson — a founding director of Creative Commons, the Free Software Foundation and Public Knowledge — provides a big-picture perspective on these efforts in the latest podcast interview from MIT Libraries in its terrific series on Scholarly Publishing & Copyright.

“The way I first got into this is with software,” explains Abelson in the interview. “Prior to [the early ’80s], if there was a program around, you could contact the author and get a copy, and you could make it better — that was the key thing, to make it better. Around the mid-’80s, that stopped…Then it became kind of clear that this attitude — not sharing your software, and thus jeopardizing any kind of collective enterprise that could exist — was also going to be true for other kinds of copyrighted works, as they increasingly got online.”

You can download the full podcast here [MP3]. If you’d like to subscribe to the series, you can paste the following link into your iTunes or another podcast reader: http://feeds.rapidfeeds.com/6772/

Over the past few months, you may have noticed that some of the posts here have been attributed to a mysterious “dwentworth.” That’s me — Donna Wentworth — and I’m here to start bringing more of your voices to the Science Commons blog.

The introduction may seem a little late, but it’s for good reason: I’ve had a lot learn. I’ve been writing about innovation and the net for ten years now — first at Harvard’s Berkman Center for Internet & Society and Corante, and then at the Electronic Frontier Foundation and Google. I’ve been a supporter of Creative Commons from the very beginning, as well as a fan of the eloquent James Boyle. Back in the fall, when I stumbled on a video of Jamie’s presentation at Google on Science Commons, I was riveted. Here, I thought, is where Creative Commons can make a difference on a whole new level — where innovative ways of licensing and sharing knowledge could actually end up saving lives.

A talk with my old friend from the Berkman Center, John Wilbanks, who now leads Science Commons, got me even more excited. Always full of infectious enthusiasm, John made it easy for me to see the possibilities for the “open science” movement — where a series of small but important changes could set in motion a profound transformation in the way research is carried out. I decided to join the SC staff to see what I could do to help, including bringing more people into a common discussion about what the next steps should be. But before jumping in, I needed to take a look around, see where the conversations were already happening and figure out how these conversations are being translated to action.

Here’s where you come in. If you’re reading this blog, chances are you’re passionate about the future of science. You may even be a part of the vast, incredibly diverse community of people that actually make science happen: scientists, publishers, research company representatives, research foundation officers, computer scientists, entrepreneurs, librarians and more. Some of you may be bloggers yourselves, who track developments in your area of science and ended up at Science Commons once or twice.

My hope is that you’ll join me in turning up the volume on the conversation surrounding open science. As part of this effort, I’m going to start profiling individuals and organizations working to open new frontiers for innovation and discovery in science. I am also building a community blog roll — or a public aggregator, if that works better — for open science. The goal isn’t to endorse particular viewpoints or blogs, but instead to showcase the work that’s already being done to midwife a new way of sharing and building scientific knowledge, as well as to start identifying ways we can all work together.

With more open research coming online, the freedom to integrate information from disparate sources, and the ability to use computers to sort through and make sense of it, scientists will be more empowered than ever to find the answers they’re looking for. Let’s figure out how we can get there faster.

Please take a few minutes to send me an email or add a comment to this post with your choices for people and organizations to profile here at Science Commons, as well as your favorite blogs and other resources on open science. I look forward to hearing from you.

Heather Morrison, who’s been tracking the growth of open access to medical literature, has posted baseline figures for the percentage of literature on cancer that’s freely available online in full text format, pre-NIH mandate:

Cancer:
13% of the literature in PubMed on cancer links to Free Fulltext.
By publication date range:
7% - within last 30 days
10% - within the last year
17% - within the last two years
21% - within the last 10 years

Opening access is the foundation for making the medical literature useful in the digital era, facilitating machine-assisted research using Semantic Web technologies — something that will become even more critical once the mandate goes into effect and the percentage of open literature starts rising.

(Hat tip to Gavin Baker @ Open Access News)

Open access leader Peter Suber answers that question in the characteristically thorough and engaging lecture he gave on March 17th at Harvard’s Berkman Center for Internet & Society. The talk, co-sponsored by the Berkman Center, Science Commons and Harvard’s Center for Research on Computation and Society, gives a tour of five ways that universities can promote open access to research:

• launching and filling their own OA repositories
• supporting peer-reviewed OA journals
• supporting OA monographs from their university presses
• fine-tuning their promotion and tenure criteria to support excellent research even in unconventional places
• educating faculty about copyright and OA itself

The Berkman Center has now posted video and audio of the entire lecture and ensuing discussion, and the slides are available here. And if you’re interested in responses, check out Stevan Harnad’s detailed commentary, as well as Suber’s reply at Open Access News.

Here at Science Commons, we’re working to improve human health — to cure diseases and save lives. And if human health is the goal, and innovation the engine, then we have to start using all the information available, and using the best technologies on that.

In that spirit, Science Commons Principal Scientist Alan Ruttenberg is participating in this year’s BioIT World Conference & Expo in Boston, where he’s conducting a pre-conference workshop entitled Harnessing the Semantic Web for Your Organization. Ruttenberg is the chair of the W3C’s Web Ontology Language (OWL) Working Group, and a coordinating editor of the Open Biomedical Ontologies (OBO) Foundry. The workshop, which takes place from 8:00 a.m.-12:15 p.m. on April 28th, will show how Semantic Web technologies are being used to solve the difficult data integration challenges that are prerequisite to making effective progress in areas such as translational medicine, understanding mechanism of action and efficient management of regulatory documentation.

If you’re going to BioIT World and you’d like to learn more about the Semantic Web approach to accelerating research and discovery, join us. We hope to see you there.

One of the biggest challenges we face at Science Commons is explaining what we do — and, much more important, why it matters.

To that end, we are publishing a series of posts to bring more clarity to the terms and phrases we use. To make sure these posts are truly useful, we’ll be asking for your feedback. Got questions? Criticism? We hope you’ll send us an email or add your comments to the post. (Note: the definitions in these posts aren’t meant to be formal; they’re aimed at sparking discussion and helping more people understand our work.)

The first time out, we took on open source knowledge management. This time, we’re tackling “cyberinfrastructure.”

According to the National Science Foundation, cyberinfrastructure is “like the physical infrastructure of roads, bridges, power grids, telephone lines and water systems that support modern society,” but “refers to the distributed computer, information and communication technologies combined with the personnel and integrating components that provide a long-term platform to empower the modern scientific research endeavor.” (People in other countries use different terms for roughly the same concept; in the UK and Australia, for instance, cyberinfrastructure is referred to as “e-science” and “e-research,” respectively.)

It’s important to note that cyberinfrastructure is distinct from the Internet, which is only one of the elements that it comprises.

To understand the difference, consider the insightful piece that Alice Park of TIME wrote last year on why the promising new vaccine for AIDS failed, which looks beyond biological factors to examine the state of scientific research as a whole. Writes Park, “Most research occurs in isolation; there’s little coordination among labs and no network through which data can be shared, making it difficult for scientists to learn from each other’s missteps” (emphasis, mine). She goes on to quote Dr. Alan Bernstein of the Global HIV Vaccine Enterprise, who describes science as an “iterative process” where, regrettably, “there isn’t a lot of iteration going on.”

Of course, there is a network that we can use for sharing scientific data: the Internet. What’s missing here is infrastructure — but not in the purely technical sense. We need more than computers, software, routers and fiber to share scientific information more efficiently; we need a legal and policy infrastructure that supports (and better yet, rewards) sharing.

At Science Commons, we use the term “cyberinfrastructure” — and more often, “collaborative infrastructure” — in this broader sense. Elements of an infrastructure can include everything from software and web protocols to licensing regimes and development policies. Science Commons is working to facilitate the emergence of an open, decentralized infrastructure designed to foster knowledge re-use and discovery — one that can be implemented in a way that respects the autonomy of each collaborator. We believe that this approach holds the most promise as we continue the transition from a world where scientific research is carried out by large teams with supercomputers to a world where small teams — perhaps even individuals — can effectively use the network to find, analyze and build on one another’s data.

If you’d like to learn more about what we’re doing, you’ll find details in Cyberinfrastructure for Knowledge Sharing, a CTWatch Quarterly piece by our own John Wilbanks If you have questions, send us an email. We’d love to hear from you.

In the past few weeks, we saw two remarkable stories emerge from research in the life sciences — remarkable not just because they made headlines, but because they give us a tantalizing glimpse of the potential for a new kind of publishing in science.

In the first, as Aaron Rowe at Wired News reported and Cory Doctorow blogged, a pair of researchers from Australia developed a blood test for African sleeping sickness — a relatively simple test that Rowe points out can be conducted without the “fancy equipment found in upscale medical labs.” Notably, the researchers published the findings at PLoS Neglected Tropical Diseases under a Creative Commons Attribution License — making freely available not only the results but the lab protocols for conducting the test itself.

In the second, we discovered that butterflies may remember what they learned as caterpillars — findings that were published (once again) by PLoS, then picked up by multiple media outlets, including New Scientist, National Geographic, Science, Wired News and NPR’s Morning Edition.

So what do these stories have to do with the future of scientific publishing? The PLoS One tagline is “Publishing science, accelerating research,” and for good reason: it is one of the pioneering open access publishers demonstrating the value of moving beyond the paper metaphor in the digital age — so that publishing can serve the progress of science, not hamper it. In the traditional publishing model, we “reward” good science by locking it up with legal and technical restrictions — making it less, not more useful to the people who can make sense of it. PLoS One makes every article it publishes available under the Creative Commons Attribution License — enabling maximum redistribution and reuse of the research while ensuring that the authors retain their copyrights and are properly credited for their work.

At Science Commons, we’re working toward a future where a published “paper” is dynamic — or as UK journalist Richard Poynder put it, “no longer simply an article to be viewed by as many eyeballs as possible,” but “the launch pad” for verifying and extending research. When a researcher clicks through to read an article, for instance, she should be able not only to see how the research was conducted, but also to click to order the research materials she needs to replicate the data.

These articles represent just a snapshot of the brilliant research that’s already being published openly. With the NIH open access mandate going into effect on April 7, we’ll start to see even more of the benefits that new models for scientific publishing can bring.