Blog archive for the ‘weblog’ Category

34 new OA journals from Academic Journals

January 23rd, 2009 by Kaitlin Thaney

Academic Journals has listed 34 new journals that will go live in the next five months – all Open Access (OA), licensed under CC-BY.

Academic Journals publishes over 50 OA journals, ranging in topic area from the biomedical sciences to arts and humanities and legal studies. All works published by Academic Journals are under a CC-BY license – the least restrictive CC license. Each published work also involves a transfer of copyright to the publisher.

The first of these journals, the International Journal of Medicine and Medicinal Science is currently available. For a complete list of journals and their anticipated launch dates, visit Open Access News’ announcement. (Hat tip to OAN).

Open Innovation, iTunes University and Science Commons

December 15th, 2008 by Kaitlin Thaney

Over the past few weeks, a number of online media components have been posted on Science Commons – from videos and features on Open Innovation over at the Kauffman Foundation’s Web site, to John Wilbankslatest talk this past November in Tampa, Fla. as part of “iTunes University” and Digital Media in Health Care Leadership Symposium. Wilbanks is the Vice President of Science at Creative Commons.

Science Commons receives generous support from the Kauffman Foundation. Visit their web site for more information on the Science Commons project, as well as their recent feature, “Open Innovation: Rx for Improved Human Health” as part of their Advancing Innovation wing. In that piece, Wilbanks lays out the underlying theory behind our Open Innovation work, its relationship to access, and its footing in network theory.

He writes:

“[…] users can spend their time and money innovating, not negotiating permission to use the network. It’s why the Web, despite its significant disadvantages in functionality and user base at launch compared to Prodigy or AOL, crushed both of them in only a few years. The access principle, as applied in the network, fostered innovation because it shifted power from the owners to the network users.”

I encourage you all to also check out the accompanying videos on the Kauffman Foundations Web site, embedded into the articles linked above.

Also available, thanks to iTunes University, is one of Wilbanks’ latest talks from the Digital Media in Health Care Leadership Symposium. The event, cohosted by USF Health and Apple, Inc., was held this past November in Tampa, Fla., bringing together over 170 participants from academia and beyond to discuss new ways of incorporating emerging mobile technology and digital learning into health care and education. For more information, visit the conference’s Web site. You can download Wilbanks’ talk here.

Supporting the Commons: Jesse Dylan and Richard Bookman

December 8th, 2008 by Kaitlin Thaney

Today, we are proud to announce the release of Science Commons’ first informational video. The video was directed by renowned director Jesse Dylan, the director of the Emmy- award winning “Yes We Can” Barack Obama campaign video with musical artist from the Black Eyed Peas. The video can also be seen on the front of

“I believe Science Commons represents the true aspiration of the web, and I wanted to tell their story,” Dylan said. “They’ve changed the way we think about exploration and discovery; the important and innovative ideas need to be shared.  I believe it’s vital to revolutionizing science in the future.  I hope this is just the beginning of our collaboration.”

This video is launched in conjunction with a letter of support from Richard Bookman, the Vice Provost for Research and Executive Dean for Research and Research Training at the University of Miami. Bookman joins a group of esteemed Commons supporters featured in this year’s “Commoner Letter” series, including this year:  Eben Moglen of the Software Freedom Law Center and Columbia University, Renata Avila – CC Guatemala Project Lead, and singer/songwriter Jonathan Coulton. More information and an archive of past letters can be found at

In his letter, Bookman writes:

“We need to find ways to make sharing research results and tools easy, trackable, and useable by scientists on a day-to-day basis. Science Commons is working on these problems in a way that few other projects contemplate: they don’t write papers, they release “running code” like contracts for sharing biological materials and open contracts for biological tools like stem cells and  genetically modified mice. […]

I support SC/CC because I think it’s the right approach at the right  time. It’s vital that we as a community support the organization – the  interstitial nature of what gets done at CC makes it harder than many  might think to raise money, which can leave the most important work  dying for lack of funds.

I hope everyone in the community can dig deep and support CC during this campaign. When you support CC, whether because of the cultural work, or the education work, or the science work, you’re supporting an  organization that is much more than contracts and websites and videos.  You’re supporting an umbrella organization working around the world that lives and breathes the “some rights reserved” philosophy.”

Our thanks to Jesse Dylan, Professor Bookman, and the broader CC community for their ongoing support. For more information about the campaign, or to show your support, visit Every little bit counts. Help support the Commons.

Open Access wins

December 5th, 2008 by Thinh

Our friend Mike Rossner from the Rockefeller University Press (RUP) has informed us that they have launched a browser-based system, called JCB DataViewer that renders in jpeg original image files associated with their articles, all of which are available under a CC-NC-SA 3.0 license after six months.

RUP recently adopted CC licensing for their journals, including the prestigious Journal of Cell Biology. Their articles are available online under NC-SA after six months from publication, whereas for the first six months, they have similar terms, but without the permission to create mirror sites.

Also, in another step forward for open access, Autism Speaks, a funder for autism research, announced last month a new policy, which went into effect as of December 3. The policy requires deposit of research articles in Pubmed, which makes it available after 12 months.

We are seeing more and more foundations that fund research taking a closer look at the need to address science infrastructure and to leverage their funding resources, by aiming not just as knowledge creation but dissemination and downstream impact.

Copyright Policy at the European Commission – Science Commons’ Response

November 24th, 2008 by Kaitlin Thaney

This past July, the European Commission released a green paper on issues pertinent to work in increasing access to scholarly content. The paper, “Copyright in the Knowledge Economy”, raises a number of questions regarding licensing schemes for scholarly content. The following is Science Commons’ submitted response to the Commission on Question 19.

The question reads:

“Should the scientific and research community enter into licensing schemes with publishers in order to increase access to works for teaching or research purposes? Are there examples of successful licensing schemes enabling online use of works for teaching or research purposes?”

Science Commons – Response to Question 19

Submitted on November 21, 2008 —

Within the scope of the Green Paper (section 1.2) is the dissemination of research, science, and educational materials to the public, and question 19 asks whether the scientific and research community should enter into licensing schemes with publishers to increase access to work for teaching and research purposes.

With respect to governmentally-funded research, the fruits of research should be openly available to the scientific community and the public, in accordance with the principles laid out in the Budapest Open Access Initiative, the Berlin Declaration on Open Access to Knowledge in the Science and Humanities, and the Bethesda Statement on Open Access Publishing. We believe that these declarations already articulate principles that are appropriate for ensuring broad, digital access to the scientific and scholarly corpus. Such access is particularly important with respect to results arising from research projects supported with government funding, because broad-based, digital dissemination serves important social and governmental purposes that motivate such funding.

We recognize that publishers have a variety of business models, and while open access models used by publishers such as Public Library of Science and BioMed Central offer the fastest and most direct means of making scholarly works available to the public, other, so-called “traditional” publishers, pay for peer-review and publication-related costs through subscription and access fees. They have argued that an exclusivity or “embargo” period is needed in order to fund investments in quality control and to support publication costs. We believe that fee-for-access publishing models are not necessarily inconsistent with the broad goals of open access, as long as the embargo period(s), if any, are reasonable, and that subsequent to the embargo period, scholarly papers published in journals are deposited in an online repository and made available for download free of charge and free of technical or legal restrictions. An example of such a policy would be the NIH Public Access Policy (April 7, 2008).

Furthermore, such works should be licensed to the public under terms that permit redistribution and appropriate reuse, including in certain circumstances, the creation of compilations, annotations, and other derivative works. Examples of licenses that support the ability to disseminate and to reuse works include the Creative Commons licenses, published by Creative Commons Corporation. The Creative Commons Attribution 3.0 license is an example of a license that is widely adopted by open access journals and recognized as consistent with the open access declarations discussed above. However, such open licenses need not be limited only to open access journals, but they can also be used a model for licensing works made available after any relevant embargo periods. Such licenses ensure that open access is not only available at a technical level through download (read-only access) but also at a legal level through appropriate licensing of copyright in order to permit the preparation of derivative works and other transformative uses (read-write access), which are central to scientific and cultural enterprises. Creative Commons has also worked with many international collaborators to make these licenses available in many languages, as well as to adapt them to the laws of many jurisdictions.

For almost two years, Science Commons has operated a portal and a tool called the “Scholars Copyright Addendum Engine,” which aggregates a wide variety of recognized “Author Addenda” by means of which scholars can enter into negotiations with publishers to retain rights of reuse for scholarly and teaching purposes. While such tools may indeed aid a few scholars in negotiation with publishers to retain rights to archive and reuse their own works for teaching and research, such case-by-case negotiations do not make a significant impact in the vast majority of cases, which represents the bulk of published research. This is due in part to the relative imbalance in negotiating power and legal expertise of the parties to such publication agreements, as well as an imbalance in incentives, with many authors having a larger stake in being accepted for publication than in promoting post-publication access. Therefore, we believe that effective policy intervention requires action at the funder or governmental level to set the appropriate standards, through mandates and incentives that ensure that fruits of research, and especially government-funded research, are disseminated as broadly as possible and with the fewest legal restrictions, consistent with sustainability and quality.

Science Commons also supports broad digital access to the scholarly and scientific corpus because we believe that many difficult and important scientific and social problems require that scientists and researchers be empowered to take advantage of software, Web tools, and other data management technologies to support advanced searching, querying, and information integration. However, in the present environment in which access to the corpus of scientific knowledge is restricted and fragmented into a variety of “wall gardens,” our ability to use that corpus and to apply modern computer technology to it is likewise fragmented and piecemeal. This has important implications for scientific productivity, impact of funding for research, knowledge dissemination and preservation, and the achievement of social and governmental goals.

Therefore, Science Commons encourages the Commission to consider strategies that incorporate the broad goals of open access, adoption of standardized licenses that facilitate appropriate reuse and exchange of knowledge and research products, and the enablement of digital information technology. We encourage the Commission to consider a variety of tools, including mandates, policies, and incentives to achieve this goal.

This can be found in our Reading Room. The Commission is soliciting feedback from the public on the questions listed in their paper until November 30, 2008. We invite your comments here, and also encourage you to submit a response to the EC on the green paper. There are a specific set of questions listed at the end of the paper, but responses may address a broader set of issues. Formal responses can be sent via email to

SEED coins Wilbanks a ‘Game Changer’ for Science

November 13th, 2008 by Kaitlin Thaney

SEED Magazine has identified John Wilbanks (VP of Science) as a “Game Changer” for science for his work as the head of Science Commons. The piece is part of their “Revolutionary Minds” series, where they profile a chosen few for their advances in a certain area. In the video and accompanying text, John describes the reasoning behind our work and why making the web work for science is important for the world of scientific research.

This segment is dedicated to “Game Changers”, which Emily Anthes of SEED describes as the following:

The ways of science are as well established as those of any human endeavor: observe, hypothesize, predict, test, discard are as good a shorthand for the scientific method as most of us could need. But science is more than that; it’s a human endeavor, with all the accompanying frailties and faculties. Competition, legal difficulties, information overload, a lack of money, and public relations problems can impede the progress of science. Fortunately, these minds aren’t willing to settle for the status quo, and instead strive for a better way for science to exist. They are prizing openness over secrecy, access over scarcity, and they are creating a future that will help science fulfill its potential to make all our lives better.

Amen to that. John joins a group of all-stars, from Carl Bergstrom (creator of the Eigenfactor) to Ilaria Capua (a viroligist known for her avian flu research – especially in making the sequence available to the public via GenBank.) Congratulations to all featured!

Knowledge wants to be connected

October 5th, 2008 by dwentworth

That was the core message of a speech by Science Commons’ John Wilbanks at the Open Access and Research Conference 2008 a few weeks ago in Brisbane, Australia. The conference was an opportunity both to celebrate Australia’s burgeoning leadership in harnessing open approaches for advancing science and scholarship, and to talk about where the global open access (OA) movement is headed.

Here’s an excerpt from an article by the Australian Broadcasting Corporation’s Anna Sellah on the speech, which provides a succinct summary of the reasons why open approaches are vital for deriving value from the vast amounts of scientific data being produced:

“The value of any individual piece of knowledge is about the value of any individual piece of lego,” Wilbanks said in a keynote address to the Open Access and Research Conference held in Brisbane last week.

“It’s not that much until you put it together with other legos.”

He says the ability to connect knowledge brings scientific revolutions. For example Watson and Crick’s breakthrough on the structure of DNA involved them reading all the scientific papers on nucleotide bonding and encoding it in the form of a physical model, says Wilbanks.

But this kind of “human scale” analysis is no longer feasible in an age when automated laboratory processes generate vast amounts of information faster than the human mind can process it.

“For example, we have 45,000 papers about one protein or one gene,” says Wilbanks.

He says a scientist might once have analysed the impact of one drug on one gene, but now pipetting robots are capable of analysing 25,000 genes at a time.

“Most of the research says the smartest of us can handle five or six independent variables at once – not 25,000,” he says

You can read the full piece at the ABC website.

Those of you following news of the conference and developments in Australia may also be interested in Open Oz and Doing things with data, two posts by OA leader Dr. Alma Swan, who was also a keynote speaker at the event.

OWLED 2008 — building the craft of reasoning on the Semantic Web

September 26th, 2008 by Kaitlin Thaney

Registration is now open for OWLED 2008 – OWL: Experiences and Directions – a workshop series for practitioners in industry and academia, tool developers and others interested in the ontology language, to describe real and potential applications, to share experience and to discuss requirements for language extensions/modifications. The forum will be held October 26-27 in Karlsruhe, Germany, co-located with the 7th International Semantic Web Conference (ISWC). The event is co-sponsored by Science Commons, and our own Alan Ruttenberg sits as the chair of OWLED.

Like its predecessors, the fifth workshop in the series aims at bringing users, implementors and researchers together in order to measure the current state of need against the state of the art, to share experience applying OWL and to set an agenda for language evolutions that satisfy users. With the specification of OWL 2 well in progress, the workshop will be an excellent opportunity to learn about, discuss and debate new developments in the language, and to give feedback to the working group.

OWLED is a forum for meeting people who have experience using OWL. Many of the designers and leading researchers who participated in the development of OWL attend, and the workshop is characterized by its interactive nature and the friendly sharing of knowledge.

To register, visit the ISWC Registration page and make your selection in the section Conferences Early Registration.

For more information about registration, including details on deadlines for discounted registration and student support, please visit this page.

Register today! The deadline for getting the best discount is coming up quickly – September 30. We hope to see you there.

Voices from the future of science: Matthew Cockerill of BioMed Central

September 18th, 2008 by dwentworth

Perhaps the best description of what scientific publishing can achieve in the digital age comes from Richard Poynder, the UK journalist who’s been interviewing leaders in the open access (OA) movement. In his interview with our own John Wilbanks, Poynder articulates the vision of a scholarly paper that is “no longer simply an article to be viewed by as many eyeballs as possible, but also the raw material for multiple machines and software agents to data mine, a front-end to hundreds of databases, and the launch pad for an ecommerce system designed to speed up the process of research.”

In this light, Poynder writes, OA is not an end in itself, but “the necessary precondition for a complete revolution in the way that science is done.”

BioMed Central (BMC) is a publisher that has taken bold steps to help realize this vision. A trailblazer in OA since the company’s inception, BMC recently launched the innovative BMC Research Notes, which aims explicitly to “complete the scientific record” by providing a venue for dark data and other kinds of useful information, and to make sure that the data are “published in standard, reusable formats and are exposed to ensure that they are searchable and easily harvested for reuse.” It is also investigating novel approaches for enriching the literature, exploring such areas as data mining and semantic technology. Under the leadership of Matthew Cockerill, who started off at BMC as its Technical Director, the company has seen remarkable growth, introducing new journals in cutting-edge fields, gaining impressive impact factors and surging in readership, submissions and revenue.

“I came into this from my own perspective as a biologist, trying to deal with a flood of data and results,” said Cockerill in an interview last year with Information World Review. “One of the founding reasons for BioMed Central was the idea that if you want to encourage the development of tools to analyze research results, as a basic starting point you need to ensure all the research is openly accessible. By opening up access to the original research, we’re helping the community develop better tools to work with that research.”

I talked with Cockerill about the progress we’re making in the OA movement, the factors behind BMC’s success and what he envisions for making OA research even more useful to scientists.
BMC has been a pioneer in road-testing models for making OA publishing sustainable, including introducing an institutional membership program. Can you tell us about some of the milestones you’ve reached? What’s driving your growth?

We’re super happy with how things are going right now — both submissions and access rates are on the rise. We’re now seeing 4 million article downloads per month, and it will be more than 50 million for the year. That’s a lot of access to research. Submissions are currently at about 1,800 per month, up from 1,500 at the same time last year. And it’s worth noting that in terms of submission rates, we expect the next year to be an even bigger growth period. The reason is simple: last year, we had one journal that got its first impact factor. This year, we have 13 journals in the same position! These include prominent titles such as Retrovirology, Journal of Translational Medicine, Biology Direct and BMC Biology. In our experience, the release of an official impact factor can triple submissions to a journal.

We now have a sustainable business model. Revenue has roughly doubled in the last 12 months — in part because we’re publishing more articles, and in part because we’ve structured our institutional membership fees so they’re proportionate to the value of the articles published, as well as realistic for covering the costs of publishing on a large scale. Our fees are still among the lowest for an open access option, and we’ve been able to maintain growth in terms of the absolute number of submissions.

Another important trend that’s going to drive submissions growth over the next year is existing journals switching across to open access with BioMed Central. Quite a few have done so already, coming from Taylor & Francis and other traditional publishers. And the pipeline for such transfers is growing rapidly, now that OA has proven itself as a viable model with many benefits for society publishers.

What’s behind the trend?

There are three factors driving it:

(1) Not all society journals are big money spinners — a large number only just break even, and this can be an unstable situation. With the majority of library serials budgets swallowed up by “big deals,” subscription cancellations are an ongoing worry for society journals. OA provides security and stability — since the publication costs for each article are covered, the society can be sure that the journal will not drain its resources.

(2) OA gives society journals the visibility that many don’t currently have, especially with a dwindling pool of subscribers. OA increases visibility and enhances dissemination, which fits well with the mission of scientific societies to advance communication within their field.

(3) Societies have, quite reasonably, taken a “wait and see” approach to open access. But now that OA journals are doing well, and some societies have led the way, the rest, I think, are seeing it as a much more viable option — just as authors no longer see choosing an OA journal as such a big risk.

So part of why we’re seeing the migration to OA is that even well-endowed libraries can no longer afford to keep the traditional publishing model afloat. And at the same time, OA is attractive to publishers because it promises to leverage the Web better for visibility and reputation building?

Yes. If you’re a publisher starting a new journal, or seeking to reinvigorate an existing journal and gain mindshare, how do you do it? Open access is the natural way to go.

All of this makes OA a much more dynamic, interesting and responsive publishing environment. It keeps us on our toes in terms of the competition, as well.

Looking ahead, do you think the Harvard faculty mandate can help change the culture and attitudes toward making OA happen — not just with words but also actions and investment?

Absolutely — the mandate at Harvard has already changed perceptions, but I think that the next steps from Harvard, in terms of practical actions, such as providing sustainable central funding for open access publication, will be even more profoundly influential.

It’s been encouraging to see the shift over the past few years in the way people think about funding OA. With OA taking off, initially there was a certain amount of concern from libraries and institutions — OA seemed to be turning from this small thing to a more substantial cost, which could be expected to grow from year to year. But now more institutions are recognizing that this is an important transition in scientific publishing. They’re working with us to bring about the changes necessary to move smoothly and progressively from a model of funding subscriptions that keep the results of research locked up, to funding the cost of publishing openly.

Foundations like HHMI and the Wellcome Trust led the way on this, explicitly setting aside and providing institutions with the extra funds to support OA costs. Now, other funders are following suit — the Research Information Network in the UK, for instance, has set up a working group that brings together publishers, university representatives and research councils to develop guidelines and best practices for efficiently channeling funds to OA. Individual institutions are also working on plans for central OA funds, along the lines of the funds at Imperial College, Nottingham and Amsterdam.

In the US, Harvard’s Stuart Shieber has signaled his commitment to putting OA journals on “equal footing” with subscription journals, calling attention to the need for institutional funding. And we also have the Berkeley Research Impact Initiative, which is funding OA and looking at the best way to make it work at the University of California.

Of course, each country has its own complications, and research and university funding in the US is very different from in the UK. So the change isn’t going to be easy, but it’s happening.

You’ve described opening access to research as laying the foundation for innovation in analyzing and working with the results. What are the next steps for enhancing the usefulness of published research?

Publication shouldn’t just be about putting words on paper, but about contributing to a structure of knowledge — more like contributing to an open source software project. We launched BMC Research Notes with a view to trying to catalyze some of the standards required for that. One of the things we want to do is enable people to share data sets — not only if they happen to fit into the narrative of a traditional paper, but just if they encapsulate useful knowledge.

To some extent, what we need to do next is connect basic scientific concepts with the kind of meaningful interconnections that exist on social network sites between people and their stuff. That isn’t easy stuff to do, in practice, but some of the underlying technologies (e.g. semantic representations like RDF) are increasingly getting towards the point of being practically useful — not least because of the massive enthusiasm for social networks, which has seen the world start looking at graph and network analysis algorithms as hot topics.

Can you elaborate on the connection you’re making between semantic technology and social networks?

The best way to explain what I mean is probably to refer you to a paper published in Genome Biology: Calling on a million minds for community annotation in WikiProteins. It’s about a project — WikiProteins — that implements some of these ideas in terms of mining the literature for conceptual relationships. The project is currently being developed to also use these conceptual relationships to connect researchers to one another. BioMed Central has worked extensively with the folks responsible for Wikiproteins, and I’m a co-author on the paper (as is Jimmy Wales of Wikipedia!).

For another perspective, Toby Segaran‘s excellent book, Programming Collective Intelligence: Building Smart Web 2.0 Applications, explores techniques to make use of information that can be mined from the pattern of connections in a network, social or otherwise. Perhaps the best known examples of this type of network mining in action are recommendation systems like Amazon’s “Recommended for You” feature, or Apple’s “Genius Playlists.”

Toby is now at Metaweb/Freebase, Danny Hillis‘s consumer-focused semantic web project. Although the extraction of semantic structure from scientific data is conceptually similar to this work in the consumer space, it doesn’t always get quite the same resources thrown at it — just as scientific computing does not get the same resources as Nintendo or Xbox. One recent case in point: Microsoft’s announcement that it is abandoning Live Academic Search, its never-quite-successful attempt at a Google Scholar-type service, because it wants to focus on consumer markets where it feels it is easier for the company to add value.

However, that said, scientific computing can and does benefit from the Nintendo/Xbox innovations, and I think the same can be said about the ingenuity being poured into developing social networks — ironically, some of the commercially-driven innovation in the consumer space gradually finds its way back to the scientific information space.

BMC is one of most prominent OA publishers using Creative Commons licenses. Do you have thoughts to share about your experience?

Returning to the theme of progress in OA, I’m happy that more people (including publishers) are starting to understand that open access doesn’t just mean not hitting a pay-wall at the publisher’s site. It’s about enabling people to get full use and value from the research that’s being conducted.

Creative Commons has it absolutely right with the idea of “some rights reserved” — providing a way for authors and publishers to allow a wide range of uses, while reserving the author’s right of attribution. There are an increasing number of scholarly publishers who embrace this principle of licensing open access content to encourage reuse. BMC is now involved in an initiative to to set up an association with these other OA publishers, analogous to associations which exist in the world of open source software. The development of such an open access publisher organization reflects the increasing importance of OA publishing, which goes beyond the activities of any one publisher.


Previous posts in this series:

Tim Hubbard on open science

September 10th, 2008 by dwentworth

Open licensing advocate and Science Commons friend Victoria Stodden is among those live-blogging the Access to Knowledge 3 (A2K3) Conference that’s wrapping up today, and she’s posted notes from a session at which the Sanger Institute’s Tim Hubbard argued for more data sharing in science — provided that the data are published in a way that makes the information (re)useful:

[Hubbard] says that openness in science needs to happen before publication, the traditional time when scientists release their work. But this is a tough problem. Data must be released in such a way that others can understand and use it. This parallels the argument made in the opening remarks about the value of net neutrality as preserving an innovation platform: in order for data to be used it must be open in the sense that it permits further innovation.

Nicely put.

You can check out more notes from the conference via the A2K3 conference blog.