Open Access News

News from the open access movement

Saturday, March 29, 2008

New OA journal of architecture

Archimaera is a new German-language, peer-reviewed OA journal of architecture and cultural history.  (Thanks to DIPP.)  The inaugural issue (January 2008) now online.

Friday, March 28, 2008

Did U.S. gov't sell out its legislative history?

Boing Boing (March 17) and Free Government Information (March 23) cover the question of a deal by the Government Accountability Office, an arm of the U.S. Congress, which Thomson West claims granted the company exclusive access to federal legislative histories compiled by GAO.

Update (4/14/08). The answer to the question is yes, the government did sell exclusive access to its legislative history to Thomson. Details at Boing Boing and FGI.

New OA database on human oral microbes

The Human Oral Microbiome Database is an OA database of information about microbes which live in the human oral cavity. The database went live on March 26. The database will contain "descriptions of the microbes, their metabolism, and their ability to cause disease ... linked to information on their DNA and proteins, as well as to the scientific literature."

The project is funded by the U.S. National Institute of Dental and Craniofacial Research, part of the National Institutes of Health, and overseen by scientists at the Forsyth Institute and King’s College London. The database is related to the Human Microbiome Project, launched in December 2007, by NIH to sequence the genomes of representative human microorganisms. (Thanks to ResourceShelf.)

New OA journal on Mormon studies

The British Journal of Mormon Studies is a new OA, peer-reviewed journal in Mormon studies. Print editions are available print-on-demand from Lulu. The inaugural issue, dated Spring 2008, is available. The journal will be published twice annually. (Thanks to John Reidelbach.)

New OA journal from Oxford on undergrad bioscience research

Oxford Journals launches first peer-reviewed journal dedicated to undergraduate bioscience research, press release, March 26, 2008.
Oxford Journals is delighted to announce the launch of Bioscience Horizons, a free online journal showcasing the best undergraduate bioscience research from the UK and Republic of Ireland.

As the first peer-reviewed journal dedicated to undergraduate bioscience research, it is the only journal to provide such a forum for students, their supervisors and universities, this journal is unique in its field. It is hoped that by publishing high quality undergraduate research work the journal will strengthen the link between teaching and research in higher education. ...
The inaugural issue is available.

York U.'s efforts for OA

Heather Morrison, York University Library - another Canadian leader in the open access movement, The Imaginary Journal of Poetic Economics, March 26, 2008.
...A link to [York University Library] Ejournal publishing support is prominently posted on the library's Services page for faculty. There is a whole page just on publishing using Open Journal Systems!.

YorkSpace is only one of York's 3 repositories, according to Leila Fernandez and Marcia Salmon, who also report that Canada is 4th among countries in societies publishing open access journals, in their presentation on Open Access Publishing.

Andrea Kosavic and Sharon Wong's Empowering Authors, a presentation for a Scholarly Communications Retreat at York, is well worth a look for some interesting approaches to explaining the key area of author rights to faculty.

Kudos to Cynthia Archer, York's University Librarian and one of the founders of the open access journal Partnership: the Canadian Journal of Library and Information Practice and Research, for a great role model!

York University Library is a member of another Canadian leading organization in open access, the Canadian Association of Research Libraries (CARL).

Statement from NIH Director Zerhouni

A Statement from the NIH Director, Elias A. Zerhouni, M.D., Welcoming Comments on the Implementation of the Public Access Policy, a press release from the NIH, March 26, 2008.  (Thanks to Heather Joseph.)  Excerpt:

The National Institutes of Health held a public meeting on Thursday, March 20, 2008, for the purpose of hearing broad comment on the implementation...of the NIH Revised Policy on Enhancing Public Access to Archived Publications Resulting from NIH-Funded Research....

NIH is applying 21st-century technology to its investment in research, becoming more transparent and accountable, and ensuring that NIH and the Department of Health and Human Services can better promote the science and health benefits derived from NIH-funded research, Zerhouni explained.

"We believe that public access after a reasonable embargo period of up to a year to research funded by NIH will help advance science and improve human health while preserving peer review and the value of scientific publishing," said NIH Director Elias A. Zerhouni, M.D. He explained that the improved access will be a "dynamic resource to not only research publications and display publications, but to link them to all sorts of knowledge that NIH has invested in making research more efficient for all scientists."

The meeting was held to ensure the policy's implementation will work as successfully as possible for all involved....

If the policy remained voluntary, Zerhouni said, about new 64,000 journal articles arising from NIH funds would not be available to the public each year....

The meeting was a listening session, and supported by 451 comments collected in advance of the meeting. Preliminary analysis indicates over 60% of these pre-meeting comments expressed support of the Policy as implemented, but approximately 15% thought the 12-month delay period was too long and 15% had concerns that a mandatory policy will be detrimental to scientific publishers....

The public may view the video cast and pre-meeting comments [here]. 

NIH is also planning a Request for Information (RFI), to be announced in the Federal Register, asking for comments on the policy's implementation. NIH's report on the meeting, pre-meeting comments and the RFI will be issued by September 30, 2008....

BMJ reviews recent OA mandates

Susan Mayor, Opening the lid on open access, BMJ, March 29, 2008 (accessible only to subscribers, at least so far).  Excerpt:

The chief public funding body for medical research in the United States, the National Institutes of Health (NIH), is introducing a mandatory open access policy from next week....

This is the latest policy from key research funders to promote open access to research findings (table). It is based on the argument that the public should have free access to results from research that it has funded, and researchers should have free access to papers they have written or reviewed rather than have to pay subscriptions or single access fees to journals. Open access publishing also makes research freely available to help advance research around the world....

Policies mandating open access to publicly funded research have been in place in Europe for some time....

Universities are also starting to require their staff members to make their papers freely available. In February Harvard University’s faculty of arts and sciences...adopted a policy that will put faculty members’ papers in an open access repository hosted by the university....

[One] problem is enforcing open access policies. “They are not easy to monitor in practice,” acknowledges Tony Peatfield, head of corporate governance at the MRC [UK Medical Research Council]....

It is still relatively early days to determine the effects of open access policies. Mr Peatfield reported that some researchers funded by the MRC have found that journals without open access arrangements have introduced mechanisms to facilitate this when necessary. Research so far has indicated that researchers may gain greater exposure for their work because studies have shown that open access articles are cited more often than non-open access articles from the same journal....

More on what universities can do to promote OA

Stevan Harnad, Peter Suber's Talk at Harvard's Berkman Center: "What Can Universities Do to Promote Open Access?" Open Access Archivangelism, March 27, 2008.

Summary.  Seven supplemental points based on Peter Suber's excellent talk (and the audience discussion) on "What Can Universities Do To Promote Open Access?" at Harvard's Berkman Center for Internet and Society.

(1) Journals vs. books: OA is only about author give-away work. Peer-reviewed journal articles are all, without exception, author give-aways, but most scholarly books are not. OA can only be mandated for give-away work. (Once OA for journal articles prevails, more authors will undoubtedly want the same for their monographs too.)

(2) Versions and Citability: The canonical version of a journal article is the final, peer-reviewed, accepted version (the "postprint"). That is what researchers need, though not necessarily in the form of the publisher's PDF. What is cited is always the published work. Researchers are infinitely better off if those who cannot afford the publisher's official PDF can always access the author's self-archived postprint.

(3) First OA Self-Archiving Mandate: Queensland University of Technology's was the world's first university-wide OA self-archiving mandate, as Peter notes, but the very first OA self-archiving mandate of all was that of the School of Electronics and Computer Science at Southampton University.

(4) Prior Evidence of Probability of Compliance With OA Self-Archiving Mandates:  Swan & Brown's author surveys found that 95% of authors would comply with an OA self-archiving mandate (over 80% willingly) but authors were not asked whether they would comply with a copyright-retention mandate. The same is true of Arthur Sale's data on actual mandate compliance rates.

(5) Deposit Mandates vs. Copyright-Retention Mandates: NIH's is not a copyright-retention mandate. It is a no-opt-out deposit mandate plus a no-opt-out requirement to negotiate with the 38% of journals who don't endorse immediate OA, so as to be able to make the deposit OA within a year. Harvard's is a copyright-retention mandate, with opt-out.

(6) Mandate Implementation Mechanisms: There are no sanctions on deposit mandates, as Peter notes; there are administrative incentives and contingencies: The IR is made the official locus for submitting publications to be assessed for performance review.

(7) Peer Review, Journals and Repositories: Journals provide peer review; IRs provide access to peer-reviewed postprints. The issue of IRs providing peer review is a red herring (raised by others, not Peter)....


  • Re #1.  Stevan and I disagree about this.  For more on my position, see e.g. my interview with Richard Poynder (October 2007, p. 40):  

    RP: Where do you draw the line (if any) between what scholarship does and does not need to be free online, and why?

    PS: For me it depends on the consent of the author or copyright holder, not the genre of the writing. The open access movement has a good reason to focus on the genre of journal articles more than the genre of books. But the common formulation of this reason is incomplete. It's true that journals don't pay authors for their articles. This economic fact matters, but mostly because it allows scholarly authors to consent to open access without losing revenue....So relinquishing revenue is only relevant when it leads to consent, and consent suffices whether or not it's based on relinquishing revenue. It follows that if authors of royalty-producing genres like books consent to open access, then we'll have the same basis for OA to books as we have for OA to journal articles....

  • Re #2.  I agree with Stevan on this and didn't discuss the subject in my Harvard talk.
  • Re #5.  I haven't watched the Harvard video.  I don't think I said that the NIH policy was merely a permission mandate; and if I did, then I erred.  I meant to say that it was both a deposit mandate and a permission mandate.  Of course it requires deposit in PMC.  But it also requires NIH grantees to retain key rights.
  • Re #6.  In my talk, I discussed various incentives including the idea that performance reviews should only consider articles on deposit in the IR.  I devoted a slide to that idea, pointing to four institutions already putting it into practice.  I recommended the policy explicitly to Harvard, and to all universities in general.

Thursday, March 27, 2008

More on the APS licensing terms

Stevan Harnad, The American Physical Society Is Not The Culprit: We Are, Open Access Archivangelism, March 27, 2008.

Summary.  A journal's copyright transfer agreement is too restrictive only if it tries to disallow author self-archiving of the accepted, refereed final draft (the "postprint"), free for all on the Web, where any user webwide can access, read, download, print-out, store, and data-mine that full-text for any research purpose whatsoever. The American Physical Society (APS) was always the most progressive of the established subscription-based publishers, and the very first to adopt a Green policy on author OA self-archiving. Today, 62% of journals are Green, but only about 15% of articles are being self-archived. Hence the first and foremost priority today is to get all authors self-archiving and all journals Green. Institutional and funder OA self-archiving mandates can and will ensure that both these things come to pass. This is not the time to be pursuing still more rights from Green publishers, particularly the most progressive one of all, APS. It's the time to self-archive and mandate self-archiving. The rest will take care of itself, but not if we keep chasing after what we don't need instead of grasping what is already within our reach....

PS:  For my comments on the same controversy, see my post from March 14.

Update (4/2/08).  Stevan has posted a follow-up to his original post:

Summary:  I agree completely with Jonathan Oppenheim's and Bill Unruh's ends: (1) that authors should be able to publish and post derivative works and (2) that they should be able to adopt the Creative Commons license of their choice. I disagree only with their means: The American Physical Society (APS), the most progressive and adaptable of traditional journal publishers and the first to have adopted a formal policy endorsing Green OA self-archiving after the practice had evolved among its authors, should not now be publicly pressured into making further formal changes as if it were the villain, while so many other publishers still aren't even Green. Evolving practice should precede formal precept in the online age, when the research community is still discovering and exploring the potential of the new medium. The APS would no more try to prevent its authors from posting derivative works than it did in the case of the posting of their preprints and postprints. The practice (and mandating) of Green OA self-archiving, once it has generated universal OA, will effectively moot everything that stands in the way of CC licensing too....

Digital scholarship in the humanities

Lisa Spiro, Becoming a “Digital Scholar”: Digital Discovery 2008, Digital Scholarship in the Humanities, March 27, 2008. Presentation at Digital Discovery (Houston, March 27).

... I’m fascinated by the question of how the abundance of digital information and the development of new technologies will affect humanities scholarship, and it seemed to me that the best way for me to understand these transformations would be to undertake a major research project myself. By revisiting my dissertation, I could build on my existing knowledge and compare my research process 5+ years ago to what’s possible today. Thus I decided to remix my dissertation as a work of digital scholarship.

... My work is still very much in process, but here are three preliminary observations:

  1. A vast amount of information is now available online. ...
  2. As we deal with the abundance of information, we need tools to find, organize, manage, analyze and share our research materials. Fortunately, those tools are beginning to be developed. ...
  3. Although the journal and monograph still dominate the humanities, new means of scholarly communication are emerging, enabling the faster dissemination of ideas, more community dialog, and the use of multimedia. ...

Lest I seem naïve, I should acknowledge that significant challenges face digital scholarship. ... As the digital environment constantly shifts and tools come and go, it’s overwhelming trying to keep up. In any case, the system doesn’t really reward faculty for experimenting with new technologies. ... Then there’s copyright: For my remixed work on bachelorhood, I’d love to provide links to the full-text of every work that I cite. I’d also like to remix those original sources to produce new works. But what I can do is constrained by copyright.

... What effect will the computer revolution have on humanities scholarship? It’s really too early to say– in a small way, that is what I’m trying to figure out in my project. In the sciences, we’ve seen the rise of new sub-disciplines and methodologies made possible through computation and data archives. In the humanities, I believe that being able to access the full text of millions of books will bring about significant changes in how research is conducted. ...

CIMP to launch IR

B K Mishra, World class library likely in Patna, Times of India, March 25, 2008. Reports that the Chandragupta Institute of Management, Patna will establish an institutional repository as part of its library, apparently to open by the end of May.

On the idea-expression divide in scientific literature

John Wilbanks, Creative works, copyrights, and publishing..., john wilbanks' blog, March 26, 2008.

This is a reply to a post over at Plausible Accuracy, asking some questions about my talk at MIT (online here) from last fall ...

I’m not arguing in my talk that copyright should not apply to the scholarly articles themselves – it’s pretty clear that articles represent creative expressions, fixed in a tangible medium, which is all it takes to get a copyright. ...

But let’s zoom in on some of the things in the article. A statement like the following is a good example.

“Transglutaminase cross-links in intranuclear inclusions in Huntington disease” (from NCBI)

Now, this statement purports to lay out a fact. Not a creative expression. Remixing this statement renders it less true and not more true. Copyright isn’t supposed to protect this statement – it’s a fact of nature, not a creative styling ...

This is what I was getting at in the talk. The copyright on the overall article, that comes from the connectors and the clause structures, is being used to control the movement of the facts of the experiment ... That seems insane to me. These are facts of nature and should be extractable separate from the copyright of the article, so that we can start to tie all the database entries about transglutaminase to all the papers mentioning transglutaminase. ...

New OA journal on molecular cytogenetics

BioMed Central announced yesterday its new peer-reviewed OA journal, Molecular Cytogenetics. The journal will publish research on "all aspects of chromosome biology and the application of molecular cytogenetic techniques in all areas of biomedicine". Three papers are now online, all published March 26.

World Health Org.: OA to promote medical research

Riaz K. Tayob, WHO: Slow progress in talks on IPRs and innovation, SUNS #6441, March 26, 2008.

Slow progress was made last week at a sub-group meeting of the [World Health Organization]'s Intergovernmental Working Group (IGWG) on Public Health, Innovation and Intellectual Property Rights.

The sub-group deals with indicators for actions in eight areas of public health, including managing intellectual property rights, research and development, technology transfer, improving access to medicines and financing mechanisms.

The IGWG is the main body under the WHO that deals with the related issues of IPRs, innovation for new medicines, and access to medicines. ...

According to delegates, during the discussions under element 2, promoting R&D, Bolivia made a proposal to promote open access publishing of research supported by public funding, and the promotion of new standards and norms at national and international levels for free access to such publications. Some developed countries opposed this, saying that they did not see it as an indicator. ...

32 OA Hamlets

Josh Fischman, Neither a Borrower Nor a Lender Be ... Unless You Have 32 Digital Versions of 'Hamlet', Wired Campus, March 26, 2008.

Thirty-two different versions of Hamlet, all printed before 1641, are held in the vaults of the Folger Shakespeare Library, in Washington, and other institutions—and all 32 are going digital with the help of the University of Maryland.

The university announced today that its Institute for Technology in the Humanities will be working with the Folger library to digitize the texts. There is no single authoritative version of the tragedy, since what survived are editions cobbled together by printers from actors’ memories or from marked-up scripts used in various productions. Digitizing the 32 texts—a project financed by the National Endowment for the Humanities—will make it easy for scholars to compare and contrast versions, noting similarities and differences.

The result will be a free, open, and interactive Web site housed at the University of Oxford. And if Hamlet‘s opening proves successful, the project will move on to Henry V, King Lear, A Midsummer Night’s Dream, Romeo and Juliet, and the other plays.

The labor of an IR

Dorothea Salo, Voice and Labor, Caveat Lector, March 26, 2008.  Excerpt:

...[We repository managers are] not talking. We’re not organizing. (The OA publishers are, but we’re not.) Even those of us who are talking are talking hardly more than happytalk. I don’t know how much more clear I can possibly make it: green open access as she is practiced (rather than merely opined about) has a severe morale problem. When I asked NISO to make me proud of what I do, I wasn’t kidding....

[R]epository labor is invisible. Just ten minutes or less per article,...the software is free and easy to set up and Just Runs, and that’s all there is to it! ...

Certain types of labor in this field are even more invisible than deposit labor. Systems administration (“it just runs!”) and design labor, certainly. Rights-clearance labor, which is picky, demanding work notable for its total lack of clarity....

Verily I say unto you: Harvard’s Provost’s office, library, and IT division had better be hard at work on citation-retrieval automation, automation that involves as little faculty labor as possible. And verily I say unto anyone who wants a mandate like Harvard’s that they’d better do likewise. And verily I say unto everyone that we (as a field) are so far from being adequately automated as to scare me....

OA at the Berkman Center

At Harvard's Berkman Center last week (March 17), Catherine Candee and I spoke about OA.  Our talks are now online.

OA to expose conflicts of interest

Jonathan Eisen, A different kind of Open Science - the need to track funding sources and conflicts of interest, Tree of Life, March 26, 2008. 

Well, the News is abuzz with discussion of a controversy involving lung cancer studies that were funded by tobacco associated money (e.g., see MSNBC and TIME and the NY Times). The issue is that apparently the source of the money was hidden through some sort of laundering of the money through a foundation.

As many readers know, I am a bit obsessed with open access to scientific research publications. This here is a case where the need for openness goes well beyond publications. Here there is a need for openness about funding and conflicts of interest and the roles of all participants. In this case, I am not sure what could have been done by the journals involved to vet the funding of the project more carefully. But nevertheless, science in general can be severely hurt whenever there are cases of even the appearance of conflict of interest. I do believe that open access journals help in this in that anyone, anywhere, can look at the publication as well as the descriptions of the funding sources and the authors contributions. The more eyes we have on research products, the more likely problems will be discovered and (possibly) the less likely it will be to happen again.

Libraries and A2K

How do you say Access to Knowledge?  A short (105 second) video from

Also see the longer announcement of the video at the UNESCO IFAP.  Excerpt:

Access to knowledge (A2K) is essential for the functioning of a healthy and democratic society....

[L]ibraries are a key component in the burgeoning social movement that is A2K....

Academics have embraced the ideas and deepened the analysis....

Members of the international consortium, Electronic Information for Libraries ( are a natural ally in the A2K movement. With millions of users in over 2,000 libraries in 50 developing and transition countries, they know only too well the value of providing access to critical educational and training materials for the scholars and researchers, doctors and lawyers, students and teachers in their countries....

They see at first hand how the digital environment has the potential to transform access and use, especially for those disadvantaged by distance or economic circumstance....

Librarians support a vibrant public domain, fair and balanced copyright laws that take into account the stage of development of a country, transparency and participation in decision-making and openness to new models, such as open access and open source software.

“Access to Knowledge” means many things to many people. First, we asked librarians how to say “Access to Knowledge” in their own language [for our video]. The variety of responses shows a rich diversity of language and culture, with the common purpose of making access to knowledge a reality for library users in developing and transition countries....

IR usage in developing countries

Bring on the IRs!  Electronic Publishing Trust for Development, March 26, 2008.

Having been alerted to the existence of statistical tools for measuring usage of articles deposited in a number of Institutional Repositories, I have collected some very encouraging statistics about how IRs are being used in developing countries.

The number of IRs using this software (developed at the University of Tasmania) is limited at present, but the following sites are among those I found that record usage by date and by country:

- University of Otago eprints Repository, New Zealand

- University of Strathclyde, UK

- African Higher Education Research Online

- Rhodes eprints repository

- E-LIS Repository

As some examples in the table below show, the full text download usage by developing countries was very encouraging indeed. India, China, Brazil, South Africa are among the busiest user-countries, and the less scientifically advanced countries are almost all represented as you go down the usage table.

Institutional repository University of Otago, based in New Zealand University of Strathclyde, based in the UK Rhodes e-Research, based in South Africa E-LIS, based in Italy
Period of usage 2007 2007 2007 ?
Number of records in repository 666 5052 808 7525
Full text downloads
From Canada 2977 2070 10413 20934
China 4673 1649 10196 22879
India 5022 1032 27609 33125
South Africa 1029 175 120598 5556
UK 8926 12664 25392 63362
USA 16830 44270 145356 1415807

. . . .and on to several hundred other countries

Encouraged, I searched other IRs and found the same story unfolding. Multiply the number of registered IRs (> 1000) by the usage figures and you can see that developing countries are using IRs a lot! ...[I]t is very encouraging to see how IRs are closing the N to S, S to N and S to S information gaps that we used to talk about. The low-cost nature of establishing IRs allows institutes in economically constrained countries to be part of the global research community, readily using and exchanging essential information....

Not only do these statistics provide a true record of the need for the research information deposited, but they even provide information on the specific research that scholars are searching, an invaluable insight into priorities for development programmes. And of course, authors will be greatly encouraged to witness usage figures of their published research, and institutes will be happy to see their organisations high on the research map.

We can earnestly hope that someone – soon – will carry out an authoritative study on the usage of IR material. This would be a magnificent contribution of value to many sectors. Perhaps someone is …?.

Wednesday, March 26, 2008

Identifying data sharing in biomedical research

Heather A. Piwowar and Wendy W. Chapman, Identifying Data Sharing in Biomedical Literature, submission to American Medical Informatics Association Symposium (November 8-12, 2008, Washington, DC). Abstract:
Many policies and projects now encourage investigators to share their raw research data with other scientists. Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations. We propose a novel approach to finding shared datasets: using NLP techniques to identify declarations of dataset sharing within the full text of primary research articles. Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision. A simpler version of our classifier achieved higher recall (86%), though lower precision (49%). We believe our results demonstrate the feasibility of this approach and hope to inspire further study of dataset retrieval techniques and policy evaluation.

Update. Also see the version at Nature Precedings.

OhioLink joins SCOAP3

OhioLINK has joined CERN's SCOAP3 project.  See yesterday's announcement from CERN:

OhioLINK [is] a consortium of the libraries of 86 Ohio colleges and universities....

Tom Sanville, Executive director of OhioLINK said: "SCOAP3, if successful, offers what we would like to all see with Open Access journals - at least a zero sum game or better. It is not a dual investment with traditional subscriptions but a replacement at not worse than the value of our current investment and hopefully better. For that reason alone the OhioLINK community thinks it worthwhile to support CERN's steps to see if this can be put into practice for important journal content".

OhioLINK joins a fast-growing number of U.S institutions which have pledged to re-direct their subscriptions to High-Energy Physics journals to SCOAP3.

Tuesday, March 25, 2008

OA for undergrad students

Gloria Tavera, Open access meets undergrad research… please?, Open Students, March 24, 2008.

You’re looking for academic articles in a peer reviewed journal, perhaps you even have some titles and authors picked out. You think you’ve found the article and…click, click, then, “Please choose the appropriate price according to the kind of subscription you like and the area of your address of residence”. At $30 a paper? Forget it. Whether you’re researching for a class or trying to look for papers related to your latest lab experiment, open access could make things a whole lot easier.

In 2006, at my own school, University of Florida, budget cuts nearly forced the library to cancel almost $750,000 in online journal subscriptions. It’s infuriating that we had to have hundreds of thousands of dollars to pay for access in the first place.

As far as I can see, the journal publisher’s business model is antiquated and counter-productive—it’s out with the old and in with the new. It practically blows my mind that such a backwards idea could persist in a community where it’s particularly important to share information and ideas. ...

OA student journals in U. Penn IR

Marjorie Hassen, The Learning Partnership, University of Pennsylvania Alamanc, March 25, 2008.
... Three student journals are currently hosted by ScholarlyCommons: the Penn McNair Research Journal, the Journal of Student Nursing Research (JOSNR), and CUREJ, the College Undergraduate Research Electronic Journal. Each of these publications showcases undergraduate research by some of Penn’s most promising students and provides an opportunity for wide exposure and discovery. Noteworthy for the breadth of its topics, CUREJ stretches the boundaries of traditional research with artwork, photographs, and video and fully exploits the benefits of an online repository. ...

Science Commons on cyberinfrastructure

Donna Wentworth, What’s “cyberinfrastructure”?, Science Commons blog, March 24, 2008.

... 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.) ...

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. ...

NEH creates Office of Digital Humanities

The U.S. National Endowment for the Humanities has created an Office of Digital Humanities, from its Digital Humanities Initiative. (Thanks to Wired Campus.)

See former OAN posts on the Digital Humanities Initiative.

On OA to environmental information

Muki Haklay, Open Knowledge - learning from environmental information, presentation at Open Knowledge Conference 2008 (OKCon), London, March 15, 2008. Does what it says on the tin.

OA to Mongolian texts

UNESCO saves rare archives in Mongolia, March 20, 2008. (Thanks to Klaus Graf.)
UNESCO is helping the main Mongolian holders of national documentary heritage, the Gandan Tegchenling Monastery and the National Archives, to preserve their unique collections. Several thousands of pages of endangered texts will be saved in digital form and be eventually open to a wider audience.

... UNESCO equipped the library of the Gandan Tegchenling Monastery with the Intranet/Internet connexion, as well as the necessary hard- and software. Six lamas received on-job training on digitalisation techniques of the original texts, e-catalogues and e-books. Until now, 23 volumes, 540 sutras and 8508 pages have been scanned – the slow progress of the work is due to extreme fragility of certain pieces and the complex scroll or tablet structures of sutras. In total 78435 pages of endangered texts will be saved in digital form and be eventually open to a wider audience who wishes to study the spiritual heritage.

UNESCO also assisted another important holder of national documentary heritage, the National Archives of Mongolia, in digitising the technical plans of palace museums of Erdenezuu, Megjid Janraisag, Amarbayasgalant and Bogda Khaan and their engineering and geological references. The biggest record, 231 x 87.07 cm, is now available in its original size. The Archives have chosen to transfer the rest of documents to A-1, A-2 and A-3 formats. Valued by the historians and archaeologists, those documentary treasures totalling to 1545 documents are now accessible on digital carriers. ...

Medical patients share data to "get help, give help"

Thomas Goetz, Practicing Patients, New York Times, March 23, 2008.  Excerpt:

...PatientsLikeMe seeks to go a mile deeper than health-information sites like WebMD or online support groups like Daily Strength. The members of PatientsLikeMe don’t just share their experiences anecdotally; they quantify them, breaking down their symptoms and treatments into hard data. They note what hurts, where and for how long. They list their drugs and dosages and score how well they alleviate their symptoms. All this gets compiled over time, aggregated and crunched into tidy bar graphs and progress curves by the software behind the site. And it’s all open for comparison and analysis. By telling so much, the members of PatientsLikeMe are creating a rich database of disease treatment and patient experience....

PatientsLikeMe is a tool that allows patients to manage their disease with a sophistication and precision that would have been unimaginable just a decade ago.... They’re not typical patients, in the sense of waiting for advice from a doctor. They are, rather, co-practitioners treating their conditions and guiding their care, with possibly profound implications. “People who use it will live longer; people who don’t won’t,” boasts Jamie Heywood, the provocative co-founder of PatientsLikeMe. “That’s evolution.” ...

The company, which is financed by private investors, eschews advertising; the business model instead seeks to exploit the value of the databank itself. By and large, this means working with pharmaceutical companies. The company has had discussions with several drug firms to sell anonymized patient data on various symptoms and treatments. They have also recruited PatientsLikeMe members to be participants in clinical drug trials. Ultimately, the company expects that the data will generate insights with considerable scientific — as well as economic — value....

The most striking notice is the company’s Openness Philosophy, a manifesto posted prominently on the site.

“Currently, most health-care data is inaccessible due to privacy regulations or proprietary tactics,” it declares. “As a result, research is slowed, and the development of breakthrough treatments takes decades. . . . When you and thousands like you share your data, you open up the health-care system. . . . We believe that the Internet can democratize patient data and accelerate research like never before.” ...

“I know it sounds like really personal information, but it’s not like I’m putting my phone number up,” says Jennifer Jodoin, a hotel manager in Palm Beach, Fla., who has changed her M.S. medications based on information gleaned at PatientsLikeMe. “I’m not posting my address and saying, ‘Come on by.’ It’s an exchange of information to get help and to give help.” ...

OA classics from Planet eBook

Planet eBook is a new portal of OA books in the public domain, launched by Richard Crocker in February 2008.  The books are well-formatted PDFs (cut/paste enabled) with no DRM and no ads.  From the about page:

...We offer an assortment of classic novels and books in electronic form which you are free give to your friends, classmates, students, anyone!

Existing free eBooks on the Web tend to be well beneath the quality of paper books, making them more difficult and less pleasurable to read. At Planet eBook we're trying to change this. Our goal is to publish a small selection of high-quality eBooks — each a genuine alternative for readers wanting to enjoy reading a book without having to pay for it. The books we publish are all in the public domain so there is no real need for readers to continue to pay for them.

You're welcome to print them out for classes and courses, distribute them on CD/DVDs, offer them for download from your website, and so on — really, you can share them however you like, as long as you don't charge money for them....

The high cost of the lack of open data

The Value of Spatial Information, a report by ACIL Tasman prepared for Australia's Cooperative Research Centre for Spatial Information and ANZLIC, March 2008.  (Thanks to Baden Appleyard.)  From the executive summary:

...Constraints on access to data are estimated to have reduced the direct productivity impacts in certain sectors by between 5% and 15%. It is estimated that this could have resulted in GDP and consumption being around 7% lower in 2006-07 (around $0.5 billion) than it might otherwise have been....

Comment.  These are big numbers and it takes a minute to put them in perspective.  In one country (Australia) in one year (2006-07), lack of OA to one kind of data (spatial data) cost the economy $500,000,000.

RLG webinar on access and digitization

Ricky Erway and Jennifer Schaffner, Out of the Stacks and onto the Desktop: Rethinking Assumptions about Access and Digitization, a webinar from RLC/OCLC.  (Thanks to Charles Bailey.)  From the blurb:

Ricky Erway and Jennifer Schaffner provide a brief overview of the outcomes of two recent initiatives undertaken by RLG Programs with contributions from staff at many partner institutions that resulted in the following reports:

Monday, March 24, 2008

J of Neuro-Ophthalmology debates OA

The March issue of the Journal of Neuro-Ophthalmology is now online.  This issue has three OA-related pieces, none of them OA, at least so far:

  • Gale A. Oren, The Crisis in Scholarly Publishing: Open Access to the Rescue?  An editorial.  No abstract.  Excerpt:  Authors reporting the results of NIH-funded research will need to comply with the forthcoming public access mandate. Regardless of the source of funding, they should look beyond getting their work published and take into consideration how accessible it will be to the scientific community after publication....Readers of the biomedical literature rightly expect to have extensive access to electronic journals in their areas of interest. Open access, in one form or other, is the best way to meet these expectations.
  • Allyson Mower and Mary E. Youngkin, Expanding Access to Published Research: Open Access and Self-Archiving.  Abstract:   Academic libraries traditionally provide access to the life science journal literature for their respective institutions by purchasing annual subscriptions to journals. However, with skyrocketing subscription prices and decreased or flattened library budgets, fewer journals are being purchased. This trend results in diminished access to the literature for members of that institution. Open access and self-archiving are possible solutions to this crisis.
  • Erin McMullan, Open Access Mandate Threatens Dissemination of Scientific Information.  Abstract:   The public good is served when researchers can most easily access current, high-quality research through articles that have undergone rigorous peer review and quality control processes. The free market has allowed researchers excellent access to quality research articles through the investment of societies and commercial publishers in these processes for publication of scholarly journals in a wide variety of specialty and subspecialty areas. Government legislation mandating "open access" to copyrighted articles through a government Web site could result in a reduction of financially sustainable peer-reviewed journals and a reduction in the overall quality of articles available as publishers, societies, and authors are forced to hand over their intellectual property or restrict the peer review process because of lost sales opportunities. The public is best served when the work of researchers advances science to its benefit. If researchers have fewer current resources, diminished quality control, or access to fewer trusted peer-reviewed journals, the public could ultimately lose more than it could gain from open access legislation.

Update.  Also see Heather Morrison's comments on Erin McMullan's article.  For my own comments on McMullan, see my article from September 2007, Will open access undermine peer review?

Digitization milestone from U. Florida

Laurie Taylor, Almost 1.5 million!, Digital Library Center Blog, March 23, 2008.

In August, the Digital Library Center proudly announced breaking the one million page mark, with over a million pages online for more than “20 collections, representing more than 44,000 titles in more than 52,000 volumes.” Now, just 7 months later we’ve added slightly over another 60% of that to the collections for a total of 1,621,841 pages, over 51,746 titles (up from 44,000) and 67,487 volumes (up from 52,000). That means we’ve been producing almost 10% of our total holdings each month for the past 7 at nearly 100,000 pages a month!

The incredible production rate is far more incredible when the types of pages are considered. Large scale digitization initiatives produce far more pages than this, but any comparison would be apples to alligators because our pages are from all sorts of documents, photographs, maps, video, audio, and more. Each file requires metadata (title, author, and a lot more) so books are relatively quick per item for page count. Letters, maps, and photographs are much slower with the same information often required for each page. ...

CC documentation project

Creative Commons Expands Documentation Project, press release, March 23, 2008.
Creative Commons today announced the expansion of a documentation project to explain various facets of Creative Commons licensing. The initiative includes links and PDF downloads to information on critical CC specifications, recommendations, research studies and tutorials. Some of the topics covered include the CC+ and CC0 projects, a simple licensing how-to, and best practices for integrating Creative Commons licensing in websites. The documentation project also offers posters, flyers and other creative media such as the “Sharing Creative Works” comic book. These documents may be downloaded directly from the Creative Commons Documentation page and are suitable for high quality printing and display. ...

Challenges and rewards of data sharing

Heather Piwowar, Eating my own dogfood, Research Remix, March 21, 2008.

... Sharing data is indeed hard. Specifically:

  • time consuming
  • decision-intensive (where to put it? what to share? what format to share it in?)
  • scary (what if someone finds a mistake?)
  • embarrassing (the data isn’t nearly as X as I wish I had the time to make it )

I also get to experience some of the first-hand benefits:

  • it forces additional organization
  • it helps me find my own data again later, from any computer!
  • it makes me feel proud to have made my science transparent (albeit after the fact, rather than as open notebook science)

I’m a firm believer in continual improvement. That means that I’ve shared my data now, in the best way that I have time for, rather than waiting until I can share it the way that I’d ideally like to. There are lots of things I’d like to improve:

  • Put it somewhere central and permanent (not clear where, for the esoteric dataset types that I have, but there are some neat possibilities)
  • Put it in a semantic format (!!!)
  • Document it better
  • Tag it so people can find it
  • ….

I’ll keep exploring and implementing these things as I get a chance.

If you want to put your data up but have hesitations about it, I say do it to the best of your ability right now given your current constraints. It isn’t perfect? I know, but perfect is the enemy of good enough. ...

See also this poster, Prevalence and Patterns of Microarray Data Sharing (Pacific Symposium on Biocomputing, Kohala, Hawaii, January 4-8, 2008), posted online March 20. .

OA textbooks at SXSW 2008

Anne Gentle has blogged some notes on the OA textbooks panel at SXSW Interactive 2008 (Austin, March 7-11, 2008).

Preview of Microsoft repository platform

Savas Parastatidis, Microsoft and "Research-Output" Repositories, Savas:web, March 24, 2008.  This excerpt omits several paragraphs of text, three images, a code snippet, and a video of a prototype.  See the original for a fuller picture.

What is Microsoft going to show at the Open Repositories 2008 conference in few days? Why is the entire "scholarly communications" section of the Microsoft Research Technical Computing team going there? ...Lee Dirks, Alex Wade, Santosh Balasubramanian (an honorary member!), and I are going to be there to interact with the community and to showcase —for the first time externally— our "research-output" repository platform....

Our goal is to abstract the use of underlying technologies and provide an easy-to-use development model, based on .NET and LINQ, for building repositories on top of robust technologies.

The platform has a "semantic computing" flavor. The concepts of "resource" and "relationship" are first-class citizens in our platform API. We do offer a number of "research-output"-related entities for those who want to use them (e.g. "technical report", "thesis", "book", "software download", "data", etc.), all of which inherit from "resource". However, new entities can be introduced into the system (even programmatically) while the existing ones can be further extended through the addition of properties.

This means, obviously, that arbitrary relationships between resources can be established. Our platform comes with a number of "known" predicates (e.g. "added by", "authored by", "cites", etc.) but it is extensible to accommodate any new predicates developers want to introduce....

Our system will be the back-end of a future version of the Microsoft Research web site. After Milestone 1, we’ll focus on an immediate public release, which is going to be free for download by the community. In fact, we are seriously thinking of even releasing the code to CodePlex for the community to take and extend....

We are already well into the process of developing a collection of tools and interfaces on top of the platform as tangible examples of how to use it.  We already have implementations of OAI-PMH...and working on Search and a simple Web UI. We are also working on WPF and Silverlight tools for visualizing the relationships between the resources within our repository....

At the Open Repositories 2008 conference, we will formally unveil our work in advance of its official release and initiate interactions/exchanges with the DSpace, EPrints, Fedora, and other players in the repository community. This is crucial to us because —like every other project our group undertakes— we are intensely focused on interoperability.

I want to be very transparent here: our effort is intended to provide a repository option to those institutions/organizations that already license or have access to Microsoft software (including the free versions of the products, like SQL Server Express). Our platform is intended to sit on top of the existing Microsoft "stack". By providing this new research-output repository platform at no cost, we can offer added value for our existing (and future) customers in the academic and research space. It is critical to point out that we are making every effort to ensure our platform is optimized to make the best use of Microsoft technologies AND to also interoperate with all other existing systems and platforms in the repository ecosystem. We are actively seeking engagement and feedback from the community! ...

UpdateTony Hey (Microsoft VP for External Research) writes to add, "My hope is that we can help create both EPrints and DSpace front ends so that librarians can choose which back end they prefer."

Sunday, March 23, 2008

OA presentations at Wake Forest

The presentations from the Scholarly Communications Workshop at Wake Forest University (Winston-Salem, North Carolina, March 13, 2008) are now online.  All three are relevant to OA:

Update (5/15/08). Podcasts for the presentations are now online as well.

Organization for OA journal editors and publishers

Dave Solomon and Gunther Eysenbach are calling for an organization of OA journal editors and publishers.  From Solomon's proposal:

...[I]t is time to start thinking about forming a professional organization of OA journal editors, publishers and those people interesting in supporting OA publishing.

Such an organization could serve a number of needed functions.

1. Education and mentoring -­ Many new OA journals fail. I believe this is largely due to a lack of knowledge and understanding of how to get a successful OA journal established and the resources and commitment it takes to sustain a successful journal. This gives gold OA a bad name and does a real disservice to the authors who had published their manuscripts in the journal. I believe a professional organization that could provide education and mentoring for individuals and groups that are considering forming an OA journal. In doing such could help alleviate this problem.

2. Setting standards and certifying journals as meeting these standards - There is still a pervasive belief that OA journals lack the quality and prestige of traditional fee for access journals. I believe gold OA has reached a point where it makes sense to develop some ethical standards and best practices as a community of OA publishers and a system for certifying that journals have met these standards and practices....

3. Coordinating the purchase of services to achieve economies of scale....

4. Advocacy - There are many organizations promoting OA. Most promote both green and gold OA. While in both are valuable mechanisms for achieving open access to research and scholarship, the issues related to green and gold OA are quite different. I feel it would be useful to have an organization that specifically focuses on promoting and educating the public and elected officials about gold OA. The intention would not be promote gold OA over green but to enlighten researchers and scholars, the public and elected officials about the value and potential of OA journals.

5. Provide a mechanism for small grant funding, research dissemination and other means of facilitating the development of electronic open access publishing....

These are just some ideas to get the discussion going. To help facilitate the process, I set up a web site with a forum and some draft documents to serve as a starting point for discussion.

Nothing is written in stone....If there is sufficient interest in forming such an organization perhaps it would make sense to try to set up a face-to-face meeting. One possibility would be at ELPub 2008 in Toronto this summer.

Buying, then liberating excellent educational content

Larry Sanger, A plea to liberate educational content, Citizendium Blog, March 22, 2008.  Sanger is the founder of Citizendium and co-founder of Wikipedia.  Excerpt:

This is a public appeal to philanthropists who are supporting education....

[T]he following is not an appeal for support of the Citizendium....

I cannot help but think that the world so far has been largely missing out on an enormous opportunity.  I am constantly fascinated by what global collaborations can do, and so when I receive a new book, I sometimes think: “How many people have bought a copy of this book?  If all those people had given their money to a web publisher to have the book released to the public for free in a digital form, would it be so released?  Sure; there’s nothing at all economically impossible about that.  So why hasn’t anyone done it?”  The answer, I think, is simply that a future universe of high-quality, free digital content is still in its mere infancy.  No one has yet been bold enough to seriously test out the new model I’m suggesting.  But if, through some sort of collective efforts, we were to liberate that excellent content I’ve paid for, then many more people could benefit from it.  This is deeply important, I think, because books and other media can change lives and indeed the whole world.  Wouldn’t the world be far better off with some of the very best educational content free to everyone?  That seems very obvious.

Well — why not pay for it then?  What’s stopping you? ...

So my suggestion is very simple: liberate truly excellent educational content.

In other words, buy or commission truly excellent content, which would otherwise be sold at the usual market rate to parents or school districts, and then simply post it online for free....

Comment.  The government of Indonesia has half the right idea.  It's buying the copyrights to selected textbooks and reprinting the books for sale at deep discounts.  Stian Håklev argues that the government should make the books OA under CC licenses.  (Blogged here on February 8, 2008.)  Sanger has the full idea.

For related projects, see my past posts on intellectual property conservancies.

Update.  Larry Sanger has now turned his argument into an online petition.  Please sign and spread the word.

Update.  Since I just mentioned the similar program in Indonesia, I should report an update from Stian Håklev based on three recent news stories in the Indonesian press.

Walt Crawford on the Harvard OA mandate and IR progress

The April issue of Walt Crawford's Cites & Insights is now online.  This issue has a lengthy section on Harvard & Institutional Repositories, reviewing a large number of recent developments and commentaries (including many by me and Dorothea Salo).  Excerpt:

...There’s a term that can be applied to any scholarly journal that boycotts work by Harvard faculty: Suicidal. Can you image the effect on any journal’s reputation once it became known that it would reject Harvard articles because it couldn’t live with Harvard’s retention of copyright?

For UC to follow suit would be wonderful: The likelihood of serious journals rejecting work from UC Berkeley, UCLA, UC San Diego or any of the other campuses in their specialties is also nearly zero. Add, say, any three or four of Yale, MIT, Cornell, Princeton, Columbia, Stanford, Michigan, Penn, Duke, Chicago, Toronto, Wisconsin and the University of Texas (I could go on…), and you’d have a clear case for journal publishers: “Deal with OA…or die.” ...

It’s enormously amusing that Patricia Schroeder, president of AAP, while saying “I don’t think anyone is quaking in their boots” because of the Harvard mandate, also said this: “publishers may not be quite as excited to take articles from Harvard.” Bwahahahah… oops, sorry....

ACRL's mixed messages on preprint access

Charles W. Bailey, Jr., College & Research Libraries Makes Preprints Available, but Restricts Access, Digital Koans, March 22, 2008.  Excerpt:

The Association of College and Research Libraries' journal, College & Research Libraries, is now offering access to preprints on its site; however, access is restricted to ACRL members.

According to the C&RL Manuscript Preparation page, the typical post-review publication delay for papers is about one year.

This preprint strategy does not appear to preclude authors from depositing preprints elsewhere after publication....

The American Librarian Library Association's author agreement that C&RL uses...says nothing about restricting the author's right to distribute digital preprints, yet the Manuscript Preparation page implies that the author is not free to do so prior to publication. Which is it?

If authors are free to distribute their own digital preprints, what good does it do to restrict access to preprints at the ACRL Website? ...

But even if [the C&RL Manuscript Preparation page is just poorly worded and needs to be clarified], it begs the question: "What is ACRL, which is actively promoting open access on many fronts, doing making C&RL's preprint service restricted?" While ACRL directly providing access to preprints at the C&RL Website is a welcome step forward, restricting access to those preprints is taking two steps back, and, although well intended, it sends the wrong message for an organization that is trying to move the open access agenda forward.

Read more about it at "C&RL Launches Preprints!"

Call for OA to midwifery courses

Sarah Stewart is looking for comments on her draft paper, Open access midwifery education.