Open Access News

Alexandre Linhares, A modest (billion-dollar) proposal, The Human Intuition Project, October 6, 2007.  Linhares is the Director-General of the Brazilian Chapter of the Club of Rome.  Excerpt:

Imagine the following scenario. A secretive meeting, years ago, when Apple's Steve Jobs, the benevolent dictator, put in place a strategy to get into the music business....I have no idea how that meeting went, but one thing is for sure: many people afterwards must have been back-stabbing Jobs, and mentioning "the music business? We're going to sell music? This guy has totally lost it."

Fact of the matter was, technology had forever changed the economics of the music business, and Jobs could see it.

Having said that, I'd like to make a modest, billion-dollar, proposal, to the likes of Adobe, Yahoo, Apple, IBM, Microsoft, and whomever else might be up to the task.

Think about science publishing....

The economics of science publishing is completely crazy for this day and age....

[T]echnology has forever changed the economics of the scientific publishing business, and it's high time for someone like Jobs to step forward.

Adobe Buzzword is specially suited to do this. Most scientific publishers (Elsevier, Springer) and societies (IEEE, ACM, APA, APS, INFORMS) have just one or two typesetting styles for papers. I imagine a version of Buzzword which carries only the particular typesetting style(s) of the final published document, and researchers would already prepare those manuscripts ready for publication....A submit button would submit the papers for evaluation, either to a journal or a conference. Referees could make comments and annotation on the electronic manuscript....

Buzzword is just my favorite option....Other options could be desktop processors (MsWord, Pages, OpenOffice, etc)....

Now, why would the people in Adobe, Yahoo, SUN, IBM, Microsoft, Google, or others actually want to do a thing like that?  There are two reasons. The first one is goodwill, the second one is money....

One crucial point is for the platform to be freely accessible to all. But you can do that, and still block the googlebot, the yahoobot, and all others "bots", but your own. Let's say, for instance, that Microsoft does something of the sort. In some years time, not only it gets the goodwill of graduate students who are studying papers published by science.microsoft.org (as opposed to hey-sucker-pay-thirty-bucks-for-your-own-paper-Elsevier), but also the way to search for such information would be only through that website. As we all know, advertising is moving online: according to a recent study, the last year saw "$24 billion spent on internet advertising and $450 billion spent on all advertising". Soon we'll reach US$100 Billion/year in advertising on the web. And imagine having a privileged position in the eyeballs of graduate-educated people, from medicine to science to economics to business to engineering to history....

Google might want to do it just to preempt some other company from blocking the googlebot to get its hands on valuable scientific research. Microsoft, the Dracula of the day, certainly needs the goodwill, and it could help it to hang on to the MS-Word lock in. Maybe Amazon would find this interesting--fits nicely with their web storage and search dreams. Yahoo would have the same reason as Google....

Comments

• I have no thoughts on Linhares' particular proposal --basically, a publisher-ready stylesheet and submit button for author apps, a platform to receive submissions and coordinate unpaid peer reviewers, open access compromised only by exclusive search indexing, and ads on search pages-- except that we're making good progress toward uncompromised OA without it. 
• But his proposal raises a larger and more important question.  I'd put it this way.  Journal publishing is dysfunctional and unsustainable in its dominant form.  Open access allows wider distribution and lower costs at the same time.  Tools to produce it, services to exploit it, and business models to support it are all multiplying fast.  There may be a trajectory in all this activity (and I believe there is), but at least there is ferment.  The ferment smells like readiness.  Now:  Is journal publishing susceptible to a sudden transformation from an unexpected player using a killer app and business plan?  Is there a Steve Jobs of journal publishing ready to act?

Charles Arthur, Free products can generate real money, The Guardian, October 5, 2007.  (Thanks to Glyn Moody.)  Excerpt:

...I once asked Google's head of open source how much it would cost the company if it ran Windows on its servers, rather than Linux. I recommend it as a question to Googlers if you want to see eyes bulge....

Ask yourself this: if Linux didn't exist, would Google? ... "Free" underpins a huge amount of effort on the internet now, and that translates into real world commerce: Amazon uses those free building blocks too for its business, which is largely about shipping atoms, not bits....

Using those free products, Google and Amazon and hundreds or thousands of other companies out there generate real value, real money, real taxes....

[Another example is the] Global Positioning Systems, aka GPS, aka sat-nav. GPS didn't just fall into the sky. It cost a lot of money to put it up there, and a fair bit to keep going - about $400m annually, including satellite updates.

But here's the thing about GPS: it's free to use, and in the short time that it's been available outside the military, its use has exploded. Figures for the value of the market are hard to come by, but EADS-Astrium estimates (in the graph at the end of the link) that this year it's worth about €40 billion. That's a hell of a multiplier on something that you give away for free, given a comparatively small investment....

Robin Peek, I Interview Me on Open Access, Wikis@GSLIS, October 5, 2007.

This is a preprint of my November column "Focus on Publishing" in Information Today....

Anyone who reads this column knows that I take on topics on Open Access (OA) frequently, increasingly frequently as OA events are occurring at an almost staggering rate. With the launch of Partnership for Research Integrity in Science & Medicine (PRISM) and some other events over the past couple of months, I have been quite peppered with questions. So, here is my salt to the dialog....

[I]t is unclear how representative PRISM is of the views of its member publishers, many of whom are engaged is some form of OA --even if it is just providing delayed access....

The publishing lobby has always been an obstacle to OA but OA started happening anyway. They are putting a higher gloss on the rhetoric but you have to remember that the publishing lobby has always had access to spin-doctors. Just try to interview a major publishing figure without their PR person listening in on the other line. OA came from much more humble roots (as in grassroots) in terms of message but its sophistication has grown. The Alliance for Taxpayer Access is one example that particularly stands out because the organizational members bring their own lobbying and PR knowledge to the discussion.

However, I think PRISM also represents the fact that the OA message is reaching beyond the usual “suspects” and they are seeking to capitalize on the fact that, sadly, people will accept spin without looking to see if there is any factual information to back it up. Frankly I have found it strange that an industry that claims to bank itself on facts are not offering much in the way of facts, particularly peer-reviewed research, to support their arguments. I defer to Peter Suber’s September issue of the Open Access Newsletter, where he outlines this in much greater detail than I have space to do here. Newcomers to OA will find this journey down the road already traveled (and traveled over again) very useful....

We already have OA and peer review is intact. The PRISM members know this as they have members who already allow the same type of OA that the National Institute of Health (NIH) puts forth as the mandate for the research it funds....The “sky is falling on peer review” is a fear tactic....

“Stop OA and everything will be okay” may well be the unofficial motto of PRISM (okay, I made up the motto) but this is like Microsoft campaigning to make Google go away....

Comment.  You don't see this everyday:  an OA preprint of a newspaper column, and one about OA to boot.  Kudos to Robin for trying it and to Information Today for allowing it.

Paul D. Thacker, Investigative reporting can produce a “higher obligation”, SEJournal, Summer 2007.  Excerpt:

...[P]ublishing executives and senior editors at ACS get bonuses based on how well the publishing operation performs. These bonuses are approved through the committee on executive compensation....

Comments

• We've long known that the American Chemical Society (ACS) pays very high salaries to its executives, at least for a non-profit scientific society.  For example, according to its 2005 tax returns, it paid Madeleine Jacobs $919,251 and Bob Massie $1,033,330.  At the time, Jacobs was the the society's CEO and Massie was president of its Chemical Abstracts Service (CAS).
• We've also long known that the ACS strongly opposed government OA policies, from PubChem to the NIH policy and FRPAA.  According to Nature, the ACS was one of only three publishers (with Wiley and Elsevier) to hear the Dezenhall proposal that recently evolved into PRISM. 
• Thacker's full article is of interest for another reason:  he explains why he was fired from his job as a reporter for one of the ACS journals --after a phone call to his editor from an industry executive who happens to chair the ACS committee on executive compensation. 
• The article includes a sidebar in which two ACS officers dispute parts of Thacker's account.  Excerpt:  "Bill Carroll, former ACS president, wrote to say...that he chaired the compensation committee but it does not evaluate or award bonuses to editorial employees."
• If your professional society has opposed government OA policies, try to find out whether its executives get bonuses based on the revenues or profits of its publications.  If they do, ask in a public meeting whether they believe this is a conflict of interest.

Taylor & Francis has added 31 journals to its hybrid OA journal program.  From yesterday's announcement:

Taylor & Francis is delighted to announce that its "iOpenAccess" option has been extended to cover 31 journals in environmental and agricultural sciences, behavioural sciences and development studies. This is in addition to the 175 journals from T&F's Chemistry, Mathematics and Physics portfolios, 7 behavioural science journals from Psychology Press, and medical and bioscience journals from Informa Healthcare....

We undertake to review the subscription prices of each journal with respect to the uptake of the iOpenAccess initiative, and the relevant information will be published [here]. The assessment of the first group of iOpenAccces titles will take place in early 2008....

Digital Library Center provides online dissertations, Inside UF, September 27, 2007.  Excerpt:

More than 9,500 dissertations from University of Florida graduate students of years gone by now languish on UF library shelves. The dissertations have been cast aside in the digital age which demands instant information.

But, if a new project at the George A. Smathers Libraries Digital Library Center is successful, decades of writings will soon be available around the world, with just the click of a mouse.

“What I’d like people to see is that the University of Florida is doing good work, and that we have in the past as well,” said Cathy Martyniak, head of the Library Preservation department.

Dissertations were first submitted electronically in 1998 at UF, and since 2001, the university required electronic submission for all dissertations. Martyniak said. Copyright restrictions require any doctoral candidate who completed work before 2001 to sign a release granting permission for scanning and Internet distribution....

Once a release form is submitted, the dissertation is scanned at the Digital Library Center and information called “metadata” provides information about the work, such as title, author, subject, year of publication and length. The work is then uploaded to the Digital Collections’ Web site, where the metadata allows for easy and accurate retrieval....

To participate in this project, UF dissertation authors are encouraged to visit [here].

Parliamentarians call for more books to be put online, EurActiv, September 27, 2007.  (Thanks to ResourceShelf.)  Excerpt:

The European Parliament has asked the Commission to speed up the process of setting up a European Digital Library, which aims to become a one-stop shop for accessing literary and scientific works online....

Digital libraries are essential for enabling scholars and students to access the rapidly growing number of scientific publications worldwide, as well as ensuring the accessibility of Europe's cultural heritage....

In a resolution adopted on 27 September 2007, the European Parliament supported the Commission's two-year old Communication....They recommended that the European Library "must initially concentrate on the potential offered by text material that is free of rights" and invited "all European libraries to make available to the European Digital Library works that are free of rights which they already hold in digital form"....

Ehud Ben Zvi, A Prototype for Further Publication Development of the Journal of Hebrew Scriptures and Other Open-Access Journals, Society of Biblical Literature Forum, September 2007.  (Thanks to Sansblogue.)  Excerpt:

Worldwide, completely free, and unrestricted access to peer-reviewed journal literature is a social and academic good. It is important for the creation and dissemination of knowledge, and as such to the academic guild and to society in general. It is important for individual researchers, students, libraries, and the general educated public.

The Journal of Hebrew Scriptures (JHS) is one of the academic, blind peer-reviewed, open access journals that provide such access electronically and whose contents are freely and permanently available to all. The number of articles and reviews it publishes yearly has grown steadily since 1996 — the year in which it is established — and so has its readership....

[T]he journal has become well-established....[T]he time has arrived to think about future developments in electronic open-access scholarly publication....

Worldwide, free, and unrestricted distribution of peer-reviewed articles and reviews using Internet technology was "revolutionary" a decade ago — and perhaps still is in many ways. However, the actual format in which the material was disseminated was, and still is, not "revolutionary" at all. We, as almost anyone else in the field of open-access journals, publish articles and reviews as PDF and HTML files....Our presentation of textual information follows the Gutenbergian model of a printed page, which in fact goes back for millennia to early writings....

The first challenge today for e-publication in our field is not to create new formats for the sake of "newness," but to think of textual presentations, or systems of textual presentations, that are more reader-friendly for the purposes, and within the mode, in which we read. In other words, we must think about how we read scholarly texts. We do read texts in linear ways, and therefore any new presentation should keep the text at least as friendly as it is now for that type of reading. But we also read texts in non-linear ways. When we read an article, we often stop to check a verse and then continue our reading; we then stop to read a footnote and at times go and grab another article or monograph to see what X or Z said about the issue....

[At JHS we decided to] keep the usual pdf format as the main way of publishing articles, but on the other we should develop and provide in our site marked xml files of the same texts.

The purpose of these xml files is to allow readers to create their own hypertexts, if they so wish, within the limitations of open access databases....[O]ur xml files should allow easy inclusion of future resources.

What kind of hypertexts do we imagine our readers would like, beyond the system of footnotes? We thought of the co-texts that people tend to have around their desks. For instance, we imagined that readers would like to be able, if they wish, to click on a reference to a verse (or verses) and view it in its original language, or gather relevant discursive, syntactical, or morphological information, or view several ancient and a variety of contemporary translations, or bibliographical databases mentioning works that deal with this verse....

We also thought that improving search capabilities would make documents more helpful....

[T]o implement all of these while keeping the journal open access, which is a non-negotiable issue for us, is a tough act. It involves technical, financial, and general resources challenges....

If you use Infomine, this tip should help:

...There are a few ways to isolate open access electronic journals in your search. From the INFOMINE Electronic Journals search page, either select "Free" in the Resource Access dropdown, or enter the term "open access resource" with your search term in the main search field. Shared Cataloging Program records in INFOMINE generally use this tag to indicate a free resource, though it may also indicate (and provide a link to) a portion of free resources within an otherwise access-restricted site. In this way, searching with the included term of "open access resource" may return a larger number of records than simply selecting "Free" in the Resource Access box....

Ulrich Herb, Online oder unsichtbar, Telepolis, October 5, 2007.  A report on the meeting, Open Access Policies deutscher Verlage (Stuttgart, September 26, 2007).  Read it in the original German or in Google's English.

PS:  If someone could post an English summary of this article, or first-hand observations of the September 26 meeting, to SOAF, then I'd link to it from this post.

Update. For a partial English summary, see Charlotte Hubbard's BMC blog post of October 9, 2007.

Under a new agreement between the University of Göttingen and Springer, all articles by Göttingen faculty published in Springer journals will be OA under the Springer Open Choice program.  Read yesterday's announcement in German or in Google's English.

Comment.  The press release doesn't say whether Göttingen is paying anything beyond its current Springer subscriptions for this extra benefit.  (The Open Choice publication fee is normally $3,000 per article.)  If so, then the deal is much like an institutional membership program.  But if not, then it's like the Springer deal with the Dutch library consortium, Universiteitsbibliotheken en de Koninklijke Bibliotheek (UKB), in which current subscription payments are considered to cover publication fees as well.

In my newsletter article Tuesday on Flipping a journal to open access, I cited the Stanford Encyclopedia of Philosophy (SEP) as an example of an OA publication adopting a strategy similar to the second stage of a two-flip conversion.  (Sorry.  I know this won't make sense for those who haven't read the article.)

SEP's Principal Editor Ed Zalta and Senior Editor Uri Nodelman believe I may have given a false impression of SEP's fund-raising program, and they may be right.  The full story of SEP's fund-raising strategy is interestingly complicated and I've often blogged the details.  However, in the Tuesday newsletter I only described it as much as necessary to show the connection to the second half of a two-flip conversion.  As a result, I omitted many details and may have created a false impression.  I'm happy to post this clarification from Zalta and Nodelman:

...We are grateful for your mention of the Stanford Encyclopedia of Philosophy, and we hope you don't mind if we clarify a few of the points you made in the newsletter.  You write:

The second flip in this process is not as novel as it may appear. The Stanford Encyclopedia of Philosophy is in the middle of something very similar right now.  To build an endowment to cover its expenses,  it's asking institutions to make payments that resemble "flipped subscriptions":  institutions make annual payments, as they  would for subscription or publication fees, but when SEP has raised enough money, the payments stop and the encyclopedia is OA, no-fee, and self-sustaining.

We'd first like to note a few minor points: (a) libraries need not make annual payments to the SEP; they may instead make a one-time payment if they can pay their membership dues in one go (indeed, many universities have done just that).  With a one-time payment, they are done.  But we also allow libraries to spread out the payment over 3 years.  (b) The SEP is OA now, and has always been so, and so the clause that starts "but when ..." might give some librarians the wrong impression that it won't be OA until we have raised enough money.  (c) It is to be remembered that the SEP never underwent the first flip: we never conceived of library membership dues as author fees.

Second, it seems to us that the result of the second flip is a situation where institutions make general payments to the OA publication instead of author-based or "upload" payments.  This resultant situation is analogous to the situation in which the SEP currently finds itself (with the caveats noted above):  namely, an OA work that accepts general payments instead of payments tied to any direct upload/download activity.

Consequently, it seems that the SEP will be doing a third kind of flip -- from one where institutions make general payments to cover expenses, to one where no payments are required at all.   One might imagine other OA publications trying to make this 3rd flip by either (a) setting the price of the expense payments to a level that will allow for some investment into an endowment or (b) finding some partner(s) or grant agencies willing to cover the cost of operating expenses so that the payments can be used wholly for endowment funds.   One reason this might be acceptable to contributing institutions is that in the case of the SEP, the money received from libraries as membership dues is put entirely into the endowment and actually *held in trust* for these institutions; it would be returned (together with any interest and appreciation in excess of the annual payout) if the publication closes down.  This is the most distinctive part of the SEP's funding model.

We think this latter idea is the one worthy of emulation.

PS:  For more background, see the SEP's page on its fund-raising strategy.

For OCA's New Partners, Scan Plan Is a Commitment of Dollars and "Sense", Library Journal Academic Newswire, October 4, 2007.  Excerpt:

Brewster Kahle can be an effective speaker, no question about it —so effective, in fact, that when he pitched the Open Content Alliance (OCA) at the Coalition for Networked Information (CNI) meeting in 2005, shortly after its inception, librarians in the Boston Library Consortium (BLC) were hooked. "Barbara Preece (BLC), Maura Marx (Boston Public Library), and I saw Brewster's presentation at CNI," Brinley Franklin, vice provost for university libraries at the University of Connecticut (UConn), told the LJ Academic Newswire. "We were immediately interested in the concept."

That concept is now being put into practice as part of a sweeping plan unveiled last week by the BLC to scan millions of pages of public domain materials in its collections in conjunction with the OCA. "In total, I believe the BLC has pledged almost $500,000 a year for two years," Franklin said, augmented by financial support offered by the Alfred P. Sloan Foundation, which has granted BLC funding to host "a summit on open access." Doron Weber, program officer at the Sloan Foundation, has also vowed "continued support in light of our recent commitment to the OCA," Franklin added.

UConn, where library budgets have remained flat in recent years, has pledged both staff and capital. The library will invest $50,000 a year for two years toward the scanning. "This is slightly less than one percent of our collections budget, which will be our funding source," Franklin said. In addition, this fall UConn will hire a full-time "digital projects librarian" as well as reallocate several existing staff, mostly from collections services, to support digitization efforts. Franklin said David Lowe, UConn's digital preservation librarian, will serve on the BLC/OCA Implementation Team, and will lead the project at UConn....

UConn joins 18 other institutions in the BLC, as pioneers of sorts. It is the first large consortium to embark on a self-funded project with the Open Content Alliance. In all, members plan to scan at least ten million pages over two years, one million pages of which are set to come from UConn, as well as major collections such as the Boston Public Library's John Adams collection; documents from the Biodiversity Heritage Library, which includes collections from Harvard; the Marine Biological Laboratory; and Woods Hole Oceanographic Institution.

Most importantly, all of the scans, Franklin stressed, will be open, accessible from any browser, downloadable, and usable, unlike competing commercial plans, which place proprietary restrictions on their scans. Franklin said UConn is committed not only financially but in principle to the OCA's efforts to keep the public domain restriction-free, a policy that seeks to ensure a vibrant role for libraries. "The library staff at UConn was unanimous in its endorsement of unrestricted access to materials we digitize," Franklin says. "We are ready to turn down funding from companies that restrict searching digital collections through their proprietary search engine."

PS:  For more on the UConn participation in the project, see the October 1 story in the UConn weekly newspaper.

Jennifer Howard, Anti-Open-Access Effort by Publishing Group Loses Another University Press, Chronicle of Higher Education News blog, October 4, 2007.  Excerpt:

Another top university press has registered its displeasure with Prism, a controversial anti-open-access lobbying effort undertaken by the Association of American Publishers. Ellen Faran, director of the Massachusetts Institute of Technology Press, has resigned from the executive council of the association’s Professional and Scholarly Publishing Division. Even so, Ms. Faran told The Chronicle in an e-mail message, “The Prism Web site continues to give the incorrect impression that it has the unanimous support of the Executive Council.”

The Web site states that Prism, or the Partnership for Research Integrity in Science and Medicine, “was established by the Executive Council of the Professional & Scholarly Publishing Division of the Association of American Publishers (AAP) to educate policy makers and the American people about the risks posed by government intervention in scholarly publishing.” The group has made some language changes elsewhere on the site since the first round of publishers’ protests.

Ms. Faran’s exit from the executive council follows that of James D. Jordan, president and director of Columbia University Press, who stepped down on August 28, five days after Prism went public.  Mr. Jordan told The Chronicle that he had resigned in part “because I had vocally opposed the launch of the Prism Web site and did not subscribe to arguments supporting it.” Other academic publishers, including Cambridge University Press and Rockefeller University Press, have also publicly criticized Prism.

Comments

• This step sends a signal about the excesses of PRISM that words alone could not send.  Thanks and congratulations to Ellen Faran.
• How many publishers have publicly disavowed PRISM or distanced themselves from it?  Nine and counting (with links to their public statements): Cambridge University Press, Cold Spring Harbor Laboratory Press, Columbia University Press, MIT Press, Nature Publishing Group, Oxford University Press, Pennsylvania State University Press, Rockefeller University Press, University of Chicago Press.  How many publishers have been identified on the PRISM web site as members of the PRISM "coalition"?  Zero.

Emma Hill, JCB content automatically deposited in PubMed Central (PMC), Journal of Cell Biology, October 1, 2007.  An editorial.  Excerpt:

Public access to JCB content

The JCB has long been a leader in providing free, public access to the science we publish. Since January 2001 we have released our content six months after publication, and we also provide immediate free-access to colleagues in 143 developing nations. And, in this my first editorial in the journal, I am delighted to announce another enhancement to our commitment to public access. As of November 2007 we will deposit all JCB content in PubMed Central (PMC), where it will available to the public six months after publication.

PMC, developed and managed by the NIH's National Center for Biotechnology Information (NCBI), in the National Library of Medicine (NLM), is a free digital archive of literature from biomedical and life science journals. Despite a previous reluctance on our side, we are now happy to provide the NLM with all of our content in XML format. The process requires a certain amount of finessing to ensure accurate conversion (hence the short delay until November). This change in our policy stems from the realization that XML content may have greater longevity than PDF files. We also recognize the necessity for multiple archives of our electronic content as print is phased out.

Additional placement of JCB content in the PMC archive ensures permanent and free access in a central repository alongside research from other leading journals. Our routine deposit in PMC represents de facto compliance for authors with policies formulated by many funding agencies requiring access to research they have funded after a short delay. This service will be free of charge to authors (although HHMI are welcome to pay us $1,000–$1,500 a pop if they so choose)....

We continue to derive our revenue from journal subscriptions in addition to author billings, and we thus delay the public release of our content for six months. However, as has been the case since July 2000, if authors want to make their papers available sooner, they may post the final, published, PDF version on their own websites immediately after publication....

Comment.  This goes well beyond standard green policies that permit self-archiving.  It even goes beyond the few that positively encourage self-archiving.  It guarantees OA archiving and doesn't leave it to the initiative of busy authors unfamiliar with their options.  Automatic deposit in PMC is routine for OA journals at PLoS and BMC, but don't forget that JCB is a TA journal.  Moreover, JCB is depositing the published editions of its articles, not the unedited author manuscripts, and doing so from self-interest, not the goad of payments from authors or funding agencies.  Compare the HHMI deal with Elsevier in which Elsevier would not deposit even the unedited author manuscripts in PMC without payment of $1,000-1,500 per paper.  If other journals follow the lead of JCB, then the OA percentage of the new literature will rapidly approach 100% and funding agencies like HHMI will never again accede to archiving demands like those of Elsevier.  Kudos to JCB and Rockefeller University Press.

Nelson Pavlosky, FreeCulture.org is now Students for Free Culture, FreeCulture.org, October 2, 2007.  Excerpt:

One result of the new bylaws that our chapters just ratified is that our name is changing officially from “FreeCulture.org” to “Students for Free Culture”....

One problem that we’ve run into repeatedly in the past is that people have been confused about the exact nature of our organization upon hearing our name. For example, at our last US national conference, many people showed up who were not aware that we were a student organization, and many of them didn’t figure this out until the end of the conference. This name change reaffirms our focus on student activism on campuses across the country and around the world....

Elodie Portales-Casamar and seven co-authors, PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation, GenomeBiology, October 4, 2007.

Abstract:   PAZAR is an open-access and open-source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools for data submission and extraction. Curated boutique data collections can be maintained and disseminated through the unified schema of the mall-like PAZAR repository. The Pleiades Promoter Project collection of brain-linked regulatory sequences is introduced to demonstrate the depth of annotation possible within PAZAR. PAZAR...is open for business.

From the PAZAR Project Outline:

PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). Our goal is to be the public repository for regulatory data.

Bond University has more than 1,000 papers in its institutional repository.  From today's announcement:

Over 1,000 papers are now available online through e-publications@Bond.

Bond’s digital repository has achieved this milestone within a year of its formal launch last November. Steady growth has been accomplished with contributions of articles from every faculty, together with the recent appearance of some notable Bond University journals such as Spreadsheets in Education and Bond University Student Law Review who have made e-publications@ Bond their official home.

The 1,000th paper in fact belongs to our latest addition to the journal fold, Bond Law Review.  This journal commenced in 1989 and it continues to be an influential publication today.  The upload of all available volumes is expected to be completed in the very near future....

Peter Monaghan, Publishers and Treasury Office Settle Suit Over Restrictions on Authors in Nations Under Embargo, Chronicle of Higher Education, October 3, 2007 (accessible only to subscribers).  Excerpt:

In steps that could help end a long-running dispute over how American publishers of academic books and journals may deal with works submitted by scholars in some "enemy" countries, the U.S. Treasury Department has issued new regulations clarifying publishers' rights, and it has agreed to settle a lawsuit brought by several groups representing publishers and authors.

The department's Office of Foreign Assets Control, known as OFAC, published the new regulations in the Federal Register on August 30, and on Monday it agreed to settle the lawsuit, which was filed by the Association of American University Presses and other groups after a series of earlier decisions by that office that had imposed various conditions on publishers regarding works by authors in countries under U.S. trade embargoes.

The earlier regulations, which dated from 1999 but were not widely publicized until 2003, required American publishers to get prior government approval, in the form of a license from the Office of Foreign Assets Control, before editing manuscripts submitted by authors in embargoed countries. The rules also restricted other services, such as paying royalties to or collaborating with such authors, and adding photographs to or otherwise enhancing the value of their work. The regulations carried stiff penalties for violators: Editors, publishers, and even officers of academic organizations that acted as publishers could face fines of up to $250,000 and up to 10 years in jail.

The regulations at first required publishers to obtain a special license on a case-by-case basis before editing or publishing work by authors in Cuba, Iran, or Sudan. In 2004 the regulation was eased to require only a more easily obtained "general license" for dealing with such works. (Burma was added to the list of restricted countries in 2005.)

In this week's settlement agreement, both OFAC and the plaintiffs have won victories, to some degree symbolic. The treasury office will keep its general-license requirement, which appears to be a formality other than in unusual cases involving military sensitivity or direct involvement of embargoed foreign governments in research papers, and it will continue to restrict publication in those cases. The plaintiffs won a stipulation that works published in electronic formats enjoy the same protections as those published in print. Previously, the regulations had not specifically included digital publications among the kinds of "informational materials" that could be freely traded by Americans.

While the lawsuit had challenged the office's authority to impose even a general-license requirement, representatives of the plaintiffs applauded the settlement....

Comment.  This is one issue on which I see eye to eye with the publishers.  It was a scandal that the Treasury Department ever applied trade embargoes to scientific editing, as if ironing out an awkward sentence or fixing a diction error were analogous to exporting munitions.  The settlement is a major step forward, but the continuing requirement for a government license to edit manuscripts submitted by scientists from "enemy" nations is a serious impediment to the freedom of the press and the dissemination of research.  For background, see my many previous posts on this long-running controversy.

Update. Also see the press release on the settlement from the AAP/PSP, AAUP, PEN American Center, and Arcade Publishing.

Richard Poynder, The IP world is not for the weak minded, Open and Shut, October 3, 2007. 

Richard interviews Peter Vanderheyden, the Vice President for Global Intellectual Property at Elsevier's LexisNexis.  At the close of the interview, Vanderheyden explains why he believes OA would not work for a high-end patent database and why he's not considering it for LexisNexis generally.

I welcome the challenge [of competition] and believe that offering "must have" value added solutions built around the way our customers work will continue to create value that customers are willing to pay for.

Yasmin Anwar, Campus launches YouTube channel, UC Berkeley News, October 3, 2007.  Excerpt:

Further expanding public access to its intellectual riches through the most popular Web destinations, the University of California, Berkeley, announced today (Wednesday, Oct. 3) that it is making entire course lectures and special events available, free of charge, on YouTube.

UC Berkeley is the first university to make videos of full courses available through YouTube. Visitors to the site at youtube.com/ucberkeley can view more than 300 hours of videotaped courses and events. Topics range from bioengineering, to peace and conflict studies, to "Physics for Future Presidents," the title of a popular campus course. Building on its initial offerings, UC Berkeley will continue to expand the catalog of videos available on YouTube....

UC Berkeley has been a leader in the open-source video movement in higher education since fall 2001, when the campus's Educational Technology Services (ETS) launched webcast.berkeley.edu, a local site that delivers course and event content as podcasts and streaming video.

In April 2006, UC Berkeley launched its audio podcast program, making audio content available as free downloads through webcast.berkeley....

Peter Becker and Jos van Helvoort, Benefits of Open Access Publishing for students in higher education, in Proceedings EADI IMWG Conference 2007, The Hague, 2007.  Self-archived October 4, 2007.

Abstract:   Most students in higher education have some experience with Open Access when doing their desk research. They appreciate the free access of scholar publications on the World Wide Web. But students in higher education also develop their competences as junior researchers and publishers. Can Open Access Publishing help them to get some reputation in the international academic society? And how appreciate they the readers’ feedback on papers published on the internet? The Millennium Generation has grown up with free accessible information. They are supposed to embrace the idea of Open Access Publishing. However, students also may be anxious for publishing (preprints of) their papers, for instance for copyright reasons. It seems that good communication about the possibilities of Open Access Publishing by their educators (tutors, professors and librarians!) is very important.

The journal Oral Tradition, which converted to OA in September 2006, has now provided OA to all 22 years of its back run.

In my newsletter article yesterday on Flipping a journal to open access, I gave a couple of examples that came close to embodying the concept. 

Here's one I missed.  Jan Velterop wrote to remind me of the Springer deal with the Dutch library consortium, Universiteitsbibliotheken en de Koninklijke Bibliotheek (UKB).   Here's the key provision in the agreement:

Within the framework of the existing licensing agreement with UKB, Springer undertakes to offer free and immediate world-wide access to articles which have been accepted for publication in one of Springer's journals in 2007 by corresponding authors whose main affiliation is with one of the UKB members....

The UKB member institutions are already paying subscription fees, and now, with no extra payment, they are considered to be paying publication fees on behalf of their faculty.  Unlike a full Rowsean flip, the journals don't become OA.  But the new articles by authors at UKB member institutions will be OA, and for the same money that formerly bought reader access (to the non-OA articles in Springer journals), the UKB member institutions are now buying both reader access to non-OA articles and author access to OA articles.

For background, see the Springer press release on the agreement (June 21, 2007) and my blog post on it.

If I missed other examples, I'd very much like to hear about them.

Stevan Harnad, Departmental Repositories, Institutional Repositories, and Research Record-Keeping, Open Access Archivangelism, October 2, 2007.

Summary:  Individual departments should not sit and wait for their university to get its act together: Unless a consensus on adopting a top-down university-wide mandate can be reached promptly, departments should go ahead and adopt their own bottom-up mandates (the "patchwork mandates" recommended by Arthur Sale), as Southampton's ECS did in 2003. Apart from maximising the visibility, accessibility, usage and impact of departmental/institutional research output, an OA Repository (with a self-archiving mandate) can serve as its internal record, ending an institution's or department's need to rely on external proprietary databases in order to monitor and assess its own research output. (Southampton now has at least 13 EPrints Repositories to date; Cal Tech has a whopping 25.) ...

Michael Wong has blogged some notes on Teaching for a World of Increasing Access to Knowledge (Vancouver, September 18, 2007).  Excerpt:

In late September at UBC, Professor John Willinsky from the Faculty of Education and Brian Lamb from the Office of Learning Technology participated in a Teaching & Learning with Technology session entitled “Teaching for a World of Increasing Access to Knowledge.” It was a remarkable discussion, mostly due to the passion and candour of the speakers as they reviewed the opportunities resulting from the emergence of open source, open access, and open educational resources.

Only 15 to 20 percent of the information available to students these days could be categorized as Open Access, and the presenters were adamant that those numbers have to go up for a post secondary education to be meaningful (and useful)....

[E]ducational institutes should be leading the way by opening up access to their research studies....

One such example of open access is a new policy adapted by the Canadian Institutes of Health Research (CIHR)....

Another example of open access can be seen with the recent development of UBC Circle, an institutional repository where scholarly publications and articles are stored, indexed, and subsequently made available to the public for free....

Dr. Willinsky noted that the UBC Faculty of Education has seen an 80% increase in citations since publications have been uploaded into UBC Circle and made available to the public. This means that more scholars and researchers are viewing their articles and are using this information in their own publications, students have access to this material to use in their own research papers, and the general public is able to access this material to get a better understanding about a certain topic....

[Brian Lamb argued that] open access education is equipping students for life-long learning, at a time when they have access to more and more information. Learning should not stop after one finishes school, and open access to information allows people to continue exploring this information....

Students and instructors need to continue to demand more open access to material, create their own weblogs and websites to share information, and continue to pursue a “right to know”. Professor Willinsky and Brian Lamb would be happy to show you how it’s done.

Elsevier has released the license it will use when it deposits articles in PubMed Central (PMC) or UKPMC on behalf of funding agencies who have paid it to do so.  Excerpt:

Elsevier has, through certain arrangements with funding agencies, agreed to post sponsored final documents (hereafter referred to as “documents”) used to generate the definitive published journal article, to PubMed Central (PMC) or PMC mirror sites for non-commercial purposes.

Documents posted to PMC are protected by copyright and are posted to PMC by permission of Elsevier. At the time of deposit, posted documents included all changes made during peer review, copyediting, and publishing. PMC and PMC mirror site host organizations are responsible for all links within the document and for incorporating any publisher-supplied amendments or retractions issued subsequently. For a document that has been sponsored, the published journal article, guaranteed to be such by Elsevier, is available for free to non-subscribers on Elsevier’s publishing platforms including ScienceDirect.

For non-commercial purposes users may access, download, copy, display and redistribute documents as well as adapt, translate, text and data mine content contained in documents, subject to the following conditions:

• The authors' moral right to the integrity of their work is not compromised....
• If documents are copied or downloaded for non-commercial research and education purposes the appropriate bibliographic citation (authors, journal, article title, volume, issue, page numbers, DOI and the link to the definitive published version on ScienceDirect) should be maintained. Copyright notices and disclaimers should not be deleted.
• Use of documents for commercial purposes is prohibited. Commercial purposes include....
• Any translations, for which a prior translation agreement with Elsevier has not been established, must prominently display the statement: “This is an unofficial translation of an article that appeared in an Elsevier publication. Elsevier has not endorsed this translation.”
• For permission to use documents beyond permitted here, visit [here]....

Documents posted to PubMed Central are without warranty from Elsevier of any kind....

Comments

• I'm glad to see that the license grants significant re-use rights, for example to "access, download, copy, display and redistribute documents as well as adapt, translate, text and data mine content contained in documents...."  It could go further but this is a notable step up not only from other Elsevier licenses but from the default deposit in PMC, which is limited to fair use.
• It seems that this license only applies when Elsevier deposits the published editions of Elsevier articles.  In that case it would apply to all articles deposited on behalf of the eight members of the UKPMC Funders Group, including for example the Medical Research Council and the Wellcome Trust.  But it would not apply when it deposits peer-reviewed but unedited author manuscripts, as it does for the NIH and Howard Hughes Medical Institute.

JISC adopted an OA policy in the April 2007 version of its Generic terms and conditions of grant[s].  I didn't know about it until today when it was added to ROARMAP.  Excerpt:

21. JISC supports unrestricted access to the published output of publicly-funded research and wishes to encourage open access to research outputs to ensure that the fruits of UK research are made more widely available.

22. JISC firmly believes in the value of repositories as a means of improving access to the results of publicly-funded research and is investing significantly in this area. As part of this, JISC is funding The Depot; a repository which can host research outputs should institutions not have a repository in which to deposit. A national support project is also available to help institutions develop repositories and share practice.

23. JISC expects that the full text of all published research papers and conference proceedings arising from JISC-funded work should be deposited in an open access institutional repository, or if that isn't available, ‘The Depot’ or a subject repository. Deposit should include biographical metadata relating to such articles, and should be completed within six months of the publication date of the paper.

24. Which version of the article should be deposited depends upon publishers’ agreements with their authors but JISC mandates that articles should be made available through publishers that adopt the RoMEO 'green' approach as a minimum. Authors should go to another journal if the journal chosen does not adopt the RoMEO 'green' conditions.

25. JISC mandates the deposit of the native version (Word, PPT, etc.), with PDF as well if wanted, but certainly with a format from which usable xml can in principle be derived (not PDF).

Comments

• There have long been rumors that JISC was planning to adopt an OA mandate.  For example, when UK PubMed Central (UKPMC) was launched in January 2007, JISC issued a press release explaining that all nine members of the UKPMC Funders Group would soon require OA for the research they fund.  At the time, JISC was a member, although it's no longer listed on the member page. All eight other members have since adopted OA mandates.
• I consider the April 2007 grant guidelines to be an OA mandate even if it's not the rumored policy.  Many other OA mandates use the same language of expectation rather than requirement, and even the policies that use stronger language succeed because they create expectations, not sanctions.  The policy has three other strengths:  the reasonable embargo, the flexibility about the destination repositories, and the firmness that asks grantees to change publishers rather than compromise on OA.  Kudos to all involved.

Scott Kiel-Chisholm, Academic Authorship, Publishing Agreements and Open Access Survey, OAK Law Project blog, October 1, 2007.  Excerpt:

The Project is undertaking a survey of academic and scholarly authors in Australia to obtain an understanding of authors’ knowledge of publishing agreements and their experience in dealing with publishers in order to provide an accurate perspective on current academic publishing practices. The results received from the survey will be used in developing model publishing agreements, toolkits and training materials for academic authors and publishers.

The OAK Law Project seeks to promote strategies for the management of copyright so as to facilitate optimal access to research output, especially that which is publicly funded.

We know that your time is valuable, yet we encourage you to complete the survey as we are confident that the results will assist us in developing practical tools that can be used by authors to better manage their copyright.

If you are an academic or scholarly author in Australia, please complete the survey by clicking here....

The latest intelligence is that the Senate will vote on the bill to mandate OA at the NIH sometime during the week of October 15-19.  That gives us more time to ask our Senators to support the bill. 

I've collected all the info you need right here.  If you haven't already contacted your Senators, please do.  And please spread the word to others.  Messages should arrive before the end of business on Friday, October 12, to be sure that Senators see them in time.  That's 10 days.

A. Hijikata and 39 co-authors, Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells, Bioinformatics, September 25, 2007.  I'm linking to the PubMed abstract because the relevant issue of the journal isn't yet online.

Motivation:  Although a huge amount of mammalian genomic data does become publicly available, there are still hurdles for biologists to overcome before such data can be fully exploited. One of the challenges for gaining biological insight from genomic data has been the inability to cross-reference transcriptomic and proteomic data using a single informational platform. To address this, we constructed an open-access database that enabled us to cross-reference transcriptomic and proteomic data obtained from immune cells. RESULTS: The database, named RefDIC (Reference genomics Database of Immune Cells), currently contains: (i) quantitative mRNA profiles for human and mouse immune cells/tissues obtained using Affymetrix GeneChip technology; (ii) quantitative protein profiles for mouse immune cells obtained using two-dimensional gel electrophoresis (2-DE) followed by image analysis and mass spectrometry; and (iii) various visualization tools to cross-reference the mRNA and protein profiles of immune cells. RefDIC is the first open-access database for immunogenomics and serves as an important information-sharing platform, enabling a focused genomic approach in immunology.

Availability:  All raw data and information can be accessed from [the RCAI RefDIC]. The microarray data is also available at [CIBEX] under CIBEX accession no. CBX19, and [PRIDE] under PRIDE accession nos. 2354 to 2378 and 2414.

Update. Rufus Pollock points out that this database does not permit commercial re-use.

Gavin Baker, Open Access Journal Literature as an Open Educational Resource, a presentation at the Advisory Committee on Open Education Resources of the Virginia Joint Commission on Technology and Science. 

See Gavin's substantial blog post on the same topic from last month.

The committee is also willing to hear comments from the public on OERs.  Send them to Patrick Cushing.

Jean-Baptiste Piggin, Book industry resists free internet access to text, EUX.TV, October 2, 2007.  (Thanks to Klaus Graf.)  Excerrpt:

Fearing that it will lose out financially, much of the book industry is resisting internet pioneers' vision of putting the world's entire store of published information online. 

Some European libraries have portrayed the bid to digitize 500 years of books and newspapers as an imperialist plot, because the big players such as Google are based in the United States.

But other libraries have signed accords with Google. Most readers and internet users who have used services like Google Book Search have been delighted at how it helps track down useful books.

Digitizing, and whether or not it is a threat to "book culture," will be an issue looming over the October 10-14 Frankfurt Book Fair....

Supporters say Google cannot proceed any other way [than with an opt-out policy], since many copyright owners are dead, no longer trading or practically untraceable. But publishers accuse Google of "stealing" the books whenever it copies the content into its huge servers....

Work began in 2005 on the VTO project, which stands for Volltextsuche Online (full-text search online). The VTO is set to be unveiled as a working system with a stock of 7,000 in-print books at the October 10-14 Frankfurt Book Fair....

Publishers' attempts to shut out the "other internet players" are also being resisted by people who say the public should have "open access" to taxpayer-funded scholarly and scientific research....

In Germany, copyright legislation is expected to come into force at the end of this year granting publishers the online rights to pre-1995 work. Before that time, online publication was undreamed of and rights to it were not mentioned in contracts.

Klaus Graf, an open-access advocate in Germany, is encouraging academics to use a one-year opt-out period to claim those online rights to their pre-1995 work and put the papers on the internet.

The prospect of scientists publishing on the internet instead of in paper journals has prompted academic publishers such as Springer to offer authors an open-access option, if they are willing to pay.

Even more worrying, from a publisher's perspective, is the prospect of expensive college textbooks being replaced by e-books that would be free to students. A British government agency, JISC, announced in September a nationwide trial with 26 books issued free....

Laying the foundations for the European Digital Library, a press release from EDLnet, October 1, 2007.  Excerpt:

A project has begun to bring the European heritage online through a single portal.

Seventy senior managers and technical experts from museums, archives, audio-visual collections and libraries across Europe came together to plan the European Digital Library. The meeting took place at the National Library of the Netherlands.

The initiative stems from the call by Viviane Reding, the European Commissioner for Information Society and Media to ‘make the wealth of material in Europe’s libraries, museums and archives accessible to all’.

This reflects growing user interest in major digitisation projects that are creating large-scale online heritage resources. However, this is the first initiative to focus on providing a multilingual interface to digital artefacts, texts and media from across the European heritage.

Such collaboration between the archival, library, audio-visual and museum domains on this scale is a significant new move....

The project – the European Digital Library network (EDLnet) – runs for two years, and will develop a prototype that demonstrates proof of concept, bringing together content from some of Europe’s major cultural organisations. The project will be run by The European Library together with the National Library of the Netherlands. 

The project will look at the political, human, technical and semantic issues that will contribute to the creation of an interoperable system able to access fully digitised content. It will invite feedback from different types of users in order to create a service that enriches the widest public and answers the needs of researchers, students, teachers and the creative industries.

EDLnet is an initiative developed following the European Commission’s recommendation on 24 August 2006 on the digitisation and online accessibility of cultural material. It is a Thematic Network funded under the eContentplus programme as part of the i2010 policy

EDLnet builds on the success of The European Library, a portal that enables people to search across 150 million titles, from 172 collections in 31 European national libraries. The European Library is a service of the Conference of European National Librarians....