Open Access News

News from the open access movement

Saturday, June 10, 2006

Another blog on OA

Zugang zum Wissen Journal is a new blog on OA by Eberhard Hilf. Posts are in German and English. The new blog takes the place of his annotated link collection, Zugang zum Wissen im digitalen Zeitalter.

PS: Good move, Eberhard! Welcome to the blogosphere.

UK group recommends anti-circumvention rights for researchers

The UK All Party Parliamentary Internet Group (APIG) has released a Report on DRM (dated June 2006). It's surprisingly friendly to user interests, as seen in the recommendation that will most affect researchers:
...that the Government consider granting a much wider-ranging exemption to the anti-circumvention measures in the 1988 Copyright, Designs and Patents Act for genuine academic research.

(Thanks to Indicare.)

More on Microsoft book search's new partners

Nancy Gohring, Microsoft takes on Google in book search, InfoWorld, June 9, 2006. Excerpt:
Microsoft is expanding its book search service, an offering that will compete with a similar service from Google, it announced Friday. Microsoft will add digitized versions of some books from the University of California Library and the University of Toronto Library to Windows Live Book Search. The program, derived from the MSN Book Search project that was launched late last year, allows users to access and search through the books online. The Open Content Alliance (OCA) will scan, digitize and index out-of-copyright books from the libraries for Microsoft. OCA, an organization supported by technology companies and libraries.

It will also work with copyright holders to gain permission to scan and include protected books. With the announcement of the MSN Book Search initiative last year, Microsoft said it would join the OCA and work with the organization to scan and digitize books....Microsoft says it will work with OCA to obtain the permission of copyright owners to legally scan and include their books.

Comment. The article title points to a real corporate rivalry but at the same time may overstate it. Let's remember one thing: book-based search engines may be competitors but book-scanning programs are complementary, at least for users. Even if the companies can't say, the more, the merrier, we can.

OA plus a CC license for a new Caltech dissertation

Oleg Evnin has put a Creative Commons license on his new Caltech PhD dissertation, On quantum interacting embedded geometrical objects of various dimensions. (Thanks to Open Access Authoring @ Caltech.)

Comment. Thank goodness OA to electronic theses and dissertations (ETDs) is on the rise. What's new here is the CC license. Caltech requires all doctoral dissertations to be submitted in electronic form, and encourages OA to them through the Caltech ETD repository, but says nothing about using CC licenses for those that are OA.

Congratulations to Evnin on the successful defense of his thesis (May 26, 2006), for choosing Caltech's OA option, and for taking the extra step of using a CC license.

Interview with Jimmy Wales

Open Business has a short interview with Jimmy Wales, the founder of Wikipedia. Excerpt:
[Open Business:] I just spoke to publishers and authors - they are afraid of new ideas such as Wikipedia and GooglePrint. Its a real question: what happens if we move further into a world of free content - how do these people get paid? Any ideas?

Jimmy: I have no opinion about this. If the old firms cannot compete, they need to find something else to do.

Evidence-based librarianship needs OA to evidence

Heather Morrison, Evidence Based Librarianship and Open Access, Evidence Based Library and Information Practice, 1, 2 (2006).
Abstract: Evidence based practice, whether in librarianship or any other profession, depends on access to the evidence, and access to opportunities to share one’s own evidence. Open access (OA) is the perfect complement to evidence based librarianship. OA provides the optimum access to the evidence for librarians everwhere, and the optimum means of dissemination. This article compares examines access to the LIS literature in the print and electronic media, and the impact of open access.

OA to electronic theses and dissertations

The digitization blog is blogging the ETD 2006 conference in Quebec City. The first post contains a good summary of my keynote address on OA for ETDs (electronic theses and dissertations). The second post contains a good summary of Art Rhyno's presentation on open source.

PS: I thank the anonymous blogger who wrote this summary. (I'd be glad to thank you directly if I knew who you were.) My slides will be online at the conference site shortly.

Florida law bars state academics from studying in six countries

Yudhijit Bhattacharjee, Florida Law Bans Academics From Doing Research in Cuba, Science Magazine, June 9, 2006. Excerpt:

Beginning next month, Florida researchers won't be able to travel to Cuba to carry out any studies. Although the United States allows such interactions, the state has banned faculty members at Florida's public universities from having any contact with the island nation under a law enacted last week. "This law shuts down the entire Cuban research agenda," says Damián Fernández, director of the Cuban Research Institute at Florida International University (FIU) in Miami.

Cuba is one of six countries that the U.S. State Department has designated as a "sponsor of terrorism," although U.S. scholars can travel to Cuba for research if they first obtain a government license. The Florida measure, which passed the state legislature unanimously, essentially closes that loophole by disallowing state-funded institutions from using public or private funds to facilitate travel to such countries. (The list includes North Korea, Iraq, Iran, Libya, and Sudan.)

A newly enacted Florida law, sponsored by David Rivera, will force the state's academics to abandon research projects such as this University of Florida-led study of Cuban agriculture.  "Florida's taxpayers don't want to see their resources being used to support or subsidize terrorist regimes at a time when America is fighting a war on terror," says David Rivera, a Republican Cuban-American state legislator who introduced the bill. Florida researchers won’t miss out on anything by not going to Cuba, he adds: "I don’t think there’s anything there that cannot be studied in the Dominican Republic or other Caribbean islands."...

Marine scientist Frank Muller-Karger of the University of South Florida, St. Petersburg, says that Cuba's plans for offshore oil exploration make scientific exchanges between Florida and the island more important than ever before. "Any major pollution event off the coast of Cuba may reach Florida, and many important fisheries in the Keys may be connected to Cuba," he says....

Fernández and others are backing a plan by the American Civil Liberties Union (ACLU) of Florida to challenge the law in court....

Comment. Rivera made a mistake to supplement his national security rationale with a supposed scientific rationale (there's nothing to study in Cuba that can't be studied in the Dominican Republic). That opens his argument to rebuttal by people who actually know what they're talking about. When will politicians learn that the threat of terrorism can justify any new prohibition all on its own?

Update (June 12, 2006). The Florida Sun-Sentinel has published a sensible op-ed against this inane idea.

OA to biotech patents

Patently Transparent, Nature Biotechnology, May 2006. An editorial. Excerpt:
With the proliferation of gene patents and the increasing profusion of biotech patents and licenses with overlapping and competing rights, the ability to interpret and filter intellectual property (IP) has never been more important. Last month’s announcement by Australian startup CAMBIA, and its initiative BIOS (Biological Innovation for Open Society), of the creation of an open-access patent database collating IP data from several national patent offices promises to radically improve that process....

[S]earching for a biotech patent has become an inexplicably frustrating and convoluted process. There is no streamlined and universal approach for searching patents filed at the various national and international patent offices....Worst of all, each patent of interest must be downloaded and printed one page at a time --even though it might be 100 pages long. The explanation is not some technical difficulty, or even a lack of funding or resources. According to the EPO, “this was done as a voluntary restriction at the request of the commercial [patent search firm] operators.” In other words, searching and accessing patents has been made difficult purposely so that patent search firms can more readily charge clients for searches.

Fortunately, help is now at hand. CAMBIA’s Patent Lens is a freely accessible IP database that contains 2.5 million patents from the USPTO, EPO and PCT, together with a powerful search engine. The interface makes possible searches of the full text of patents from all these patent databases.... It is estimated that underexploitation of technical information (an estimated 80% of which is published in patent documentation and nowhere else) costs European industry alone $20 billion each year—simply because the inability to access relevant patent information results in duplication of effort or the creation of products that overlap with prior art.

Draft book chapter on access to knowledge

Ray Corrigan has posted a draft book chapter to his blog and seeks comments from readers. This excerpt begins after he finishes telling the very interesting story of Colmcille, a sixth-century Irish monk devoted to multiplying hand-transcribed copies of the Bible, frustrated by pre-copyright permission barriers to his work, and subject of one of the first legal decisions on access barriers to public-domain literature.
The Colmcille story is about a struggle over access to information. Access to information underpins the themes of this book which is about decision making related to and involving important socio-technological information systems....[I]n a knowledge society the default rules of the road are the laws governing the flow of information and the restrictions built into the architecture of technology. These laws and technologies are shaping up to be a bottleneck, particularly for decision making and education. It might be reasonable to stick a digital lock on an electronic version of some educational material and make it a crime to bypass the lock, but people need to be aware of this....

The third idea in the book is that changes in law and technology could be leading to a kind of “second enclosure movement” which threatens not only our ability to make informed decisions about those complex information systems, but even something as fundamental as our access to the basic raw materials of education. This is something which has been a problem in the developing world for generations. Relative to average incomes, a student paying $80 for a book in Indonesia would be the equivalent of a US student paying nearly $3200 for the same book in the US. A vibrant information ecology is at the foundation of our knowledge society, just as a vibrant natural environment is at the heart of a healthy society....

New hybrid OA journal on nanotechnology

Nanoscale Research Letters is a new hybrid OA journal from Springer and the Nano Research Society. From yesterday's press release: Excerpt:
Springer and the Nano Research Society have announced a new partnership to publish Nanoscale Research Letters (NRL), which will be the first nanotechnology journal from a major commercial publisher to publish articles with open access. The new journal provides an interdisciplinary forum for the open communication of scientific and technological advances in the creation and use of objects at the nanometer scale. The first open access articles are scheduled to appear on Springer’s online platform, SpringerLink, in July 2006....

“This new journal and the open access articles will cross disciplines, conventions, and mind-sets to uncover new rules of science and technology,” said Professor Greg Salamo, President of the Nano Research Society. “Springer is one of the preeminent publishers in the nanosciences, and we look forward to providing a publishing platform for scientists from all disciplines.”...

"We are very excited and proud to bring ’Springer Open Choice’ to the field of nanoscience and technology. Open access is increasingly seen as a high impact way of publishing scientific research and we are in the business of serving the publishing needs of the scientific community, whatever its requirements," said Jan Velterop, Director of Open Access at Springer.

Friday, June 09, 2006

Federated searching of OA repositories

Santiago Chumbe and five co-authors, Overcoming the obstacles of harvesting and searching digital repositories from federated searching toolkits, and embedding them in VLEs, in Proceedings 2nd International Conference on Computer Science and Information Systems, Athens, 2006.
Abstract: This paper addresses two important needs. The first one is the need to alleviate the resource discovery task across digital repositories by subject, which includes the ability of searching heterogeneous sources that apply to a specific audience (e.g. engineering academics) or purpose (e.g. research, teaching) from one access point. The second need is to provide toolkits for federated searching which are able to be embedded in electronic learning environments used by lecturers, students and researchers. Most of these environments are institutional Virtual Learning Environments (VLEs) and Portals. Our study will show that the satisfaction of both needs faces important obstacles. On one side, standard exchange formats such as Z39.50 or OAI, developed precisely to facilitate the transfer or sharing of data between computer systems, present obstacles that make the harvesting and searching of data from digital repositories a challenging process. On the other side, VLEs are often restricted in their ability to allow the sharing and re-use of external e-learning sources discovered by federated searching toolkits. A solution for these obstacles, based on a service-oriented architecture approach, is suggested and explored on a pilot system. The aim of our research is the realisation of the concept of flexible federated searching. The intention is that the VLE user should be able to use whatever search tool he/she likes for whatever repositories he/she needs to search, without concern for how the tool and the repositories manage to communicate, or how the tool makes search results available to other VLE components. The pilot system attempts to demonstrate that most of the flexible federated searching concept can be achieved by making proper use of current interoperability standards for digital repositories and e-learning systems.

A generic ontology for experimental science

Brock Read, A New Tagging System Could Help Computers Understand and Compare Research Results, Chronicle of Higher Education (accessible only to subscribers), June 9, 2006. Excerpt:

[Ross] King and Larissa Soldatova, professor[s] at Aberystwyth, have designed a framework that could help computers understand and analyze scientific papers and make useful comparisons among them. The framework -- an ontology, as the researchers call it, named EXPO -- allows scientists to document the essential details of their experiments with keyword descriptions known as metadata. A software program designed by Mr. King and Ms. Soldatova can then "harvest" those metadata tags, using them to look for specific kinds of research and compare the researchers' results.

According to Mr. King and Ms. Soldatova, the metadata their program relies on describes "generic knowledge about scientific experimental design, methodology, and results representation" -- information about what hypothesis was formulated, how it was tested, and what results the experiment achieved.  Mr. King and Ms. Soldatova made a point to keep the tagging data general because they want EXPO to pull together research from different sciences. Scholars in several disciplines -- like biology and genomics -- have worked to create their own ontologies, Mr. King says, "but they're doing that sort of individually in their own little silos....We tried to identify the key objects that are common to all experiments, whether they're biology, chemistry, or what have you," he says.

Computers that routinely read research reports might help keep scientists abreast of the work of scholars in other fields, and they could keep researchers from duplicating experiments conducted by their colleagues, Mr. King said. Of course, scientists must first be convinced to start using the EXPO framework -- which, for the time being, requires people who write research reports to input all of the required metadata themselves.

Comment. Just like text-mining software, article-reading and semantic-crunching software help OA by providing one more incentive for authors and publishers to make their work freely available on the open web for analysis and processing. I call this the software strategy for OA: build spectacular tools optimized for OA literature and add to the compelling incentives that already exist.

New OA journal on cell division

Philipp Kaldis and Michele Pagano, Cell Division, a new open access online forum for and from the cell cycle community, Cell Division, April 3, 2006. An editorial in a new journal from BioMed Central.
Abstract: Cell Division is a new, open access, peer-reviewed online journal that publishes cutting-edge articles, commentaries and reviews on all exciting aspects of cell cycle control in eukaryotes. A major goal of this new journal is to publish timely and significant studies on the aberrations of the cell cycle network that occur in cancer and other diseases.

New OA journal on multidisciplinary medical ethics

Dan J. Stein and four co-authors, Philosophy, Ethics, and Humanities in Medicine: Expanding the open-access conversation on health care, Philosophy, Ethics, and Humanities in Medicine, March 17, 2006. An editorial in the inaugural issue of a new OA journal from BioMed Central.
Abstract: Natural philosophy once spanned the fields of philosophy, science, and medicine. Scientific disciplines and medical specialties have rapidly achieved independence, and the availability of the internet and open-access publishing promises a further expansion of knowledge. Nevertheless, a consideration of the grounding concepts and ethical principles that underlie health care remains paramount. It is timely, therefore, to contribute to the global conversation on health care with an open-access journal that focuses on addressing the conceptual basis of medicine and related disciplines, considering the ethical aspects of clinical practice, and exploring its intersection with the humanities (including history of medicine).

OA web site on pain research and treatment

Pain Treatment Topix is a new OA web site on pain. From today's accouncement:
It provides evidence-based clinical news, information, research, and education on the causes and effective treatment of all pain conditions.

According to Pain Treatment Topix Publisher/Editor, Stewart B. Leavitt, MA, PhD, “In many ways, acts as a clearinghouse gathering and logically organizing all the clinical essentials of pain management at one website; thereby, visitors can make the most of their time on the Internet. This is an open-access website –– all of the resources are available free of charge, without restriction or required registration –– and we are not promoting or selling any products or services.”...

Pain Treatment Topix is modeled after another successful project –– Addiction Treatment Forum –– which Leavitt and colleagues started in 1992. This has become a leading noncommercial educational program in the addiction treatment field worldwide.

More on the AAP opposition to FRPAA

Mark Chillingworth, AAP science publishers club to fight US Fed Research Act, Information World Review, June 8, 2006. Excerpt:
STM publishers are coming together within the Association of American Publishers (AAP) to fight the proposed Federal Research Public Access Act 2006. The US Act aims to ensure that all research papers funded by the US government are made publicly available within six months.

The Professional Scholarly Publishing Division (PSP) of the AAP, which boasts McGraw Hill, Springer, John Wiley & Sons and Elsevier as members, is fighting the Act. Brian Crawford, chairman of the PSP, said: “If passed, the legislation will seriously jeopardise the integrity of the scientific publishing process.”...

PS: I responded to the AAP arguments back on May 10.

Major book-scanning partners for OCA and Microsoft Book Search

Microsoft to Collaborate With University of California and University of Toronto Libraries for Windows Live Book Search, a press release from Microsoft, June 9, 2006. Excerpt:

Microsoft Corp. today announced two key advances in Windows Live(TM) Book Search, a service that will enable Web searchers to find answers from authoritative, trusted book content. The addition of two new participants, the University of California and the University of Toronto libraries, will result in an addition of digitized material, primarily out-of-copyright books, from these two institutions to the Windows Live Book Search service. Also, the recently debuted Windows Live Books Publisher Program enables publishers to submit in-copyright material to become part of Windows Live Book Search....

With collections totaling more than 34 million volumes in the more than 100 libraries on its 10 campuses, the University of California library is the largest research and academic library in the world. In addition, the University of Toronto’s library network, the largest in Canada, has more than 15 million holdings and is one of the top-four research libraries in North America. These important collections will greatly expand the depth and breadth of content available through Windows Live Book Search....

With the support of the Open Content Alliance (OCA), publicly available print materials in UC and U of T libraries will be scanned, digitized and indexed to make them readily accessible to customers. OCA also works with copyright holders to legally scan protected materials.

"This announcement reflects the growing momentum of OCA," said Brewster Kahle, director of the Internet Archive, where OCA resides. "It is both encouraging and helpful to have Microsoft as an anchor in this effort to make public domain material freely available to consumers on the Internet."...

Boosting discoverability through search and OA

Susan Mayor, Search engines increase online journal use more than open access, BMJ, June 10, 2006 (accessible only to subscribers). Excerpt:
The ability of internet search engines to find journal articles has considerably increased the readership of academic journals, a detailed analysis of the internet use of one particular research journal has found. Introducing open access publishing achieved a smaller additional increase in journal use, the analysis showed.

Researchers at the Centre for Publishing at University College London used a deep log analysis, which collects “digital fingerprints” of users of specific internet sites, to track use of the online version of Nucleic Acids Research. They assessed use before and after the journal introduced an “author pays” open access publishing system, in which authors pay a fee to cover the cost of publishing their paper, which is then made available for free to readers. This was the first time that this technique had been employed to analyse the use of a single academic journal.

Comment. Without a subscription, I can't read the whole article. But it appears that the authors conclude that search introduces a bigger jump in discoverability than OA. What's key is that OA was introduced second. So the real conclusion appears to be that OA boosts discoverability even for a journal that's already searchable.

U of Zurich is implementing its OA mandate

Villö Huszai, Die Universitäten öffnen sich dem Internet, Neue Zürcher Zeitung, June 9, 2006. The University of Zurich is preparing to launch its OA repository this fall, as the first step toward implementing its OA mandate. Read the original German or Google's English.

New OA database of genetic and protein interactions

First comprehensive literature-derived database of yeast interactions, a press release from BioMed Central, June 8, 2006. Excerpt:
Researchers have built the first comprehensive manually-generated, literature-based, database of genetic and protein interactions. The database, which doubles the amount of information available on interaction networks in the yeast Saccharomyces cerevisiae, will be a useful resource for both the yeast and the systems biology community. In a study published today in the open access journal Journal of Biology, researchers manually curated the entire literature for genetic and physical protein interactions in the yeast Saccharomyces cerevisiae, an important model system for human cells. The database enabled better predictions of gene functions and protein interactions than all previous data collections combined....

The literature interaction dataset is publicly available at the BioGRID database and at the Saccharomyces Genome Database.

Elsevier and its critics discuss the future of journals

Matt Krupnick, Academic journals' futures up in air, ContraCostaTimes, June 7, 2006. Excerpt:

"We think the model of scholarly publishing is broken and needs to be changed," said Thomas Leonard, UC Berkeley’s head librarian. "Once you think about material delivered digitally, you start to think whether a journal is needed at all."

Leonard and others from the academic and corporate worlds will meet today on the Berkeley campus for a forum on the journal industry's future. The event is sponsored jointly by UC Berkeley's Center for New Media and Elsevier, one of the world's largest publishers....

In the 1980s and 1990s, universities balked at the publications’ rapidly rising prices. Some librarians, including those in the UC system, talked more openly about boycotting expensive titles. But faculty members, especially those at research-oriented institutions such as UC, simply cannot do without academic journals. Without access to research available only in journal articles, promotion and tenure is out of reach....

The pressure to provide the latest research to instructors and students has led institutions to continue to pay for the expensive publications, but not without a fight. When it came time for the UC system to renew its approximately $6 million contract for a wide range of Elsevier titles, university officials bargained aggressively until the company lowered its asking price. The Netherlands-based company does the best it can to limit annual price increases, said Karen Hunter, an Elsevier senior vice president who will speak at the Berkeley seminar. But the priciest journals can produce more than 300 new pages per week, she said....

But critics remain steadfastly opposed to such business practices. Publicly traded publishers such as Elsevier charge four or five times as much for their journals as nonprofit publishers, said Ted Bergstrom, a UC Santa Barbara economics professor who has studied journal prices since 2000. With technology evolving, publishers will need to innovate themselves to survive, Bergstrom said. "I wouldn’t underestimate them," he said, "but I would worry if I were one of the stockholders."...

More on OA to law

Jim Miles, Redefining Open Access for Legal Information, podcast of a paper presented at the 2006 Libraries in the Digital Age (LIDA) Conference (Dubrovnik, June 6, 2005).

An ambitious search engine for the worldwide deep web of science

The US Department of Energy has released a new report, DOE Science Accelerator: Advancing Science by Accelerating Science Access, June 2006. Excerpt:
To accelerate discovery, it is essential to accelerate the diffusion of science knowledge. This calls for a new era in the sophistication and breadth of the tools to access and use scientific knowledge. Herein, the Office of Scientific and Technical Information (OSTI), an organization of the U.S. Department of Energy (DOE) Office of Science, proposes the “DOE Science Accelerator.”

Why build the DOE Science Accelerator? Because it is impractical for researchers to spend time finding and sifting through hundreds, if not thousands, of information sources in various disciplines and still have time for life-altering discoveries of their own. Scientists and science-attentive citizens need a time-saving single-search interface for the whole of science. They need to explore the deep Web, where specialized databases are beyond the reach of surface Web crawlers such as Yahoo! and Google. They need transformational knowledge-diffusion technologies that enable robust and rapid scientific discovery. The DOE Science Accelerator will meet those needs....

A significant milestone was achieved in 2002 when introduced the capability to search 30 major databases of federal science agencies. OSTI pioneered this effort, but it has taken the cooperative effort of 16 information organizations from 12 executive branch agencies to successfully launch and sustain this authoritative gateway to scientific knowledge. It is estimated that there are as many as 1,000 additional sources of scientific merit throughout the world of university, non-federal and foreign research entities....[T]o accelerate advances in science and maximize the return on research investment, it is essential to create a global search capability to make these resources searchable and accessible....Just as science advances only if knowledge is shared, accelerating the sharing of knowledge will speed up the advancement of science. The DOE Science Accelerator will accelerate the sharing of knowledge by converting comprehensive cross-community searches from the impractical to the routine.

Comment. Under Director Walter Warnick, OSTI has built up a superb track record in federated searching and open access. OSTI is the only player on the scene willing to take on this ambitious project and it's in a good position to pull it off.

Update. Also see the June 8 press release from Deep Web Technologies, which got one of the key contracts to help OSTI develop the new search engine.

Update. For some reason, the document I excerpt above has been taken offline. But here's an older one, by Walter Warnick, on some of the same material, Enabling Scientific Discovery through a Science Information Infrastructure, March 18, 2002. (Thanks to Bob Calder.)

Update. The original document is still online but has been moved to a new location. (Thanks to Cathey Daniels.)


PLoS has issued a press release on PLoS ONE (June 7, 2006). Excerpt:
The Internet-fueled reinvention of the scientific journal took an important step forward with the announcement of PLoS ONE, a pioneering system for the publication and creative use of scientific and medical knowledge. PLoS ONE is the latest innovation from the Public Library of Science, a non-profit organization making the world's research literature a freely available public resource. PLoS ONE will return control over scholarly publishing to the research community by bringing together research from all areas of biology and medicine, offering authors an efficient and highly effective means to communicate their results and ideas, and providing the community with powerful new tools for navigating and adding value to the published research literature. "Scientists are eager to apply the awesome power of the Internet revolution to scientific communication, but have been stymied by the conservative nature of scientific publishing," said Michael B. Eisen, co-founder of PLoS and an assistant professor at the University of California, Berkeley. "PLoS ONE redefines what a scientific journal should be – eliminating needless barriers between authors and their audience and transforming the published literature from a static series of articles into a dynamic, interconnected, and constantly evolving resource for scientists and the public." ...

PLoS ONE will launch later this year and will be accepting submissions from the beginning of August.

More on the growing pains at BMC

Mark Chillingworth, Open Access publisher BioMed upbeat despite content overlap concerns, Informatin World Review, June 9, 2006. Excerpt:
Concerned voices of dissent from the editors of BioMed Central journals are merely part of the process of creating a new publishing business model, publisher Matthew Cockerill has told IWR....Three areas of worry have been highlighted [by BMC editors]: increases in the article processing charge (APC); a new code of conduct; and increasing overlap between existing and new journals from the stable....

“That BioMed Central is publishing more journals is positive for open access,” Cockerill said of the charges. “We have a lot of evidence that where we are strongest as a publisher is where we have clusters of journals and there is some overlap.” He added that clusters enabled BioMed Central to create gateways to content rather than to cannibalise. He also said that the code of conduct was circulated for feedback and is constantly being added to in response to feedback. “We are working on a new model of publishing. There are many issues that need improving and we are working on them.”

Remaining upbeat, he said the company has seen no detrimental effect on submissions since the dissent entered the public arena through The Scientist journal in May. Cockerill said he welcomed the current debate (click here for Cockerill on viability of OA publishing). “We have a shared interest with OA and it’s important that BioMed Central creates a viable business model for OA.”

A French publisher sues Google

Danny Sullivan, French Lawsuit Over Google Book Search, Search Engine Watch, June 6, 2006. Excerpt:
French publisher sues Google for piracy from AFP and French book publisher sues Google from the BBC cover how a French publishing group becomes the third to sue Google over its book scanning program. La Martiniere alleges the indexing project violates copyright. Association of American Publishers Sues Google over Library Digitization Plan and
Google's Library Scanning Project Heads to Court (action by the Authors Guild) covers the two other suits that I know of, which we've blogged about before.

Defending net neutrality

Lawrence Lessig and Robert W. McChesney, No Tolls on The Internet, Washington Post, June 8, 2006. An op-ed defending net neutrality. (Thanks to SaveTheInternet.) Excerpt:
Congress is about to cast a historic vote on the future of the Internet. It will decide whether the Internet remains a free and open technology fostering innovation, economic growth and democratic communication, or instead becomes the property of cable and phone companies that can put toll booths at every on-ramp and exit on the information superhighway.

At the center of the debate is the most important public policy you've probably never heard of: "network neutrality." Net neutrality means simply that all like Internet content must be treated alike and move at the same speed over the network. The owners of the Internet's wires cannot discriminate. This is the simple but brilliant "end-to-end" design of the Internet that has made it such a powerful force for economic and social good....

Update (June 9). Net neutrality suffered a serious setback in Congress today. Follow the details and help the continuing fight at SaveTheInternet.

Advantages of Fedora

Michael, The Jester’s Case for Fedora, Technosophia, May 2, 2006. The advantages of building an institutional repository with Fedora. (Thanks to Gayle.)

UK still wants to sell public info, not give it away

Heather Brooke, Make it work for us, Ms Tullo, The Guardian, June 8, 2006. Another article in The Guardian's excellent series on the Free Our Data campaign. Excerpt:
It may be a modern version of squaring the circle. According to the director of the Office of Public Sector Information (Opsi), Carol Tullo, it is feasible to open up the government's stores of data, uphold copyright and charge the public for official information. Speaking recently at a conference of freedom of information officers from government, she said: "Why should we be gatekeepers? We have enough to do in our day jobs than to worry about what the local economy may find interesting." The default position of government should be to trade in information, Tullo said, adding that transparency and openness benefits government in many ways....

More on permission barriers to online scholarship

Kristin R. Eschenfelder, An Assessment of Access and Use Rights for Licensed Scholarly Digital Resources, a poster for presentation at JCDL 2006. Self-archived June 7, 2006.
Abstract: This is a poster in a VERY large powerpoint slide. To view it, you should choose a 33% view option. To print it on one page, you need to choose a "scale to fit paper" option in print options. The poster contains more data than the accompanying document from the proceedings which is also available in dLIST. The poster reports the initial results of a study investigating how technological protection measures (TPM), or digital rights management systems, are used on licensed full-text digital scholarly resources from history, health sciences and engineering. The study results describe the range and variation in access and rights restrictions experienced by a typical user of assessed resources. Results also summarize librarian perceptions of the interactions between the restrictions and learning, teaching, scholarship and library management. Methodological lessons learned are also described.

More on the Linking UK Repositories report

JISC has issued a press release (June 7) on its recent report (June 5) on the OA repository infrastructure in the UK.

Coalition of society publishers opposes FRPAA

The DC Principles Coalition has released its June 7 letter to to Senators Cornyn and Lieberman, opposing the FRPAA. The society publishers in the coalition oppose the OA mandate, want to lengthen the six month embargo, assert that the bill will harm them, and nevertheless assert that it duplicates much of what they already do.

Comments. Three quick comments:

  1. I've responded to all these arguments already, e.g. in my comments on the AAP.
  2. "Scientific societies fully support the goal of increasing access to research..." This is true except for the word "fully". As their letter shows, these societies compromise their support for the goal of increasing access to research in order to support their revenue streams.
  3. I repeat my assessment that "publishers who object to [national OA policies] are defending the remarkable proposition that they should control access to research conducted by others, written up by others, and funded by taxpayers." They are putting their interests as publishers ahead of their interests as scientific societies.

Playing catch up

The posts to follow will be unusually short. I'm still on the road and should finish catching up over the weekend.

Thursday, June 08, 2006

One way to support no-fee OA journals

Heather Morrison, Open Access: the Membership Fee Subsidy Model, Imaginary Journal of Poetic Economics, June 7, 2006. Excerpt:
The majority of open access journals do not charge processing fees. Such journals operate on a variety of models and combinations of approaches. This blogpost looks at the simple membership-fee-subsidy model. For a very large society, a small subsidy from membership fees could create a very substantial pool of money for open access publishing. For example, if the world's largest scientific society, the American Chemical Society, were to set aside $10 from the fees of each of its 158,000 members, this would create an annual fund of $1.5 million to subsidize open access publishing. For an organization of this size, it is not out of the question to find such money by shifting internal priorities, without raising membership fees by so much as a penny.

Tuesday, June 06, 2006

On the road

My blogging and emailing may be a little slow and late for the next few days. I'll be on the road at a conference.

More publisher opposition to FRPAA

Rudy Baum, Take A Stand, Chemical & Engineering News, June 5, 2006. Excerpt:

The federal government is taking another stab at socializing scientific, technical, and medical (STM) publishing in the U.S. This time the effort arrives in the form of S. 2695, the Federal Research Public Access Act, introduced in early May by Sens. John Cornyn (R-Texas) and Joseph I. Lieberman (D-Conn.) (C&EN, May 8, page 28)....

The Professional & Scholarly Publishing Division of the Association of American Publishers ( has taken a strong stand against S. 2695. Recently, the division's Executive Council wrote a letter to Sen. Susan M. Collins (R-Maine), who chairs the Committee on Homeland Security & Governmental Affairs, the committee to which S. 2695 has been referred, urging her "to oppose S. 2695 and to prevent any attempts to advance this legislation."...

If you care about the future of ACS publishing operations-indeed, if you care about the timely and accurate dissemination of the scientific literature-I urge you to contact Sen. Collins and your state’s senators to oppose S. 2695.

Comment. Since the ACS is urging its members to write to Sen. Collins in opposition to FRPAA, it's more important than ever to write to her and your Senators to support it. The ATA has a template for contacting your Senators and asking them to co-sponsor the bill.

I really thought that not even the most raging and riled opponents of FRPAA would call John Cornyn a socialist.

NSB letter and McCain amendment call for scientific openness

Ted Agre, Panel faults U.S. science policy, The Scientist, June 6, 2006. Excerpt:

The U.S. government risks jeopardizing the "quality and credibility" of Federally sponsored scientific research by failing to encourage the open exchange of scientific information, according to the National Science Board (NSB)....The NSB, an independent panel that provides advice to the president and Congress on science policy issues, surveyed nine Federal agencies that conduct or support research, and found "no consistent Federal policy regarding the dissemination of research results by Federal employees."

"An overarching set of principles for the communication of scientific information by government scientists, policy makers, and managers should be developed and issued by the Administration," the NSB reported in a letter last month to Federal government agencies and to Sen. John McCain (R-Ariz.), who had requested the NSB study in February....

The Bush administration for years has been stung by criticism that it has censored government scientists, manipulated research results, and conducted political "litmus tests" of prospective scientific advisory board members.

The NSB surveyed policies at the National Institutes of Health (NIH), National Aeronautics and Space Administration (NASA), National Oceanic and Atmospheric Administration (NOAA), the Environmental Protection Agency (EPA), among others. NASA and NOAA, in particular, have come under recent scrutiny following reports that senior officials had barred agency scientists from discussing climate change with reporters or from presenting scientific papers without prior approval. NASA has since developed new policies on scientific openness....

Benjamin Fallon, a spokesman for the White House Office of Science and Technology Policy (OSTP), did not respond to requests for comment. Last month, after receiving the NSB letter, McCain, ranking member of the Senate Committee on Commerce, Science, and Transportation, inserted an amendment to a Senate bill that would require the Bush administration to formulate an "overarching set of principles" to foster open exchange of data and research results. The bill, the American Innovation and Competitiveness Act of 2006 (S 2802), was approved by the full committee on May 18 but has not yet been sent to the Senate floor for a vote. McCain spokesperson Andrea Jones did not provide further information....

Here's the key passage from the NSB letter to Sen. McCain (May 10, 2006):

Overall conclusion. Upon review as per your request, the Board finds that there exists no consistent Federal policy regarding the dissemination of research results by Federal employees. An overarching set of principles for the communication of scientific information by Government scientists, policy makers, and managers should be developed and issued by the Administration to serve as the umbrella under which each agency would develop its specific policies and procedures. The Board believes a need exists for all Federal agencies that conduct research to establish policies and procedures to encourage open exchange of data and results of research conducted by agency scientists, while preventing the intentional or unintentional suppression or distortion of research findings and accommodating appropriate agency review. A clear distinction should be made between communicating professional research results and data versus the interpretation of data and results in a context that seeks to influence, through the injection of personal viewpoints, public opinion or the formulation of public policy. Delay in taking these actions may contribute to a potential loss of confidence by the American public and broader research community regarding the quality and credibility of Government sponsored scientific research results.

Here's the key passage of McCain's amendment to the American Innovation and Competitiveness Act of 2006 (S 2802):

[Section 104.a] Within 90 days after the date of enactment of this Act, the Director of the Office of Science and Technology Policy, in consultation with the Director of the Office of Management and Budget, shall develop and issue an overarching set of principles for the communication of scientific information by government scientists, policy makers, and managers to the public. The principles shall encourage the open exchange of data and results of research by Federal agency scientists....[Section 104.b] The Director shall ensure that all civilian Federal agencies that conduct scientific research develop specific policies and procedures regarding the public release of scientific information consistent with the principles established under subsection (a) within 180 days after the date of enactment of this Act. These agency-specific policies shall be uniformly applied across the agency, widely communicated, and readily accessible to all employees and the public. They shall specifically address what is and what is not permitted or recommended.

Comment. The openness at issue here is not open access. It's the freedom of government-employed scientists to report the results of their research without interference from uneducated political appointees with a contrary religious or political agenda. But open access could be part of the solution sought by the NSB and Sen. McCain. The FRPAA would make an excellent foundation for a "consistent Federal policy regarding the dissemination of research results by Federal employees."

Update. Also see Andrew Revkin's story on this in the June 8 New York Times.

Call for student support for FRPAA

Gavin Baker, Research will suffer if UF cuts journals, Alligator Online (student paper at the U of Florida), June 6, 2006. Excerpt:
If you're like most students, you'll write a research paper during your time at UF. More than likely, you'll need to access articles published in academic journals, which you'll do thanks to a subscription by the UF libraries. But what do you do when the library doesn't have a subscription?

That situation is today's reality. Last year, UF's library materials budget was well under the average of the top 10 public universities, and just more than half the budget of the University of Michigan. Next year, the library is planning to cancel $750,000 in journal subscriptions due to funding constraints. Ultimately, UF will never be able to afford all the research materials we might need. The question is not, "What if we didn't have access to research?" but, "How can we make things better?"

Today, Congress has the opportunity to improve access to vital research. Every year, the U.S. government invests more than $55 billion in research, which results in thousands of journal articles published annually. In fact, the federal government is by far the biggest financial backer of scholarly research. If researchers were required to make their findings available online as a condition of funding, access to research could be greatly improved.

A bill recently introduced by Sen. John Cornyn, R-Texas, and Sen. Joe Lieberman, D-Conn., would do just that. The Federal Research Public Access Act would require research-funding agencies to establish policies that ensure that the fruits of the research they fund are made available to every American. The bill has been supported by researchers and librarians - and students should support it, too.

Research assessment, impact factors, and OA

Colin Steele, Research with purpose, The Australian, June 7, 2006. Excerpt:

The UK Research Assessment Exercises and the projected Australian Research Quality Framework have given impetus to the existing "publish or perish" syndrome by researchers. An analysis of the increasing trend to measure research effectiveness also could lead to a situation where "publish and perish" may prevail....

Eugene Garfield, the creator of the Science Citation Index, now part of Thomson Scientific, notes: "Like nuclear energy, the [journal publication] impact factor is a mixed blessing. I expected it to be used constructively while recognising that in the wrong hands it might be abused."...

The selectivity of journals by Thomson is also a problem in that it has a distinct bias towards northern hemisphere and English language journals. Thompson covers fewer than half of the roughly 22,000 peer-reviewed journals currently published. Australian coverage is limited outside the science area. Where you publish is now almost as, if not more, important than what you publish. The assessment process has arguably distorted an original purpose, namely the effective dissemination of researcher output. Analysis of library data globally tends to show that a significant amount of purchased material is little used. Thomson statistics also show that 80 per cent of citations come from 20 per cent of articles. Nature revealed that 89 per cent of its citations in 2004 were generated from just 25 per cent of the papers....

Mike Sargent, chairman of the National Collaborative Research Infrastructure Scheme, stated to the 2005 National Scholarly Communication Forum that "the Government regards publicly funded research as a public good" and that "as a general statement of principle, researchers ought to be able to find out what research is going on and gain access to that research. Use of open access regimes and institutional repositories will be critical to both the development of the AF [Accessibility Framework] and the RQF."

Ultimately, it must be remembered that what's important is to disseminate research knowledge as effectively and openly as possible, rather than for that knowledge simply to be seen as a static and dormant symbol of research ranking, both individually and collectively.

More OA data from the NBII

The spring issue of NBII Access Newsletter is now online. Each of its articles is about some OA database (often a new OA database) hosted by the US National Biological Information Infrastructure (NBII).

John Blossom on the impact factor problem

John Blossom, Impact Factors: Scientific Publishers Face Uncomfortable Truths About Citation Policies, Shore Communications ContentBlogger, June 6, 2006. Excerpt:
The Wall Street Journal (subscription) reports on the troubling revelation that impact factors, the calculations used to calculate the value of a scientific journal based on the frequency of citations to its content, may have been manipulated by some publishers by their pressuring of article authors to increase their citations of a particular publication....[The problems] presented are part of a broader picture of established publishers trying to shore up their value in an era in which competitive outlets challenge their supremacy....

In the process of moving from traditional review and ranking techniques with only the greatest of reluctance many scholarly publishers are missing enormous opportunities to redefine how scientific thought can be made available and useful in much more efficient, effective, reliable and valuable ways. It's not a matter of paid-versus-free, either: it's not clear that "open access" journals offer any significantly better review and impact measurement value, only a new way to subsidize existing review and ranking techniques....

[I]ntelligent publishers should be working now to develop more efficient ways to evaluate the ongoing value of scholarly content that take far more advantage of the online technologies that have made advances in much of today's scientific thought possible. There will be far more premium value to be obtained from a superior method of bringing good scholarly thought to market more quickly and effectively than from defending a system that is in danger of hurting the cause of progress as much as it helps it.

To those publishers who feel that markets have no alternative but to play by this game, I'd urge them to recognize that in an increasingly global publishing marketplace alternative systems are going to evolve more quickly than one may imagine - especially when emerging economies can provide themselves with more advantage when they do so. The Western style of scholarly publishing is likely to be challenged in the years ahead by Asian markets that want to accelerate their progress in bringing products and services to market based on advances in scientific thought....

PS: See my comments on the same WSJ story earlier today.

OA research on academic search, from Microsoft

Microsoft has announced the 12 winners of its funding competition, Accelerating Search in Academic Research. (Thanks to ResourceShelf.) From the June 2 announcement:
Researchers from 36 countries submitted proposals for research to advance the field of search. The 12 winners will receive grant money from Microsoft Live Labs and access to a set of MSN Search query logs in order to push forward our understanding of the Internet, search, and online social behaviors.

The results of the research we’re funding are intended to be totally open to the public. We’re encouraging the awardees to publish what they find in peer reviewed journals and at conferences. Nothing about this is proprietary. It’s our gift back to the research community.

PS: Congratulations to the 12 winners and kudos to Microsoft for its commitment to provide to open access to the research results.

Richard Poynder interviews Harold Varmus

Richard Poynder has posted his interview with Harold Varmus, Nobel laureate, former director of the NIH, and co-founder of PLoS. This is the latest installment of The Basement Interviews, Poynder's blog-based OA book of interviews with leaders of many related openness initiatives. Read the whole interview for more on the origin of E-Biomed, PubMed Central, and PLoS, and Varmus' views on the Bethesda statement, the prospect of TA journal conversions to OA, the moral arguments for OA, and the pace of progress. Excerpt:

RP: Currently PLoS charges $1,500 for each paper it publishes.

HV: Yes. There are other ways to cover our costs too, including advertising on the web site of the journal, and through various kinds of memberships and sponsorships. We also think that open access journals will be able to increase their revenues by the same kind of philanthropic mechanisms that national public radio uses in America....

RP: ...What are your views on [the NIH] policy?

HV: I would argue that the policy he came up is not as strong as it ought to be....[R]ight now NIH is not getting compliance with its public access policy, and I think there will be repercussions from that....Congress is going to say: "What is in this database?" And when people take a look they will see that very little is going into PubMed Central that was not already being contributed before the new policy came into effect....

RP: ...[T]here has been a long-standing and vigorous debate within the OA movement about the respective merits of the so-called Green and Gold roads....What are your views on that debate?

HV: My views are very clear: at this point self-archiving is not Open Access....One of the important components of the definition of Open Access that we have all agreed on is that research information should be placed in a searchable database. Right now the only way to be confident that you can do that effectively is by using a large public digital library like PubMed Central....Some day perhaps we will be able to just self-archive, and it will all work fine; but we're not there today....

RP: I'm curious about your motivation for supporting Open Access so vigorously....

HV: I believe that science is one of those activities that improves the state of the world, and once you realise how important publication is in the series of acts that constitutes the doing of science, and once you understand the incredible transformation of that publication process that the Internet, and software, and the whole digital world, now promises it is hard not to be pretty passionate about trying to make that part of the scientific universe work more effectively.

Comment. With respect, Varmus is wrong to say that self-archiving is not OA. OA is a kind of access, not a kind of venue, and "OA repositories" deliver this kind of access as well as "OA journals", and distributed repositories deliver it as well as central repositories. Repositories certainly count as "searchable databases". If he wants to say that PMC searching is better than OAI searching, or that gold OA is more urgent than green OA, that's quite different. We should be discussing those propositions, but they have no bearing on the definition of OA.

New methods to peer-review OA preprints

Herbert Van de Sompel, Certification in a digital era, Nature, June 2006. A contribution to the Nature debate on peer review. An updated look at what are sometimes called overlay journals, which apply peer review to articles already on deposit in OA repositories. Excerpt:
A core inspiration [of his Digital Library Research and Prototyping Team at LANL] is that the digital environment allows for (indeed, requires) systemic changes in scholarly communication procedures. This potential for fundamental change is related to two properties of the digital environment that were unavailable in the paper world. First, the core functions of our scholarly communication system can be separated (at least theoretically) in the digital environment1. Second, we will be able to record in a machine-readable form, then aggregate, and later data-mine the collection of events of this system.

One line of investigation led us to define a framework in which peer review is an autonomous service overlaid on scholarly repositories hosting unreviewed manuscripts, with the repositories and reviewing services linked together for an integrated view of the distributed information. Another effort automatically identifies possible reviewers based on extractable information from the digital environment, such as a manuscript’s subject area and citation pattern, and the existing body of literature in the subject area....

The digital, networked environment allows for the functions of scholarly communication to be individually implemented by multiple parties in different ways, and then combined as alternative or companion services in what can effectively be regarded as a network-based value chain. This may seem far-fetched, but examples of such deconstructed value chains are already emerging....

Add to this the ability to track the use of digital manuscripts, and even to aggregate such usage information across distributed systems, combined with the intriguing correlations between readership counts and citation counts, and one can imagine the emergence of some new facet of certification provided by readership information. Collaborative environments in which peers can grade each other's manuscripts (like viewers rating movies in the Internet-based Netflix movie-rental system) could provide yet another certification indicator....Especially intriguing is whether automatically extractable quality metrics could be used as parallel facets of certification. If so, could such metrics be less prone to deficiencies resulting from the human-driven nature of peer review? Understanding that most, if not all, papers get published somewhere, could such automated metrics be more indicative of the actual quality of manuscripts?

More on peer review and OA

Nature has launched a debate on peer review just like its two earlier debates on open access (October 2001 and March 2004). At the same time, it is conducting an experiment in open review.

Comment. First I'll make my usual point that achieving OA and reforming peer review are independent projects. OA is compatible with every kind of peer review, from the most conservative to the most innovative. Tying OA to just one model of peer review doubles the difficulty of persuading institutions to adopt or endorse OA. There's no need to agree on the best model of peer review --ever, let alone before we take a step achieve OA. If we had to do so, we wouldn't be able to take a single step.

But having made that point, let me add that there are a lot of exciting synergies to explore between OA and different models of peer review, and the Nature debate is one good forum in which to explore them. For one example, see Herbert Van de Sompel's contribution to the debate, Technical solutions: Certification in a digital era. (I'm blogging an excerpt immediately after this post.)

"We have become whores to the impact factor"

Sharon Begley, Science Journals Artfully Try To Boost Their Rankings, Wall Street Journal, June 5, 2006. (Thanks to ARCLog.) Excerpt:

After [John B. West] submitted a paper on the design of the human lung to the American Journal of Respiratory and Critical Care Medicine, an editor emailed him that the paper was basically fine. There was just one thing: Dr. West should cite more studies that had appeared in the respiratory journal...."I was appalled," says Dr. West of the request. "This was a clear abuse of the system because they were trying to rig their impact factor."...

[T]here is mounting concern that attempts to manipulate impact factors are harming scientific research....

Impact factors matter to publishers’ bottom lines because librarians rely on them to make purchasing decisions. Annual subscriptions to some journals can cost upwards of $10,000. The result, says Martin Frank, executive director of the American Physiological Society, which publishes 14 journals, is that "we have become whores to the impact factor." He adds that his society doesn’t engage in these practices.

Journals can manipulate impact factors with legitimate editorial decisions. One strategy is to publish many review articles, says Vicki Cohn, managing editor of Mary Ann Liebert Inc....Since it is easier for scientists to cite one review than the dozens of studies that it summarizes, reviews get a lot of citations, raising a journal’s impact score....

Journals also can resort to "best-of" features, such as running annual summaries of their most notable papers. When Artificial Organs did this in 2005, all 145 citations were to other Artificial Organs papers....Self-citation can go too far. In 2005, Thomson Scientific dropped the World Journal of Gastroenterology from its rankings because 85% of the citations it published were to its own papers and because few other journals cited it. Editors of the journal, which is based in Beijing, did not answer emails requesting comment.

Journals can limit citations to papers published by competitors, keeping the rivals’ impact factors down. An analysis of citations in the Journal of Telemedicine and Telecare shows very few citations of papers in a competitor, Telemedicine and e-Health, "while we cited them liberally," says editor Rashid Bashshur, director of telemedicine at the University of Michigan, Ann Arbor....

Scientists and publishers worry that the cult of the impact factor is skewing the direction of research. One concern, says Mary Ann Liebert, president and chief executive of her publishing company, is that scientists may jump on research bandwagons, because journals prefer popular, mainstream topics, and eschew less-popular approaches for fear that only a lesser-tier journal will take their papers. When scientists are discouraged from pursuing unpopular ideas, finding the correct explanation of a phenomenon or a disease takes longer....As examples of that, Ms. Liebert cites early research on AIDS, gene therapy and psychopharmacology, all of which had trouble finding homes in established journals. "How much that relates to impact factor is hard to know," she says. "But editors and publishers both know that papers related to cutting-edge and perhaps obscure research are not going to be highly cited."...

Comment. What's the OA connection? A journal isn't even eligible for an impact factor until it's two years old, and even then Thomson Scientific is very selective about the journals it selects for tracking. Because most OA journals are new, most don't have impact factors --though the ones that do have them are very competitive as Thomson itself has shown in two studies (one, two). The culture of chasing the impact factor therefore deters authors from publishing in most OA journals. Note that it also deters authors from publishing in any new journals, whether they are new because they're trying a new business model or new because they're exploring a new methodology or topic. For the same reason, it deters the launch of new journals. The impact factor does much more to entrench existing journals than to support much-needed change.

If the impact factor were an accurate measure of quality, then we might have to live with this problem. But in fact, it's a measure of impact (or more precisely, a mixture of real and illusory impact) that is systematically misused as a measure of quality. If this isn't already clear, I can add two problems to the good list Begley provided in her article. (1) When an article is cited to criticize it for error or fraud, the citation still boosts the journal's impact factor. (2) Impact factors measure the average citation impact of a whole journal but are often used to judge the impact (or worse, the quality) of an individual article or author when we have no idea whether they brought the average up rather than down.

One of the most effective steps we could take to help the cause of OA (and the cause of good science) is to get promotion and tenure committees to look for signs of true quality rather than settle for this crude surrogate.

IAA comments on the EC report

The Information Access Alliance has publicly released its May 23 Comments to the European Commission on "Study on the Economic and Technical Evolution of the Scientific Publication Markets in Europe. Excerpt:
Since the IAA exists to advocate for change in antitrust enforcement, our comments are focused on those analyses and recommendations relating most directly to antitrust issues....We particularly want to express our agreement with the study’s findings regarding “the broad facts about the market for journal publications” (Section Two). The IAA was organized in recognition of these facts to work within the United States to seek adoption of a new standard of antitrust review by state and federal antitrust enforcement agencies. One of the IAA members, SPARC, was created in 1997 specifically to be a constructive response to market dysfunctions in the scholarly communication system. The members of the IAA share the concern expressed in the Study’s analysis that the market for scholarly journals, particularly as regards STM publishing, is increasingly dysfunctional....Therefore, we enthusiastically support Recommendation B2 to reconsider historic approaches to merger review and increase scrutiny of future mergers. We too believe that evidence suggests that past mergers have substantially increased journal prices and that further mergers of large publishers will have similar effects.

Preview of PLoS ONE

The Public Library of Science (PLoS) has released a prototype of PLoS ONE, its big new project to launch later this year. PLoS ONE will offer multidisciplinary scope, rapid turn-around, open review, and powerful personalization and discussion tools. Here are some details from the site:

Inclusive scope. The boundaries between different scientific fields are becoming increasingly blurred. At the same time, the bulk of the scientific literature is divided into journals covering ever more restrictive disciplines and subdisciplines. In contrast, PLoS ONE will be a venue for all rigorously performed science, making it easier to uncover connections and synergies across the research literature.

Objective peer review. Peer reviewers are routinely asked to comment on whether papers are sufficiently novel or immediate to justify publication. Such subjective judgements can seriously delay the publication of good science. PLoS ONE will concentrate on identifying those papers that are rigorously and technically sound. Such work will be rapidly published and presented for open and continuous review so that the whole community can be involved in judging impact....

Interactive papers. A paper in a traditional journal is a static marker in an ongoing process. Authors looking back on papers written 6 months or a year ago will see things that they might now have written differently. New data may have arisen to strengthen or alter some of the conclusions. We will provide authors with ways to make those changes and so acknowledge the evolution of their ideas. This doesn't alter the scientific record—the original paper is still the original paper—but authors and readers can build upon it.

PLoS ONE will offer a new approach to the way that scientific research is communicated. Like all revolutions, this will take time, and the launch of PLoS ONE will only be the first step. New features and functionalities will be continually added to PLoS ONE while existing ones will be applied to an ever-increasing body of literature. We cannot do this alone and want to invite all members of the scientific community to help us shape the development of PLoS ONE and the future direction of scholarly publishing.

Toward shared norms on sharing

Science Commons has launched a major new project called Scholar's Copyright. It consists of three short amendments or Author Addenda that researchers may attach to their copyright transfer agreements with publishers. The addenda let authors retain the rights they need for OA. Like Creative Commons licenses, each of these will come in lawyer-readable, layperson-readable, and machine-readable forms. So far, only the lawyer-readable forms are available.

Here's a rundown on the three, from the new site:

  1. The OpenAccess-CreativeCommons 1.0 Addendum reserves the right for the author to post the published version (for example, as a .pdf file) immediately and to grant others a Creative Commons "Attribution NonCommercial" license to use the article.
  2. The OpenAccess-Publish 1.0 Addendum reserves the right for the author to post the published version immediately upon publication.
  3. The OpenAccess-Delay 1.0 Addendum reserves the right for the author to post the author's final manuscript version immediately and the published version six months after publication.

For a good discussion of why they're needed, how they differ from previous author addenda, and why we need three rather than just one, the background briefing paper is very helpful. Excerpt:

[T]he full powers of new technological approaches, such as text mining and semantic indexing, are not resulting in powerful new public resources. Contracts between publishers and universities can explicitly forbid such use of technology on scholarly resources, and the opportunities implicit in the Internet fall by the wayside. Efforts to create an "open access" movement have shown real success. But unfortunately the majority of scholarly research is unavailable, either for reading or for processing in software....

[M]ore than 90% of journals allow some form of archiving. In theory then, most authors in most journals can indeed legally self-archive. In practice, whatever the journals may state as a policy, many scientists are deterred by the legal issues, which are not well understood by authors. The Wellcome Trust has commissioned a special effort to examine, clarify and update the existing policy research.

Restrictions against archiving arise from the industry practice of requiring copyright assignments from the authors of scholarly papers to the publishers....These agreements do often allow authors to make archive copies available on the Internet, but with inconsistent policies and terms on timing of release, file formats, and location of archives. Some journals obscure their archiving policies on back pages of websites or don’t publish a policy at all....

The legal friction has not gone unaddressed. Several Addenda to copyright transfer agreements and suggested contract language to make compliance rights explicit have come from funders, librarians and universities. These proposals provide a mechanism and tools to negotiate and modify an existing copyright transfer agreement. Other approaches include replacing the copyright alienation systems with non-exclusive grants of a “license to publish” wherein the author retains ownership of the copyright and thus the rights to archive the article.  Early anecdotes suggest some success in terms of publisher acceptance of these new approaches, but none of the existing legal tools rises to the level of a standard. This creates, in turn, the risk of exacerbating the level of confusion, inconsistency, and arbitrariness of the present system.

Authors need to have the clear and unambiguous freedom to engage in their normal everyday scholarly activities without contending with complex technology, continuous amendments to contracts, or the need for a lawyer.

Although institution, funder, and policymaker may craft different legal text to reserve archiving rights for different classes of journal policy, these variations reveal clear patterns of use: the key variations are time to release an archived document, the format of the archived document, and the location of the archived document. These patterns can be identified and expressed in standard contract language. With significant community participation, the scientific community can build a new set of shared norms instead of wasting valuable resources through repeated negotiations....

For more, see the Scholar's Copyright FAQ.

CPTech joins the ATA

The Consumer Project on Technology (CPTech) has joined the Alliance for Taxpayer Access.

PS: This is a good time for other US-based non-profits to join the ATA, which works for open access to publicly-funded research in the US. The ATA is one of the most effective voices in Congress for the CURES Act and FRPAA, and its effectiveness grows when it can speak for a wider range of membership organizations. Joining the ATA costs nothing.

Monday, June 05, 2006

Fund-raiser for OA-committed autism organization

Cure Autism Now (CAN) is "is an organization of parents, clinicians and scientists who believe in urgency, excellence in science, research, treatment, collaboration and open access to information." Tomorrow it's launching a fund-raiser with ONCOR Entertainment. See the details in today's press release.

CAN maintains the Autism Genetic Resource Exchange (AGRE), an OA database clinical data and DNA samples. For details, see the AGRE FAQ.

JISC report on linking OA repositories

Alma Swan and Chris Awre, Linking UK Repositories: Technical and organisational models to support user-oriented services across institutional and other digital repositories, a JISC Scoping Study Report (111 pp.), June 5, 2006. Excerpt:
The JISC commissioned the project partners to undertake a scoping study whose aim is to identify sustainable technical and organisational models to support user-oriented services across digital repositories. Open access repositories of interest to UK further and higher education communities were cited as having particular relevance. The study is intended to inform strategies to support access and use of repositories, with a view to the establishment of a national repository services infrastructure or framework....

The following have been identified as top priorities:

  • interim ‘catch-all’ repository (or repositories) for authors whose institution does not yet have a repository
  • national resource-discovery service
  • meta-analysis services, specifically citation analysis and bibliometric analysis services that can inform future national research assessment exercises
  • repository usage and statistics services....

The full list of recommendations made to the JISC is as follows:

  1. The research community should be engaged at the highest level to encourage the establishment of repositories in all HE and FE institutions and the development of policies that will ensure the collection of content....
  2. Developments of repositories, aggregators, end-user services, and intermediary services should move towards a service-oriented architecture and establish separate layers for the aggregation model to maximise the flexibility available for building end-user services to meet user requirements....
  3. Additional means to generate metadata using automatic means are required. It is recommended that investigations into relevant techniques and tools be taken forward with some urgency....
  4. It is recommended that the use of RSS and ATOM be investigated as additional standards to OAI-PMH for use in aggregating metadata and content. They offer the potential of targeted exposure of repository resources that may be beneficial in the development of end-user services targeted at specific communities. It is also recommended that the exposure of repository contents within web search engines be examined in closer detail to assess the paths of exposure that exist and the implications for repositories of exposure via this route....

Sunday, June 04, 2006

California Medical Association endorses PLoS

Quality Matters: Open-Source Medical Journal Helps Physicians Translate Clinical Research into Practice, CMA Alert, April 13, 2006. CMA Alert is a publication of the California Medical Association. (Thanks to George Porter.) Excerpt:

The Internet is awash with medical information. But the most reliable medical information on the web-the contents of peer-reviewed medical journals-is hidden from the public and most of the world’s physicians. Although most medical journals are available online, their publishers limit access to those who choose, and can afford, to pay for access.

Unlike traditional medical journals, which limit access to maximize subscription revenue, the Public Library of Science’s journal PLoS Medicine is a free, open-source, peer-reviewed medical journal. The journal, launched in October 2004, is an international, multidisciplinary medical journal. It publishes studies designed to enhance the understanding of human health and disease and help physicians translate clinical research findings into clinical practice.

Because PLoS believes that medical research is an international public resource, its articles can be downloaded and distributed without restriction as long as the author is given proper credit. Publishing costs are offset by a publication fee charged to authors. PLoS waives the fee for authors with insufficient funds. The ability to pay is not known by the editors, and never affects the decision whether to publish an article....

OA and global civil society

Michael Schiltz, Gert Verschraegen, and Stefano Magnolo, Open Access to Knowledge in World Society? Soziale Systeme, 11 (2005) H2. I'm linking to a self-archived version. Despite the official date on the journal, the issue will appear later this month.
Abstract: This paper examines the societal significance of the Open Access movement and especially addresses its role in the public domain and in what’s commonly called ‘global civil society’. Taking advantage of the opportunity to study the emergence of a potentially transformative communicative technology in situ, we explore the social and evolutionary potential of Open Access, demonstrating how the global spread of technologies and associated semantics of ‘openness’ are giving new content to the concepts of the public sphere, civil society and social inclusion. In a first step, the paper argues that classical concept of civil society is less and less convincing and not adapted to the features of modern world society. In a second step the paper proposes different ways to rethink the notions of ‘civil society’ and the ‘public’ to fit the reality of a world society where knowledge is increasingly a resource for creating associations and networks. We argue that the Open Access and Creative Commons movement have contributed to the proliferation of non-localised, global ‘epistemic communities’ and have created new definitions of information and ownership. The paper also tackles misunderstandings of Open Access as a radical denial of copyright or revenue (and even profit), but demonstrates how Open Access is very well compatible with current economic realities and the emerging structure of world society.

Update (8/24/06). The published edition of this article is now OA at the journal site.

More time to comment on EC report

Comments on the EC report and its OA recommendations were originally due on June 1. But the deadline has been extended until June 15.

The original report is long. For a short summary of the OA highlights, see my SOAN story from May 2 or my blog posting from April 3. Note especially recommendation A1, which would mandate OA for publicly-funded research.

Please send a supportive comment to before June 15. You can be sure that OA opponents are sending in their comments.

Even a short comment in support of recommendation A1 would be better than no comment at all. It doesn't matter whether you live in a European country.

Review of Quosa

Mark Chillingworth, Quosa’s sharing habit will be hard to resist, Information World Review, June 2, 2006. Excerpt:

Quosa is an information management application that offers search, organising and sharing tools for the scientific, technical and medical (STM) online information sources Ovid, PubMed and Google Scholar.

At last year’s Online Information show, Quosa was one of the highlights of the Ovid stand, following a deal between the two companies in the autumn. Quosa is basically a desktop plug-in that wraps itself around your browser. It does not replace the search engine of the information source; Quosa’s search facilities are text mining tools that let you dig deeply into the content once it has been retrieved.

The main driver for adopting Quosa is its ability to create an information sharing environment. It lets users create virtual libraries of information that other members of a team or organisation can access and share....

You can share the results of your research with your peers by setting up virtual libraries in the My Article Organizer panel. Once you have selected the information you want to save and share, you click on the Save button and set up a folder in your folders list using the same Windows Explorer navigation tools most people are familiar with....[C]lick on the Publish button, choose which library you want to publish to, and it’s all done. Everyone in your team who is a member of that library will now have access to your research.

Comment. Interesting product. There are three aspects of OA interest here.

  1. When Quosa shares downloaded articles, how does it handle copyright and licensing restrictions? Does it make sure that every user with access to the shared library also has acccess privileges under the relevant license? (What a headache.) If so, does it let users share OA content without any kind of user-authentication?
  2. Can Quosa let users share info with the world and not just with lab partners? Apparently not. But if it had a bridge to an OA repository, and not just a private library, then it could easily do so. Of course, that would aggravate the copyright and licensing problems --but only for non-OA content.
  3. Like virtually all text-mining tools, Quosa tilts the balance of advantage at least slightly in favor of OA. It may work equally well with free and licensed content (whatever can be downloaded to a browser by a licensed user). But since all users have access to all OA content and only some have access to TA content, Quosa automatically adds utility to all OA content while it only adds utility to TA content for some users. This gives authors and publishers one more incentive to make their work OA, an incentive roughly as large as Quosa is useful. (Quosa would add nothing to the utility of OA content if it did nothing but enable sharing, but don't forget that it also does text mining.)

OA to data through blogs

Jean-Claude Bradley has been blogging raw experimental data since February 2006. Yesterday he blogged a few more notes on the project:
I think that the part [of OA] that we have yet to embrace is the posting of work fresh out of the test tube. As long as scientific research is published in an article format and its value is determined by a popularity contest of citations and peer-reviewed blessing, there will be little motivation to post work fresh out of the test tube. Especially when issues like competition and tenure are at stake.

The reality is that the impact of raw experimental data is usually unknowable at the time when it is generated. It may never be used by anyone (which is a guarantee if kept in a private lab notebook) or it may at some point answer a key question for an agent (human or otherwise) looking for a solution to an important problem.

My opinion at this point is that publishers or any kind of central repositories are not going to be as effective in communicating this kind of raw scientific data, unless it is readily available on the uberdatabases like Google or MSN. That's why Blogger makes an optimal vehicle to communicate raw experimental data: no cost, no gatekeeper and anyone looking on an uberdatabase will find your stuff.

OA coming to the University of Liege

The University of Liege will soon launch an OA repository for the scientific publications of its faculty and the doctoral theses of its graduate students. Read the announcement (June 3, 2006) from the "OA rector" Bernard Rentier in French or read Google's English.

Comment. This is very good news. Can Pr. Rentier tell us anything about the underlying policies? For example, will the university require or merely encourage OA to journal postprints and doctoral theses?

New OA database on small molecules

ChemBank is a new OA database from the Broad Institute's Chemical Biology Program (at Harvard University) and funded by the U.S. National Cancer Institute's Initiative for Chemical Genetics (ICG). (Thanks to ResourceShelf.) From the site:

This knowledge environment includes freely available data derived from small molecules and small-molecule screens, and resources for studying the data so that biological and medical insights can be gained....

Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the ICG in collaborations involving biomedical researchers worldwide. These scientists have agreed to perform their experiments in an open data-sharing environment (data-sharing agreement).

The goals of ChemBank are to provide life scientists unfettered access to biomedically relevant data and tools heretofore available almost exclusively in the private sector. We intend for ChemBank to be a planning and discovery tool for chemists, biologists, and drug hunters anywhere, with the only necessities being a computer, access to the Internet, and a desire to extract knowledge from public experiments whose greatest value is likely to reside in their collective sum.

Update. ChemBank structures are now updated in PubChem.

"Tragic missed opportunity" for OA

Glyn Moody, Open Access: If Not Now, When? Open..., June 3, 2006. Excerpt:
Against a background of growing fears of an imminent pandemic triggered by avian 'flu, the announcement that a new journal, Influenza and Other Respiratory Viruses, is being launched by Blackwell Publishing to serve precisely this area, is welcome news. As the press release notes, quoting the editor the new title:
"There is considerable concern among experts working in the fields of influenza and respiratory medicine that there is an urgent need for international collaboration on research and development" says Alan Hampson....

Given this "urgent need for international collaboration on research and development" you might think that Influenza and Other Respiratory Viruses would be open access to allow that collaboration to be as wide and rapid as possible; indeed, it is hard to think of another area in medicine today in which free access to the latest information could be considered such a matter of life and death - not just for a few patients, but for entire populations. And yet nowhere does the press release utter the magic words "open access".

It is true that Blackwell announced its "Online Open" last year, whereby authors can choose to pay a fee so that their article is immediately made freely available for all to access online. But this is not quite the same thing, and it places the onus on the author. Far better for Blackwell to make OA the default for this title: it would receive huge kudos for the move, and earn the world's gratitude.

It would be sad, to say the least, if the title were to go down in history as a tragic missed opportunity to mitigate or even avert an influenza pandemic that later cost so many millions of lives.

Comment. Exactly.