May 2008 | Issue 2.08

Hardin Scholarly Communication News brings together a variety of topics that affect the current system of scholarly communication, with emphasis on new developments, open access and alternative publishing models in the health sciences. This newsletter aims to reflect the interests of its readers so please forward comments, suggestions and entries to include to karen-fischer@uiowa.edu.

Table of Contents:
Harvard FAS and Law School Pass Open Access Mandates
Rockefeller University Press Gives Away Copyright on Journal Articles
Progress Towards Public Access to Science - Harold Varmus on the NIH Policy
Journals Find Fakery in Many Images Submitted to Support Research
Are Impact Factors Inflated?
Comparison of SCImago Journal Rank Indicator with Journal Impact Factor
Introduction to the Health Commons
The Importance of Open Access for Taxonomy Research
Four Elsevier Perspectives on Open Access
Medical Patients Share Data to “get help, give help”

In a historic measure, the Harvard University Faculty of Arts and Sciences (FAS) in February unanimously approved a motion that compels Harvard researchers to deposit their “scholarly articles” in an open access (OA) repository to be managed within the library and to be made freely available to anyone via the Internet. Faculty members, however, can opt-out of compliance by obtaining a waiver, a point some OA advocates say could potentially undermine the policy’s effectiveness. Nevertheless, the Harvard vote provided a resonant “shot heard ’round the world” for the open access movement.

“This is a large and very important step,” said Stuart Shieber, professor of computer science at Harvard, who put forth the motion. “It should be a very powerful message to the academic community that we want and should have more control over how our work is used and disseminated.” In a statement released following the vote, Shieber cited serials costs that have “risen to such astronomical levels,” forcing cancellations and “reducing the circulation of scholars’ works.”

Specifically, the Harvard motion resembles a publishing contract of sorts; it compels faculty to give Harvard non-exclusive, irrevocable permission to distribute their articles online, which Harvard intends to do, as well as permitting others to use the works as well, as long as those uses are non-profit. In legal terms, the permission granted by each Faculty member is “a nonexclusive, irrevocable, paid-up, worldwide license to exercise any and all rights under copyright relating to each of his or her scholarly articles, in any medium, and to authorize others to do the same, provided that the articles are not sold for a profit.” Faculty members retain their copyrights in the articles, subject to the university’s license and are free to publish in other journals. The legislation does not apply to articles completed before adoption of the motion, and does not apply to Harvard’s professional schools.

Curiously, the policy also, “when preferable,” allows faculty to opt-out of compliance. All one has to do, is ask. “The policy specifies that a waiver of the license for an article will be granted by request of the faculty author,” Shieber told the LJ Academic Newswire. “This is in keeping with the principle that the policy should serve the faculty, and faculty members are in the best position to determine that in individual cases.”

Critics, however, including OA pioneer Stevan Harnad, questioned whether “potential author resistance to perceived or actual constraints on their choice of which journal to publish in,” could hamper the policy—in other words, if the most prestigious journal in a researchers’ field requires exclusivity, will that be enough to motivate a researcher to opt-out?

Valid questions, among many others, that will surely be examined in practice: the motion provides for an analysis of the legislation’s effectiveness, with a report to be delivered in three years. “There are of course many details of implementation still being worked on,” Shieber told the Newswire. “In general, these will be worked out under the principle of serving the faculty best in the distribution of their scholarly writings.”

Following suit, the Harvard Law School unanimously voted to mandate OA on May 7th.

From Harvard Law School Press Release:

In a move that will disseminate faculty research and scholarship as broadly as possible, the Harvard Law School faculty unanimously voted last week to make each faculty member’s scholarly articles available online for free, making HLS the first law school to commit to a mandatory open access policy.

“The Harvard Law School faculty produces some of the most exciting, groundbreaking scholarship in the world,” said Dean Elena Kagan ‘86. “Our decision to embrace ‘open access’ means that people everywhere can benefit from the ideas generated here at the Law School.”

Under the new policy, HLS will make articles authored by faculty members available in an online repository, whose contents would be searchable and available to other services such as Google Scholar. Authors can also legally distribute the articles on their own websites, and educators here and elsewhere can freely provide the articles to students, so long as the materials are not used for profit.

“This exciting development is something in which the whole Harvard Law School community can take great pride,” said John Palfrey ‘01, executive director of the Berkman Center for Internet & Society and newly appointed vice dean of library and information resources. “The acceptance of open access ensures that our faculty’s world-class scholarship is accessible today and into the future. I look forward to the work of implementing this commitment.”

The vote came after an open access proposal was made by a university-wide committee aimed at encouraging wider dissemination of scholarly work. Earlier this semester, the Faculty of Arts and Sciences voted to adopt a policy similar to the Law School’s new initiative.

Similar initiatives are underway to promote free and open access to scholarly articles elsewhere, although no initiative extends as far as Harvard’s. Legislation before Congress would mandate that all federally funded research be available in open access.

Library Journal Academic Newswire, Feb. 14, 2008
Harvard Law School Press Release, May 7, 2008

Under the new policy, instead of giving up their copyrights to the journals, authors will now provide the journals with licenses to publish their papers. The authors may reuse their work any way they like, as long as they provide attribution to the journals. Six months after publication, third parties may use and redistribute the papers under a Creative Commons license.

The press places one thing off-limits: creating Web sites that mirror the contents of a journal within six months of its publication. The press hopes to retain subscribers because of that six-month delay.

In the world of scientific publishing, the three journals — The Journal of Cell Biology, The Journal of Experimental Medicine, and The Journal of General Physiology — may be unique in that they are maintaining subscription access but are giving up copyright. Many open-access scientific journals also allow authors to keep copyright. —Lila Guterman

The Chronicle News Blog, May 5, 2008

Emma Hill and Mike Rossner, You wrote it; you own it! Journal of Cell Biology, April 30, 2008. An editorial. Excerpt:

Authors of papers published in Rockefeller University Press journals (The Journal of Cell Biology, The Journal of Experimental Medicine, or The Journal of General Physiology) now retain copyright to their published work. This permits authors to reuse their own work in any way, as long as they attribute it to the original publication. Third parties may use our published materials under a Creative Commons license, six months after publication….

Preying on authors’ desire to publish, and thus their willingness to sign virtually any form placed in front of them, scientific publishers have traditionally required authors to sign over the copyright to their work before publication….

At The Rockefeller University Press, we have followed this tradition in the past and obtained copyright from authors as a condition of publication. Several years ago, however, we recognized that the advent of the internet had irrevocably changed the nature and mechanisms of knowledge distribution, and we returned some of those rights to authors. Since July 2000, we have allowed our authors to freely distribute their published work by posting the final, formatted PDF version on their own websites immediately after publication.

With the growing demand for public access to published data, we recently started depositing all of our content in PubMed Central. In a further step to enhance the utility of scientific content, we have now decided to return copyright to our authors. In return, however, we require authors to make their work available for reuse by the public. Instead of relinquishing copyright, our authors will now provide us with a license to publish their work. This license, however, places no restrictions on how authors can reuse their own work; we only require them to attribute the work to its original publication. Six months after publication, third parties (that is, anyone who is not an author) can use the material we publish under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License….

The Creative Commons License will apply retroactively to all work published by The Rockefeller University Press before November 1, 2007….Authors who previously assigned their copyright to the Press are now granted the right to use their own work in any way they like, as long as they acknowledge the original publication….

Full text of our new copyright policy is available here.

Varmus is the President of the Memorial Sloan-Kettering Cancer Center, co-founder of the Public Library of Science, former director of the NIH (1993-1999), and the 1989 Nobel laureate for physiology or medicine.

The National Institutes of Health (NIH) is about to cross an important threshold. Starting April 7th, the authors of research reports that describe work supported by the NIH will be required to deposit accepted manuscripts into PubMed Central (PMC), the NIH’s public digital library of full-text articles, with the understanding that the articles will be freely available for all to view no later than 12 months after publication.

This is a landmark event from several perspectives. Most obviously, it further accelerates the world-wide movement toward greater access to the scientific literature, markedly increasing the number of articles freely available to read online. By taking this step, the NIH will join other funding agencies—including the Wellcome Trust, the UK Research Councils, the European Research Council, and the Howard Hughes Medical Institute—all of which have recently required their investigators to deposit publications in PMC or equivalent public libraries, such as UKPMC, within six months to a year. Since NIH-supported investigators publish about 80,000 papers each year, many of them in journals that currently do not contribute their articles to PMC, the library will soon grow at about twice its already impressive rate. With an enlarged PMC, the virtues of full-text searches and ready access will be more obvious, encouraging still greater participation by authors of work not funded by the agencies that mandate deposition. As we all know, scientists want their work to be found, read, and cited.

The new NIH policy is especially gratifying to those of us who founded the Public Library of Science eight years ago with the goal of promoting greater access to and better use of the scientific literature through libraries like PMC. Still, not all articles in PMC are accessible on the same terms or timelines, and the public libraries and the laudable new policies from funding agencies still fall short of the full potential envisioned for a digital world of science. For articles in traditional, subscription-based journals, there is normally a six- to 12-month interval between publication and posting for public access. For that reason, the libraries are inherently archival—they are useful for searching relatively recent papers, but not for browsing most of the world’s newly published work. Furthermore, not every important new article will have been supported by enlightened funding agencies and fall within the reach of their mandates; those may not appear in PMC at all. The libraries are also limited as archives—the new policy is not retroactive, and few of the journals that participate in PMC have contributed their older papers. This is a pity, given the potential for preserving our scientific legacy in a searchable, digital form, especially at a time when most academic libraries are placing their old paper volumes in distant warehouses. So, for various reasons, the public libraries will remain incomplete, even with respect to recent work, until all authors—and publishers—commit to ensuring access to their work. Finally, unless authors modify their copyright agreements with journals before publication—something they are urged to do—journals will continue to retain inappropriate control over the use of their articles, which is currently confined largely to reading online for most articles in PMC.

In contrast, open-access journals, like those published by PLoS or BioMed Central, make their articles immediately and freely available in PMC, eliminating any extra work by the authors and any delay before the articles are fully accessible. Furthermore, these journals permit far greater use of their articles, by allowing readers to explore and reuse the texts under the terms of a Creative Commons license. These degrees of freedom are possible because access and use do not diminish revenues: open-access publishers recover their costs upfront, frequently by charging a publication fee that is paid from research expenses, rather than with subscription charges to libraries and readers. Thus the distribution and reuse of open-access content can be without limit, just as scientists and the public would wish.

The issue of ownership of published scientific papers is a vexing one, and it could pose difficulties for another recent and exciting initiative that promises to enlarge access to scholarly work. Last month, Harvard’s Faculty of Arts and Sciences (FAS) voted unanimously to require that its members provide the university with a nonexclusive license to post all their accepted articles on an openly accessible, university-maintained Web site. Because the policy might prevent some faculty, especially scientists, from publishing in journals that will not allow early free access, the policy was written to include an “opt-out” provision. This is, of course, not ideal, but much better than a policy that asks faculty to “opt-in.” Moreover, the nuisance of writing to the Provost every time a desired journal refuses to conform to the Harvard policy may cause faculty members to rethink their choice of venue, thereby minimizing use of the “opt-out” option.

As savvy journals will soon recognize, if faculty members choose to publish in other journals to comply with the new Harvard policy, the consequences will be significant—to be respected, journals need respected authors. Nevertheless, in a news article about the new Harvard policy in Science, former Congresswoman Patricia Schroeder, the chief lobbyist for the Association of American Publishers, says that, in view of the policy, “publishers may not be quite as excited to take articles from Harvard”[1]. This seems very unlikely, especially if the Harvard FAS is joined by other Harvard faculties and those on other prestigious campuses, where similar policies are under consideration.

The ownership issues are also not new. A decade ago, the American Academy of Arts and Sciences proposed that the nation’s academic work could be made more widely available through posting on university web sites. In a subsequent Policy Forum in Science [2], the authors of the Academy report recognized that this could not happen without recommended reform of copyright practices. Unfortunately, little progress has been made, largely because, then as now, traditional publishers fear major losses of subscription revenues if their journals’ articles are made freely available at the time of publication. Such losses are, of course, not going to occur if only some Harvard professors post their work in the university repository; but signs now point to more widespread participation in the United States, and some European institutions have already adopted such practices.

Open-access publishing offers a way out of this dilemma in academia, just as it offers solutions to the shortcomings of public libraries like PMC. When costs of publication are recovered from publishing fees instead of from subscriptions, and when authors retain copyrights and grant licenses to publishers, both of which happen with open-access publishing, then articles can be placed immediately in open university repositories (or in public libraries) without threats to revenues or infringements of ownership. We at PLoS celebrate these principles, while also applauding the new policies at Harvard, the NIH, and elsewhere, as welcome signs of continued progress toward public access to research literature.

Excerpt:

Kristin Roovers was a postdoctoral fellow at the University of Pennsylvania with a bright career ahead of her—a trusted member of a research laboratory at the medical school studying the role of cell growth in diabetes.

But when an editor of The Journal of Clinical Investigation did a spot-check of one of her images for an article in 2005, Roovers’s research proved a little too perfect.

The image had dark bands on it, supposedly showing different proteins in different conditions. “As we looked at it, we realized the person had cut and pasted the exact same bands” over and over again, says Ushma S. Neill, the journal’s executive editor. In some cases a copied part of the image had been flipped or reversed to make it look like a new finding. “The closer we took a look, the more we were convinced that the data had been fabricated or manipulated in order to support the conclusions.”

As computer programs make images easier than ever to manipulate, editors at a growing number of scientific publications are turning into image detectives, examining figures to test their authenticity.

And the level of tampering they find is alarming. “The magnitude of the fraud is phenomenal,” says Hany Farid, a computer-science professor at Dartmouth College who has been working with journal editors to help them detect image manipulation. Doctored images are troubling because they can mislead scientists and even derail a search for the causes and cures of disease.

The Abstract:

The impact factor of an academic journal for any year is the number of times the average article published in that journal in the previous two years are cited in that year. From 1994-2005, the average impact factor of journals listed by the ISI has been increasing by an average of 2.6 percent per year. This paper documents this growth and explores its causes.

Thanks to AccessDenied blog.

Abstract:

The application of currently available sophisticated algorithms of citation analysis allows for the incorporation of the “quality” of citations in the evaluation of scientific journals. We sought to compare the newly introduced SCImago journal rank (SJR) indicator with the journal impact factor (IF). We retrieved relevant information from the official Web sites hosting the above indices and their source databases. The SJR indicator is an open-access resource, while the journal IF requires paid subscription. The SJR indicator (based on Scopus data) lists considerably more journal titles published in a wider variety of countries and languages, than the journal IF (based on Web of Science data). Both indices divide citations to a journal by articles of the journal, during a specific time period. However, contrary to the journal IF, the SJR indicator attributes different weight to citations depending on the “prestige” of the citing journal without the influence of journal self-citations; prestige is estimated with the application of the PageRank algorithm in the network of journals. In addition, the SJR indicator includes the total number of documents of a journal in the denominator of the relevant calculation, whereas the journal IF includes only “citable” articles (mainly original articles and reviews). A 3-yr period is analyzed in both indices but with the use of different approaches. Regarding the top 100 journals in the 2006 journal IF ranking order, the median absolute change in their ranking position with the use of the SJR indicator is 32 (1st quartile: 12; 3rd quartile: 75). Although further validation is warranted, the novel SJR indicator poses as a serious alternative to the well-established journal IF, mainly due to its open-access nature, larger source database, and assessment of the quality of citations.

For more detail, see the white paper Wilbanks co-authored with Marty Tenenbaum, Health Commons: Therapy Development in a Networked World, May 2008. Tenenbaum is the founder of CommerceNet and CollabRx. Excerpt:

The current path to drug discovery also perpetuates old traditions of information and intellectual property control. This deeply set inability to capture collective learning dooms everyone to revisit infinitely many blind alleys. The currency of scientific publication encourages individual scientists to hoard rather than share data that they will never have the time or resources to exhaustively mine. And, the wealth of “negative” information gleaned from clinical trial data is mostly lost to the need for companies to safeguard their commercial investments. Although computational and systems biology, aided by Moore’s law, make it feasible to systematically search the vast space of targets, leads, and interactions, this potential is limited in practice by lack of access to data, compound libraries, specimens, and shared services essential for economies of scale. As a result, many biological promising leads, and the knowledge surrounding them, are ultimately discarded.

Thankfully, we have a rare moment in time where we can change the entire system in one motion by establishing a collaborative ecosystem of knowledge and research services that can be rapidly assembled to develop new therapies with unprecedented efficiencies and economies of scale. We can create the same radical increase in efficiency for scientific research that commerce saw in the 1990s, as secure Internet transactions transformed many vertically integrated industries into horizontally integrated ecosystems of service providers and consumers. The explosion of contract vendors in biotechnology, covering the spectrum from gene to protein to drug discovery, development and trials, is one factor. The emergence of the Semantic Web for science is part of the story, as is the existence proof that common use licensing can create explosive value in software and culture. And the power of the network to bring these elements together into a unified system, a Health Commons, is the final piece of the puzzle….

Health Commons is a coalition of parties interested in changing the way basic science is translated into the understanding and improvement of human health. Coalition members agree to share data, knowledge, and services under standardized terms and conditions by committing to a set of common technologies, digital information standards, research materials, contracts, workflows, and software….

Scientific publishing is integral to the drug development process. But in the digital age, we must question whether the unit of a published paper is really the most efficient means of disseminating scientific knowledge. The elegance, clarity, and value of a carefully assembled, constructively peer-reviewed, professionally copy-edited and laid-out research article is clear. However, in this process, much information is delayed, or worse, lost. Interim data and results are typically discarded, especially the results of failed experiments, dooming others to waste time rediscovering them over again. Clinical trial data may never be published; a trial that fails because of an unknown toxicity, for which data has been captured previously, is both expensive –– and tragic for the patients involved. Although journals and funding agencies are committed, in principle, to requiring data associated with publications be made available, in practice, this only succeeds in the few cases for which community endorsed repositories exist. And beyond access to data, there’s the deeper issue of making the conclusions conveyed in a scientific paper available in a structured form that can be understood and manipulated by computers as well as human scientists.

In Health Commons, all this will be different. By integrating the TOPAZ publishing platform, which currently supports PLoS ONE, into Health Commons, publication of research results will be a visible and automatically staged process. Knowledge will simply be promoted from one’s personal repository in the Commons to be shared with one’s laboratory, shared with one’s collaborators, and ultimately to be made publically accessible. PLoS, along with other participating publishers, will provide vetting at many levels from community voting to review boards, as appropriate. Review by one’s peers will occur at many stages: formal editorial boards could still provide traditional journal imprimaturs alongside more radical experiments in community voting….

Beyond ensuring timely access to knowledge by humans, semantic annotation is also the key to making that knowledge machine-understandable….

Because the range of potential applications is unlimited, computer access to published data and knowledge is likely one day to be at least as important as eyeball access….

The Health Commons is too complex for any one organization or company to create. It requires a coalition of partners across the spectrum….

Health Commons is a new and very practical project, not just a plan or vision. The founding partners are Science Commons, CommerceNet, Public Library of Science, and CollabRx .

Thanks to Peter Suber, Open Access News, May 25, 2008

Kevin Zelnio, PLoS ONE Publishes First Taxonomic Paper, The Other 95%, May 28, 2008. Excerpt:

[PLoS ONE just published its first species description:] an excellent paper by Fisher and Smith on the ants of Malagasy region….

Why should one support open access publishing of taxonomic papers?

Visibility is important to the field of systematics, where the relevance is often lost amidst the taxonomic jargon. By removing the subscription barrier, taxonomists make their work accessible and noticeable to researchers all over the world. Increasingly, the need has never been greater for high quality taxonomy. The treatment of neglected tropical diseases relies on proper identification a the pathogen or parasite. Species form the fundamental unit of much of evolution and ecology. Sound knowledge of species and their attributes is basic to all other fields of biology ranging from the molecular to the metacommunity. While scientists might not agree on what a species is, there is no doubt about their importance and the necessity to identify and describe them.

The time is now for taxonomy and taxonomists to enter the digital age. New web technologies can prove effective at linking papers, potentially increasing readership and bringing disparate fields together. For instance, a paper describing a new species of pathogenic nematode can have hyperlinked keywords that summarize the findings, i.e. “Nematoda” “Genus species sp.nov.” “Genus species (of host)” “Pathogenesis” “Endoparasite” “Locality Information”, etc. Other articles of interest with hyperlinked keywords can be linked together for researchers to uncover. Species names themselves can be linked to the original paper, so one can find basic information about that species. This will make it easier to ground-truth simple observations about a species that can affect interpretations in other research, such as where it has been described from, variation in characteristics between sexes and sites, behavioral and diet observations and life history traits….

Should taxonomists forego traditional publishing outlets?

The better option would be for those outlets to go online and open access! If there is some success to PLoS ONE in their venture to publish papers of a taxonomic nature, hopefully it will inspire established journals to follow suit. If you believe strongly in the force of the digital age to implement positive change in science, support open access initiatives by publishing your articles there. One may posit that hybrid journals, where authors may elect to pay an additional fee to make their article accessible online for free, is a step forward in the right direction….Peter Suber notes one should proceed with caution when electing to publish in a hybrid journal for several reasons. In particular, hybrid journal options do not free up subscription money from libraries. Because it is a risk-free strategy for journals, there is not an incentive to get rid of subscriptions fees all together, since most authors do not elect the free-access option. Many publishers still do not make their publishing model or data on the efficacy of the hybrid option available. This makes it difficult to police whether they are reducing subscription fees in relation to author uptake of the free-access option, where high fees are paid to offset subscription fees….

* Gary Rudland, Models for better access and dissemination. “Director of Strategy, Nick Fowler, reviews existing and new models for disseminating scientific information.”
* Kirsten Spry, Disseminating science & health research to a wider audience. “Subscriptions drive Elsevier’s successful publishing machine. But did you also know that there are initiatives underway to test new access models?”
* Francis Cox, Behind the Scenes…Funding Bodies. “How funding Body Agreements provide wider access to research.” [PS: Focusing on the Wellcome Trust.]
* Toni Bellanca, Internet Innovations. “Elsevier’s most recent innovations in Internet dissemination & online access.”

Thanks to Open Access News, May 12, 2008