Hardin Scholarly Communication News

A Newsletter for the Health Sciences Campus at the University of Iowa

February 2008 | Issue 1.08

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:

NIH Mandates Open Access to Researchers’ Publications
NIH Public Access web site
What’s Next, Post-NIH Mandate?
Jane: A Tool for Suggesting Journals and Finding Experts (and Facilitating Peer-Review)
Questioning the Impact Factor (and new alternatives)
Harvesting and Organizing OA Blog Discussions of Peer-reviewed Research
Together Again: Springer, Max Planck Agree To New “Experimental” Deal
Open Access Portal to Medical Education
Students for Free Culture – FreeCulture.org
Cost Profiles of Alternative Approaches to Journal Publishing
Ethics of Open Access in Biomedical Research
Petition to Free Up Access to the Cochrane Library

PUBLIC ACCESS MANDATE MADE LAW
President Bush signs omnibus appropriations bill,
including National Institutes of Health research access provision

Alliance for Taxpayer Access
News Release

Washington, D.C. – December 26, 2007 – President Bush has signed into law the Consolidated Appropriations Act of 2007 (H.R. 2764), which includes a provision directing the National Institutes of Health (NIH) to provide the public with open online access to findings from its funded research. This is the first time the U.S. government has mandated public access to research funded by a major agency.

The provision directs the NIH to change its existing Public Access Policy, implemented as a voluntary measure in 2005, so that participation is required for agency-funded investigators. Researchers will now be required to deposit electronic copies of their peer-reviewed manuscripts into the National Library of Medicine’s online archive, PubMed Central. Full texts of the articles will be publicly available and searchable online in PubMed Central no later than 12 months after publication in a journal.

“Facilitated access to new knowledge is key to the rapid advancement of science,” said Harold Varmus, president of the Memorial Sloan-Kettering Cancer Center and Nobel Prize Winner. “The tremendous benefits of broad, unfettered access to information are already clear from the Human Genome Project, which has made its DNA sequences immediately and freely available to all via the Internet. Providing widespread access, even with a one-year delay, to the full text of research articles supported by funds from all institutes at the NIH will increase those benefits dramatically.”

“Public access to publicly funded research contributes directly to the mission of higher education,” said David Shulenburger, Vice President for Academic Affairs at NASULGC (the National Association of State Universities and Land-Grant Colleges). “Improved access will enable universities to maximize their own investment in research, and widen the potential for discovery as the results are more readily available for others to build upon.”

“Years of unrelenting commitment and dedication by patient groups and our allies in the research community have at last borne fruit,” said Sharon Terry, President and CEO of Genetic Alliance. “We’re proud of Congress for their unrelenting commitment to ensuring the success of public access to NIH-funded research. As patients, patient advocates, and families, we look forward to having expanded access to the research we need.”

“Congress has just unlocked the taxpayers’ $29 billion investment in NIH,” said Heather Joseph, Executive Director of SPARC (the Scholarly Publishing and Academic Resources Coalition, a founding member of the ATA). “This policy will directly improve the sharing of scientific findings, the pace of medical advances, and the rate of return on benefits to the taxpayer.”

Joseph added, “On behalf of the Alliance for Taxpayer Access, I’d like to thank everyone who worked so hard over the past several years to bring about implementation of this much-needed policy.”

For more information, and a timeline detailing the evolution of the NIH Public Access Policy beginning May 2004, visit the ATA Web site at http://www.taxpayeraccess.org.

Revised Policy on Enhancing Public Access to Archived Publications Resulting from NIH-Funded Research, Release date January 11, 2008 | Effective Date April 7, 2008

Summary

In accordance with Division G, Title II, Section 218 of PL 110-161 (Consolidated Appropriations Act, 2008 ), the NIH voluntary Public Access Policy (NOT-OD-05-022) is now mandatory. The law states:

The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

Specifics

1. The NIH Public Access Policy applies to all peer-reviewed articles that arise, in whole or in part, from direct costs 1 funded by NIH, or from NIH staff, that are accepted for publication on or after April 7, 2008.

2. Institutions and investigators are responsible for ensuring that any publishing or copyright agreements concerning submitted articles fully comply with this Policy.

3. PubMed Central (PMC) is the NIH digital archive of full-text, peer-reviewed journal articles. Its content is publicly accessible and integrated with other databases (see: http://www.pubmedcentral.nih.gov/).

4. The final, peer-reviewed manuscript includes all graphics and supplemental materials that are associated with the article.

5. Beginning May 25, 2008, anyone submitting an application, proposal or progress report to the NIH must include the PMC or NIH Manuscript Submission reference number when citing applicable articles that arise from their NIH funded research. This policy includes applications submitted to the NIH for the May 25, 2008 due date and subsequent due dates.

Objections to the NIH Mandate from Publishers:

STM comments on U. S. National Institutes of Health Unfunded Mandate, Jan. 4, 2007 Press Release

American Association of Publishers (AAP), Jan. 3, 2007 Press Release

NIH has put together a web site to explain compliance and provide instructions on submission guidelines. Submission takes about 10 minutes, but there are also many journals that do the submission to PubMed automatically.

The NIH Public Access Policy ensures that the public has access to the published results of NIH funded research. It requires scientists to submit journal articles that arise from NIH funds to the digital archive PubMed Central (http://www.pubmedcentral.nih.gov/). The Policy requires that these articles be accessible to the public on PubMed Central to help advance science and improve human health.

For Submission process, policy details, and FAQ, visit: http://publicaccess.nih.gov/

Robin Peek, What’s Next Post Mandate? A preprint of her Focus on Publishing column to appear in the March issue of Information Today. The preprint will come down at the end of February and the postprint will go up three months after publication. Excerpt:

…NIH tells submitters that: “Before you sign a publication agreement or similar copyright transfer agreement, make sure that the agreement allows the article to be submitted to NIH in accordance with the Public Access Policy.’ However what the NIH does not explain how the mandate will work with publishers who are not already in compliance with the guidelines. The NIH notes that,” Institutions and investigators are responsible for ensuring that any publishing or copyright agreements concerning submitted articles fully comply with this Policy.

Peter Suber, author of the SPARC Open Access News, observes “the policy makes no exceptions for dissenting publishers, does not depend on publisher consent, and simply requires grantee compliance. This clearly implies that if a publisher does not accommodate the NIH policy, and grantees cannot obtain special permission to comply with it, then they must look for another publisher.” …

One thing to keep in mind is that not all publishers object to this law as a good number of biomedical research journals…[already] submit [their articles] to PMC. Despite the strongly worded press releases from the major lobbying groups such the Association of American Publishers and the STM Publishers vowing to keep up the fight opposing the law…fighting the Congress and the President really has become old and its time to move on to other things. For example, Martin Frank, executive director of the American Physiological Society, noted in a January 11, 2008 issue of Science. ‘Journals will have to step up their policing by asking NIH to remove articles that have been mistakenly posted because they are still under embargo or are too old to fall under the policy.”

The later part is just plain strange –where is logic of vanquishing the items submitted voluntarily? I am sorry, when did this become as issue? …I wish that the enlightened publishers who are already successfully working with the voluntary policy try to positively influence the implementation plan and not participate with publishing lobbies who provide us with more silly side street distractions.

But with the law will come the necessity to charge up the education machine. As Heather Joseph, the Director of SPARC stated in an interview with LJ Newswire: “In terms of the immediate future, librarians are going to be extremely busy educating their administrators, faculty members, researchers, and students as to how to comply with the policy, and also on what it means to each constituency. Successful implementation of this policy must be a high priority for the coming year.” …

Open Access News, February 3, 2008

Bioinformatics Advance Access published online on January 28, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn006

Martijn J. Schuemie and Jan A. Kors

Department of Medical Informatics, Erasmus University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands

Summary: With an exponentially growing number of articles being published every year, scientists can use some help in determining which journal is most appropriate for publishing their results, and which other scientists can be called upon to review their work.

Jane (Journal/Author Name Estimator) is a freely available web-based application that, on the basis of a sample text (e.g., the title and abstract of a manuscript), can suggest journals and experts who have published similar articles.

Availability: http://biosemantics.org/jane.

A December editorial in the Journal of Cell Biology questions the data behind the ISI Journal Citation Rankings (the impact factors published by ISI).

Related topic:

Declan Butler, Free journal-ranking tool enters citation market, Nature News, January 2, 2008. Excerpt:

A new [OA] Internet database lets users generate on-the-fly citation statistics of published research papers for free. The tool also calculates papers’ impact factors using a new algorithm similar to PageRank, the algorithm Google uses to rank web pages. The open-access database is collaborating with Elsevier, the giant Amsterdam-based science publisher, and its underlying data come from Scopus, a subscription abstracts database created by Elsevier in 2004.

The SCImago Journal & Country Rank database was launched in December by SCImago, a data-mining and visualization group at the universities of Granada, Extremadura, Carlos III and Alcalá de Henares, all in Spain….

The new rankings are welcomed by Carl Bergstrom of the University of Washington in Seattle, who works on a similar citation index, the Eigenfactor, using Thomson data. “It’s yet one more confirmation of the importance and timeliness of a new generation of journal ranking systems to take us beyond the impact factor,” says Bergstrom….

Thomson is also under fire from researchers who want greater transparency over how citation metrics are calculated and the data sets used. In a hard-hitting editorial published in Journal of Cell Biology in December, Mike Rossner, head of Rockefeller University Press, and colleagues say their analyses of databases supplied by Thomson yielded different values for metrics from those published by the company (M. Rossner et al . J. Cell Biol. 179, 1091–1092 ; 2007).

Moreover, Thomson, they claim, was unable to supply data to support its published impact factors. “Just as scientists would not accept the findings in a scientific paper without seeing the primary data,” states the editorial, “so should they not rely on Thomson Scientific’s impact factor, which is based on hidden data.”

Citation metrics produced by both academics and companies are often challenged, says Pringle. The editorial, he claims, “misunderstands much, and misstates several matters”, including the authors’ exchanges with Thomson on the affair. On 1 January, the company launched a web forum to formally respond to the editorial.

More Alternatives:
Eigenfactor.org: the Eigenfactor score is a measure of the journal’s total importance to the scientific community (includes citation ranking, journal price, disciplinary differences, etc.)
H-index: for the impact factor of individual scientists, rather than journals.

After a few months of community comment and collaboration, ResearchBlogging officially launched on January 21, 2008. From the about page:

Do you like to read about new developments in science and other fields? Are you tired of “science by press release”? Research Blogging is your place. Research Blogging allows readers to easily find blog posts about serious peer-reviewed research, instead of just news reports and press releases.

How it works

* Bloggers — often experts in their field — find exciting new peer-reviewed research they’d like to share. They write thoughtful posts about the research for their blogs.
* Bloggers register with us and use a simple one-line form to create a snippet of code to place in their posts. This snippet not only notifies our site about their post, it also creates a properly formatted research citation for their blog.
* Our software automatically scans registered blogs for posts containing our code snippet. When it finds them, it indexes them and displays them on our front page — thousands of posts from hundreds of blogs, in one convenient place, organized by topic.
* The quality of the posts listed on our site is monitored by the member bloggers. If a post doesn’t follow our guidelines, it is removed from our database. Borderline cases may be discussed in our forums.

We also provide bloggers with an icon they can use to show when they’re talking about a peer-reviewed work that they’ve read and analyzed closely….

If you’re a blogger who writes about serious research, Research Blogging offers you a way to distinguish your serious posts from news, politics, family, bagpipes, and so on. We can direct your regular readers — and new readers — to the posts you’ve worked the hardest to create. All you need to get started is a blog and our guidelines… and a peer-reviewed research report that you’d like to discuss.

Open Access News, Jan. 26, 2008

After a highly-publicized split last October, Springer announced this week that it has won back a key subscriber, Germany’s prestigious Max Planck Institute (MPS), with an innovative two-year deal that features Springer’s open access (OA) option. The new agreement, signed last week, was billed as a “mix” of open access and subscription models under which Max Planck researchers will have access to all 1200 Springer journals in SpringerLink as well as having author charges waived for researchers choosing to publish in journals under Springer’ OA option, Open Choice. Financial details, however, were not disclosed.

Though billed as “a two-year experiment,” the new deal represents a significant reconnection for Springer, a leading STM publisher, and the well-funded Max Planck, one of the world’s most prestigious research institutions with more than 12,000 staff members, 9000 Ph.D. students, post-docs, guest scientists and researchers, and student assistants working in over 80 affiliated research institutes. The agreement, however, was billed as “a two-year experiment.” Over the duration of the deal, noted Peter Hendriks, Springer’s president of STM publishing, both sides will “evaluate the effects of open access on both authors and users.”

Springer spokesman Eric Merkel-Sobotta told the LJ Academic Newswire the deal was along the lines of two other recent “experimental” deals Springer has struck, one with UKB, a consortium of the Universities and the Royal Library of the Netherlands, and one with the Georg-August University of Göttingen, both of which also waive author fees for those institutional researchers choosing to submit to Springer journals using Open Choice. The standard Open Choice author fee is $3000.

Springer’s Jan Velterop, an OA pioneer during his years at BioMed Central wrote on his blog that the new deal “could quite conceivably yield an increase in article submissions to Springer journals by authors from Max Planck Institutes…in fact, such an increase is expected, over time.” On his blog, OA advocate Peter Suber noted that this kind of deal “helps create a new body of OA content articles by faculty at participating institutions for about the same price that institutions currently pay for subscriptions.” Velterop added that such deals could reconcile “the desire for universal and immediate open access to peer-reviewed scientific journal articles with the need to ensure the economic sustainability of peer-reviewed journals.”

In October, 2007, after negotiations had broken down, MPS VP Kurt Mehlhorn said Springer was intent on charging “approximately double the price” the organization regarded as “reasonable.” In a statement, MPS officials suggested the breakdown in negotiations with Springer was representative of “extreme price developments in the supply of information, as well as usage restrictions,” and suggested scientific organizations throughout the world should “rethink” their information policies.

Chalk it up to all’s fair in negotiation. Merkel-Sobotta said Springer has always been open to open access, so long as any such system recognizes the value added by journal publishers and said that despite the public perception of acrimony, the two sides continued to talk and that Springer was “very pleased” with the eventual, innovative deal—and also interested to see what the next two years will look like. “If researchers really want open access,” he noted, “we’ll see.”

Library Journal Academic Newswire, Feb 5, 2008

Vangelis G. Alexiou and Matthew E. Falagas, e-meducation.org: an open access medical education web portal, BMC Medical Education, January 24, 2008. Abstract:

Background: Internet can serve in opening the door to a brand new world of high quality medical information. However, the chaotic size of data available in the WWW is often misleading. We sought to provide the world medical community with a web portal that may be used as a clearinghouse providing the outlet for dissemination of high quality WWW educational products.

Methods: Directories of the relevant WWW resources have been compiled and others are being currently under development to cover most medical fields. A custom-built medical search engine was created. Really Simple Syndication (RSS) feeds and video sharing services were reviewed for their quality and were presented along with case-based educational presentations through a user-friendly web portal interface. A directory of guidelines database is currently under development.

Results: The educational portal e-meducation available [here] has been launched in December 2006 and at the moment, provides links to more than 800 educational web-pages, more than 2100 clinical practice guidelines, 32 news feeds, and 14 educational videos. The web site also hosts 40 case-based presentations and a custom medical search engine.

Conclusions: Based on the incorporation of simple and tested educational strategies such as case based instruction and interactive learning, e-meducation.org aims to become a prototype platform that offers a more convenient interface to existing products, resources and medical contents.

Students for Free Culture (SFC) is a diverse, non-partisan group of students and young people who are working to get their peers involved in the free culture movement. Launched in April 2004 at Swarthmore College, SFC has helped establish student groups at colleges and universities across the United States. Today, SFC chapters exist at over 30 colleges, from Maine to California, with many more getting started around the world.

Free Culture Manitfesto, excerpt:
The mission of the Free Culture movement is to build a bottom-up, participatory structure to society and culture, rather than a top-down, closed, proprietary structure. Through the democratizing power of digital technology and the Internet, we can place the tools of creation and distribution, communication and collaboration, teaching and learning into the hands of the common person — and with a truly active, connected, informed citizenry, injustice and oppression will slowly but surely vanish from the earth.

read more…..