www.openbiomed.info

Anti-RWA fervor, meet self-reliance: Pre-Prints and Post-Prints can change the world

Ralph Waldo Emerson (1803 – 1882)

It is easy to see that a greater self-reliance must work a revolution in all the offices and relations of men; in their religion; in their education; in their pursuits; their modes of living; their association; in their property; in their speculative views.   Ralph Waldo Emerson- Self-Reliance (1841)

Obscured  in all the concern and unhappiness with the introduction of the anti- NIH Public Access Policy Research Works Act and its primary supporter, the Association of American Publishers (AAP), is the fact that PubMed Central is not the only place to find  free full-text articles and archives of biomedical research results.

Institutional repositories, internet-based document servers sponsored by a university, non-profit, or for-profit organizations, allow authors to distribute authorized copies of their scholarship before or after peer review, provided that an author has implicit or explicit permission by contractual arrangement made with a publisher. There are competing definitions for pre-print and post-print, but the most popular assumption is that pre-prints are the author’s version of the scholarly paper before submission to a journal for peer review,  while post-prints are the version of the paper after peer-review corrections recommended by the journal editors but still lacking journal typesetting and other publication enhancements.

ResearchGate

According to a fast-growing, self proclaimed repository called ResearchGATE,

Self-archiving is a cost-free way to make your publications more visible. By improving access to your articles, you can help increase the citations your research receives and improve your position in the field. But self-archiving is not only for the benefit of the author – by making your work freely accessible, you give back to the field and aid new research. Indeed, this greater community benefit is the reason behind the recent mandates for public access that many funding bodies and institutions have established (including the NIH, Wellcome Trust and the UK Research Councils). More and more, open access is part of grant requirements, usually because public sources fund the projects and the managing institutions believe that the public deserves access to the research they helped facilitate.

The simplest way to determine how a prospective publisher will react to your desire to deposit a pre-print or post-print is to look up the publisher in  RoMEO to find out if your publishers’ copyright rules allow you to deposit your scholarship elsewhere. RoMEO summarizes publishers’ rules and categorizes publishers by colours, indicating what level of author author rights exists.

On January 7th,  Stevan Harnad was commenting on Research Works Act (H.R.3699) (“Research Works Act H.R.3699: The Private Publishing Tail Trying To Wag The Public Research Dog, Yet Again“) and concluded with his well-know perspective of a green world transforming publishing:

“What the research community needs, urgently, is free online access (Open Access, OA) to its own peer-reviewed research output. Researchers can provide that in two ways: by publishing their articles in OA journals (Gold OA) or by continuing to publish in non-OA journals and self-archiving their final peer-reviewed drafts in their own OA Institutional Repositories (Green OA). OA self-archiving, once it is mandated by research institutions and funders, can reliably generate 100% Green OA. Gold OA requires journals to convert to OA publishing (which is not in the hands of the research community) and it also requires the funds to cover the Gold OA publication costs. With 100% Green OA, the research community’s access and impact problems are already solved. If and when 100% Green OA should cause significant cancellation pressure (no one knows whether or when that will happen, because OA Green grows anarchically, article by article, not journal by journal) then the cancellation pressure will cause cost-cutting, downsizing and eventually a leveraged transition to OA (Gold) publishing on the part of journals. As subscription revenues shrink, institutional windfall savings from cancellations grow. If and when journal subscriptions become unsustainable, per-article publishing costs will be low enough, and institutional savings will be high enough to cover them, because publishing will have downsized to just peer-review service provision alone, offloading text-generation onto authors and access-provision and archiving onto the global network of OA Institutional Repositories. Green OA will have leveraged a transition to Gold OA.”

This message needs to get out in many formats and forums. Berlin 7 was one  high-profile 2009 forum. At Berlin 7,  Christ Ambruster, a Research Associate from the Max Planck Society, presented a review of the PEER project titled “Green Open Access as a global solution? Some reflections based on the PEER Project“. PEER has been investigating large-scale, systematic depositing of  final peer-reviewed manuscripts and effects on reader access, author visibility, journal viability, and the evolution European research policies . The project has run since September 2008 and will conclude with a conference in May 2012.

Tags: AAP, Berlin 7, Chris Ambruster, Green OA, PEER Project, Ralph Waldo Emerson, Research Works Act, Stevan Harnad

Stepping into the Light: AAP members part ways with RWA

Kurt Elling playing “Steppin’ Out” (Joe Jackson) at the New Morning in Paris on May 26, 2011.

“We so tired of all the darkness in our lives

With no more angry words to say can come alive

Get into a car and drive to the other side”

You may not learn anything new in this post if you are already following this issue, but I imagine some readers are not and need some pointers.

NATURE PUBLISHING GROUP AND DIGITAL SCIENCE

“Nature Publishing Group (NPG) and Digital Science note the concern amongst the scientific and library communities about the Research Works Act (H.R. 3699), currently under consideration by the U.S. federal government, and wish to clarify our position.

NPG and Digital Science do not support the Research Works Act. ”   READ THE ENTIRE STATEMENT

AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE (AAAS)

“The nonprofit American Association for the Advancement of Science (AAAS), the world’s largest general scientific society and publisher of the journal Science, today reaffirmed its support for the current public access policy of the U.S. National Institutes of Health (NIH).

Contrary to recent news reports, AAAS does not endorse the Research Works Act, which would prevent the NIH from requiring its grantees to make biomedical research findings freely available via the National Library of Medicine’s Web site.”   READ THE ENTIRE STATEMENT

ROCKEFELLER UNIVERSITY PRESS

“Dear Representative Maloney,  I am the Executive Director of The Rockefeller University Press, a nonprofit organization that publishes three biomedical research journals. I am contacting you as a publisher and as your constituent in the 14th Congressional District of New York to express my strong opposition to the Research Works Act (H.R. 3699), which you and Representative Issa introduced into the House on December 16, 2011.  I want to state emphatically that I support the NIH Public Access Policy and think it should be expanded to other federal funding agencies.”   READ THE ENTIRE LETTER

The Harvard Open Access Project (HOAP) at the Berkmann Center for Internet & Society is tracking other publishers that  step into the light  at their Notes on the Research Works Act page, including:

• AAP members who reject the RWA and publicly disavow the AAP position on RWA
• AAP members who apparently reject the RWA, but whose positions require confirmation.
• Publishers who reject the RWA but are not members of AAP

Tags: AAAS, AAP, berkman center, Harvard Open Access Project, Kurt Elling, Nature Publishing Group, Research Works Act, Rockefeller U. Press

Public health becoming more public: open access options in top-10 public health journals

The SCImago Journal & Country Rank allowed me to drill down into 2011 citation data for Public Health, Environmental and Occupational Health.  Here are the top 10 cited journals in 2011:

Here is a description of how these journals offer or encourage open access (or not).

So eight out of these 10 public health  journal sources could produce open access content, depending on what authors do.  In case you were wondering what happened to the American Journal of Public Health, it does show up at at no. 20.

Tags: opemaccess. publishing, open access, Public Health, publishing

Resisting open access, publishers dangle free access in front of readers

I was looking at the SCImago 2011 journal ranking for Obstetrics and Gynecology and noted that the top six journals were either open access or had an open access option for authors.

Of course, in position 7, is a notable non-open access journal , Obstetrics and Gynecology, that does not have an open access option. Obstetrics and Gynecology is also known as the “Green Journal” for the color of its cover, not green open access.  Obstetrics and Gynecology is a core journal any physician specializing in women’s health.  As I scrolled down home page I eventually encountered a MOST POPULAR box highlighting most viewed, most emailed, and highest impact:

For the top ranked articles, it should come as no surprise that free articles are going to get read, emailed, and cited more. This has been the promise of the open access movement.  The world likes free. So how does an article become free without an author subsidized open access option?

I decided to search free access in the publisher’s help pages.  I found the answer: “Content should only be set free at the request of the Journal’s Publisher….Using the Free (Open Access) Content Rules, you can create a rule to set a specific article, issue, or supplement free. Please note that only one item can be selected per rule, but you can create multiple rules to set free more than one article, issue, or supplement….The new Free Content rule will now appear in the “Free Content” list, and all content specified in the rule will now be marked “Free” and available to anyone accessing the journal site.”

So it seems that the publisher decides what is set free, but the readers are voting for the popularity of free articles with their clicks.

The publisher, the Lippincott, Williams, and Wilkins division of Wolters Kluwer, has also taken a similar tact with the journal CIN: Computers, Informatics, Nursing , creating an ad-hoc collection of free articles that  are labeled the “open access collection.”

Wolters Kluwer and all of its U.S.  imprints are listed in the membership of the Association of American Publishers (AAP)  and  therefore in the hot seat over the Research Works Act, a bill that seeks to remove government competition with private publishing and  overturn the current NIH public access policy requiring timely deposit of papers supported by NIH research grants.

Free access is not really a substitute for the systematically developed open access collections made possible by the NIH open access policy and successful open access publishers.  I think it is only a matter of time before a publisher like LWW begins to offer authors a true open access option.

Tags: free access, Lippincott, LWW, OB/GYN, SCImago, Wolters-Kluwer

Library organizations unanimous: Oppose H.R. 3699, The Research Works Act

The Medical library Association issued an Action Alert on January 12th, asking their membership to contact House Representatives and urge them to oppose H.R. 3699,  The Research Works Act. MLA suggested using the talking points developed by the Alliance for Taxpayer Access:

• The bill would prohibit federal agencies from conditioning their grant funding to require that all members of the public be guaranteed online access to the research findings that their tax dollars fund;
• The bill would reverse the NIH Public Access Policy and stifle critical advancements in life-saving research and scientific discovery;
• The NIH Public Access Policy currently provides millions of Americans with access to vital health care information from the NIH PubMed Central database;
  • Under this policy, more than 90,000 new biomedical manuscripts are deposited for public accessibility each year
• H.R. 3699 would prohibit the deposit of these manuscripts, seroiusly impeding the ability of researchers, physicians, healthcare professionals and patients from accessing and using this health-related information in a timely manner;
• H.R. 3699 would also affect scientific research coming from other federal agencies including information on energy, the environment, climate change, and other areas that impact the well being of th epublic
• Address how our library and community have benefited from the NIH Public Access Policy

The Special Libraries Association (SLA) used their public policy blog to make the same points as MLA and points to the taxpayer access draft letter to Oppose H.R. 3699.

The American Library Association (ALA) was out in front as early as January 9th, writing in the District Dispatch about  ALA’s  long-time, ardent support of increasing access to information of all types, including federally funded research.   This latest bill, the Research Works Act, would act in direct contradiction and therefore the ALA vehemently opposes the bill.

SPARC®, the Scholarly Publishing and Academic Resources Coalition suggested on January 6th that “Supporters of public access to the results of publicly funded research need to speak out against this proposed legislation. Contact Congress to express your opposition today, or as soon as possible. “

Here is how you can speak up, courtesy of www.taxpayeraccess.org:

• Representative Issa 
  @DarrellIssa
  http://issa.house.gov/index.php?option=com_content&view=article&id=597&Itemid=73
  Fax: (202) 225-3303
• Representative Maloney 
  @RepMaloney 
  https://maloney.house.gov/contact-me/email-me (Using zip code 10128-3679)
  Fax: (202) 225-4709
• Members of the House Oversight and Government Reform Committee – especially if you’re a constituent.
  http://1.usa.gov/zDqnne 
• Your representative – through the ATA Action Center: http://www.congressweb.com/cweb2/index.cfm/siteid/sparc

Tags: Alliance for Taxpayer Access, libraries, mla, sla, SPARC

Are we open access fanatics… or PTSCB survivors?

There are actually observers and players in scholarly communication  that think the 100 or so open access blogs out there are merely a bunch of shrill malcontents bent on breaking up the marriage of convenience between overburdened faculty and experienced publishers that have historical precedent to prosper and profit from selling it right back to the institutional libraries of those that created it, or merely vending  individual articles, easily discovered through PubMed or Google Scholar.

Clicking on this image will download a 20MB PPT Morality Tale of innocence, vanity, greed, betrayal and hope as a series of photo-slides with toy animals.

I think many librarians blog about open knowledge and open access, not as uninformed agitators, but rather as concerned  survivors of  the extraordinary last decade of the old millenium and first decade of the new millenium that saw the exponential growth of the digital library and the exponential demand by institutional clients for electronic journals and their cost.  When the cost of electronic journals began a rapid escalation at a much greater rate than inflation, coupled by the initial need to subscribe to both print and electronic,  the so-called serials crisis in library expenditures became a budgetary crisis as well.

Source: ARL Statistics 2003-04, Association of Research Libraries, Washington, D.C. *Includes electronic resources from 1999-2000 onward. http://www.arl.org/bm~doc/monser04.pdf

Inevitably, there are limits to what any library can afford. Biomedical libraries are also charged with maintaining subscriptions to an increasing variety of research databases and electronic clinical bedside tools at a time when budgets are finite or shrinking.  The ability to maintain popular subscriptions and tactfully drop subscriptions to under-utilized resources (complemented by funding inter-library loan for articles from dropped titles) continues in most academic medical libraries.

The reaction in 2004 by the Dartmouth Biomedical Libraries was typical.  There was awareness of open access alternatives and great trepidation from faculty used to a longstanding publishing-editorial partnership that created predictable and useful knowledge distribution on a need-to-know basis among peers, with libraries buying back from publishers the content and editorial expertise “donated”  by faculty.  The taxpayer access advocacy movement had not gained the traction and attraction it has now. There was still uncertainty voiced about whether the author-pays open access business model of PLoS or BioMed Central could survive.  Still, at that moment at Dartmouth in 2004, four years before the dawn of the economic crisis, there was still concern:” …there is one matter on which research librarians, academicians, government officials, openaccess proponents, and journal editors are in agreement: the current cost of biomedical journals is too high and not in the best interests of medicine, science, or the public.” (source)

In 2012, there is still a serials crisis, because there are even greater demands on  medical libraries to afford new products and face the unpleasant reality of reducing journal subscriptions as an offset for trying new things:

• The Columbia University Health Sciences Library in 2012 can only afford new titles by cutting underutilized titles
• The City of Hope Hospital Graff Library is also cutting journal titles and packages in FY2012.
• the University of Texas Health Sciences Center in San Antonio is initiating cuts in FY2012
• The UCSF Library proposed 2012 cancellations that essentially eliminated print where electronic existed and was waiting for faculty response.

However, in 2012, there are successful open access publishers, and since 2009 some very important universities have been nurturing the Compact for Open Access Publishing Equity. The number of academic medical center and university institutional repositories and their use has steadily increased, providing a place for faculty to deposit open access copies of articles from an Elsevier published journal since 2004, even from Elsevier journals that the university had to cut.

Given all this trending toward multiple versions of open access and the ongoing existing problems with library resource budgets, there is a lot of education that has to take place. So think of occasional shrill and fanatical behavior as PTSCB… Post Traumatic Serials Crisis Behavior and generally well-intentioned attempts to educate scholars and librarians to open access alternatives.  I mentioned Green open access publisher behavior to some colleagues, and one person thought no publisher was trying to cut down less trees.  I did reorient this sincere person.

Tags: City of Hope, COPE, Dartmouth, Elsevier, Gold OA, Green OA, serials crisis, UCSF, UTHSCSA

opacmo release 2 promotes biological text-mining in PMC open access subset

I completely missed the first release of opacmo: the open access mortar.  The first release of this PubMed Central text-mining tool took place at the end of July 2011, when I was gearing up to teach my August-December library school class by learning another course management system (DesireToLearn), as well as preparing the details of my participation at ETD2011.  The fall flew by in a blur, but thankfully opacmo has reached its next milestone.

The Open Access Mortar (opacmo) is a text-mining database programming project that features

• a named entity recognition system for biological terms, both formal and informal
• a web-site which describes and defines the project
• a programmatic search  interface and to discover publications linked to genes, proteins, species, diseases and other ontological terms
• an open-source tool suite and download center

Here’s the original introduction to opacmo:

The Open Access Mortar, a.k.a. opacmo, is a mash-up of several bioinformatical assets. opacmo links open access publications to biomedical resources and provides a search interface for easy information retrieval. opacmo lets you carry out searches for officially named terms and presents you the publications that are linked to these terms. opacmo also accounts for unofficial synonyms or common names that might be used instead of the officially accepted terms.

In a nutshell that I can get my head around, opacmo offers a new way of drilling down into the PubMedCentral Open Access Subset by using official (MeSH) terms or even common names for established or emerging biological knowledge.  I really like this colorful table which shows the Subset assets harvested at the end of November:

open access subset of PubMed Central (22 Nov 2011), Courtesy of opacmo http://joachimbaran.wordpress.com/2012/01/04/opacmo-release-2-of-the-open-access-mortar/

There is much more technical explanation of the text-mining and output functions in the release 2 blog post. Naturally, the attraction I have to this project is the global potential of combining a a free text-mining search tool with the PubMedCentral Open Access Subset. Both the subset and opacmo project should evolve and expand at  at a similar rate.  One useful way to promote this project would be to create some searching demonstration videos  that could be deposited in Vimeo or YouTube. As far as I can tell now, none are there yet.

Tags: opacmo, open access subset, PubMed Central, text-mining

Let’s not lose track of these immediate defenders of taxpayer access to tax-subsidized scholarship

Click on this image to get to the page with contact information for writing or tweeting to Bill sponsors or the House Committee

I don’t have much to add when there are already very articulate opinions supporting the case for retracting or opposing the Research Works Act. If you care about this and are a U.S. constituent of a House Member, please let them know your opinion.

• Michael Eisen, Associate Professor of Molecular and Cell Biology, UC Berkeley On January 5th: Why does the University of California Press support reactionary legislation opposing public access to scientific research?  Also see Michael’s personal blog for a related piece.

• Rebecca J. Rosen, The Atlantic, On January 5th, Why Is Open-Internet Champion Darrell Issa Supporting an Attack on Open Science?

Tags: AAP, NIH Public Access Policy, Research Works Act

What’s new with the predator InTech? Not much…apparently

I have well over 5,000 page views for my posts about the open access publisher InTech. More than 80% of them come from internet users that do a google search for InTech and find my postings that I have effectively tagged.   That would lend credibility to the idea that InTech is continuing to use direct email marketing to find authors, and some authors want to know more about InTech and start searching.

Reading Richard Poynder’s interview with Intech’s Nicola Rylett back in October, I had some hope that the issue of insufficient editing, a form of non-service for authors and a poor publishing practice that could reflect badly on all open access publishing,  would be addressed in the future  books to be released.   As I have said in my previous posts on InTech, I stick to looking at biomedicine and health topics in my blog.  In the first week of the new year, I decided to see what was new at InTech.

I found a number of biomedical titles released in December 2011, including one that I decided to take a closer look at: Medical Imaging, edited by “Okechukwu Felix Erondu”.  Dr. Erondu has certainly published a few articles on medical imaging, and his editorial role is featured on the cover image:

My concern starts when I see no editorial introduction or preface to this field, other than the 75-word  blurb on the title page, and no chapter authored by Dr. Erondu.  Here are my other observations:

• There are 18 chapters, a few suitably general to what seems like a general textbook, but several on specific topics such as “Fast MRI Methods for the Clinical Evaluation of Skeletal Disorders” or “Assessment of Human Skin Microcirculation and Its Endothelial Function Using Laser Doppler Flowmetry.“   Comparing this to a general textbook on medical imaging, Handbook of medical imaging: processing and analysis (not an open access book, but previewed in Google Books and subscribed in my library), we find in the typical medical imaging text 53 chapters and 900 pages.  My conclusion:  there is no apparent intent by the InTech editor or publisher  to define the true content with a realistic title for this volume.  Instead, there is a general title which misleads or obscures the nature of the content from potential readers.
• I looked carefully at one chapter, Safety of Interactive Image-Guided Surgery, by Alain Beaulieu.  The author relied on research sources from the 1990′s, nearly exclusively, with only two references out of more than 50 being 2006 or after.   Other evidence of outdated research was the term “image-guided”.   The MeSH term established in 2002 for image-guided surgery is Surgery, Computer-Assisted.  There are hundreds of articles on this topic in the year 2010 alone.
• I actually found, with a little digging around. that the author Alain Beualieu had created a very similar presentation in 2008 for a IEEE symposium, A Process Control System Model for Interactive Image Guided Surgery, with identical figures and some very closely resembling descriptions.  In 2011, the InTech chapter does not cite this article at all, so what we have [and what an editor with curiosity could have discovered] is a kind of self-plagiarism.   As long as the IEEE doesn’t mind…

So I think I can confirm that as far as I can tell from looking at this recent open access book from InTech , we have not seen a changeover to more effective and honest editorial practices.  These still seem to be packaging disparate submissions into a convenient hodge-podge, calling it an electronic book, and encouraging readers to take advantage of something free, something that would be hard to sell.  The only person paying and subsidizing InTech are authors. This is not credible open access, when the content is just so questionable.

Tags: IEEE, intech, intechweb, medical imaging

A tale of three cities: three upstart OA journals want to own “open” and “biology”

I received a copy of the publicity for a new open access journal from Royal Society Publishing, Open Biology®. The registration symbol (®)  is attached to the name, and with good reason.   There are a couple of other open access journals that have very similar names, as you can discover with a google search:

•  The Open Biology Journal (ISSN: 1874-1967)from Bentham Open
• Biology Open (ISSN: 2046-6390)from The Company of Biologists

Bentham Open started Open Biology in 2008, and publishes over 239 other titles.   The Company of Biologists started Biology Open in September 2011.  The Royal Society’s Open Biology also launched officially in September 2011.   Here is a brief comparison of these three journals and their most formidable open access competition, BMC Biology and PLoS Biology.  The last quarter article count is for research articles only.

*all author charges for Open Biology will be waived for submissions received before the end of February 2012

So it appears that the three upstarts have recruited a significant editor in chief, and their article processing charges are certainly not out of line, considering where the fees are with the two established leaders of biology open access.   Please remind me to revise this chart in another 6 months to see where submissions are going.

Tags: Biology Open, BMC Biology, Open Biology, PloS Biology, Royal Society Publishing