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December 28, 2006

Scholarpedia Launches

Scholarpedia feels and looks like Wikipedia - the free encyclopedia that anyone can edit. Indeed, both are powered by the same program - MediaWiki. Both allow visitors to review and modify articles simply by clicking on the edit this article link.
However, Scholarpedia differs from Wikipedia in some very important ways:
• Each article is written by an expert (invited or elected by the public).
• Each article is anonymously peer reviewed to ensure accurate and reliable information.
• Each article has a curator - typically its author -- who is responsible for its content.
• Any modification of the article needs to be approved by the curator before it appears in the final, approved version.

…Currently, Scholarpedia hosts Encyclopedia of Computational Neuroscience, Encyclopedia of Dynamical Systems and Encyclopedia of Computational Intelligence. Although all three will eventually be published in a printed form, they will also remain freely available and modifiable online. (Producing a hard copy of each encyclopedia is important for archiving; besides, many academicians have a preconception that the prestige of an online article is not as high as that of a printed one.)

If there is enough interest and support from the public, Scholarpedia will grow in the following directions:
• The neuroscience chapter of Encyclopedia of Computational Neuroscience will be a seed to start Encyclopedia of Cognitive Neuroscience, and then Encyclopedia of Neuroscience
• Encyclopedia of Dynamical Systems will be a seed to start Encyclopedia of Applied Mathematics, and then Encyclopedia of Mathematics.
• Encyclopedia of Computational Intelligence will be a seed to start Encyclopedia of Computer Science.

Read more at Scholarpedia

Posted by P. Kaufman at 1:55 PM

December 27, 2006

Second Nature: PLoS One Picks Up Where Nature Left Off

The launch of the new PLoS ONE scholarly research portal looks like a big win for open access research content from a number of angles. PLoS ONE is posting research and will allow interactive review before and after publication for scientific articles via a very sophisticated publishing environment. The PLoS ONE platform applies many of the best practices of social media, providing ready access to comments posting and awareness of active discussions to draw in more active discussions. PLoS ONE will publish all papers that are judged to be rigorous and technically sound, and had already posted more an 100 papers by its launch - a remarkable number for a just-launched scholarly journal of any kind. By contrast Nature's recently shuttered open-review portal trial, which ran for around four months, attracted only 71 authors willing to post their work online and attracted 92 technical comments.

As we noted in our latest news analysis article one of the keys to successful social media products is a dedicated core of trusted contributors who will be able to ensure editorial success. PLoS ONE starts with a global editorial board of more than 200 scholars, ensuring a broad array of inputs for reviewing content. Some of the fears about having content rejected after having had it exposed to comments prior to publication may be relieved by the PLoS ONE policy that allows papers that have been already rejected by PLoS Biology and Medicine journals to be re-submitted via PLoS ONE. This is a potentially valuable feature, allowing research that may not have yet reached the highest levels of acceptance to mature through its exposure to comments from a broader audience.

PLoS ONE is finally opening the doors to the potential for fundamental changes in how scholarly research proves its worth. With an open exchange of ideas and commentary facilitated by technologies long available to the general public and a solid body of research and reviewers PLoS ONE holds out the potential to liberate the highest levels of scholarly innovation from the regimen of the printing press. Changing the way that research is paid for was a good first step for open access, but with the ability to eliminate artificial distribution bottlenecks that choke off natural conversations PLoS ONE may do for scholarly research what Wikipedia has done for reference materials - with much more integrity in the underlying editorial processes.

John Blossom, Content Blogger 12/22/06

Posted by P. Kaufman at 9:39 AM

December 26, 2006

Nature Ends Open Peer Review Experiment

Scientific journal Nature has announced plans to abandon an online experiment, which allowed scientists to comment on their peers' research before publication, due to lack of participation.

In a four-month trial, which began in June, a group of select scholars reviewed scientific manuscripts and decided what should appear in print. In the experiment, authors whose manuscripts were selected for traditional peer review could also opt to have them simultaneously posted on the Internet for feedback from scientists.

According to the British publication, although the experiment generated high online traffic, it was ultimately canceled because only a few authors participated and many of the online comments were nothing more than nice work.

Published by an arm of Macmillan Publishers Ltd., Nature is highly selective of the research it publishes. Of the 10,000 papers it receives every year, the journal rejects nearly 60 percent, and only about 7 percent of submissions are published.

From Knowledgespeak, 12/25/06

Posted by Katie Newman at 10:30 AM

December 20, 2006

"Our Cultural Commonwealth"

The American Council of Learned Societies has just issued a report, "Our Cultural Commonwealth," assessing the current state of scholarly cyberinfrastructure in the humanities and social sciences and making a series of recommendations on how it can be strengthened, enlarged and maintained in the future.

John Unsworth, Dean and Professor, Graduate School of Library and Information Science here at Illinois, chaired the Commission that authored the report.

if:book 12/19/06

Posted by P. Kaufman at 1:47 PM

Update on USGS Scientific Review Process

Contrary to what the Washington Post and other press reports including an item in this blog have implied, the Director of the USGS (U.S. Geological Survey) has asserted that Bush administration is NOT trying to muzzle scientists at the USGS by placing new controls on the approval and release of research plans and products. See:

Statement from USGS Associate Director for Biology Dr. Sue Haseltine Regarding the USGS Scientific Review Process

Rather, Dr. Haseltine asserts that

Research supervisors in the review chain are simply charged with ensuring all USGS information products have addressed peer comments and are in compliance with USGS procedures with regard to the review and release of scientific information.

Posted by Katie Newman at 11:07 AM

Counter Crusade to Google Book Digitization

Already facing a legal challenge for alleged copyright infringement, Google's crusade to build a digital library has triggered a philosophical debate with an alternative project promising better online access to the world's books, art and historical documents.

The latest tensions revolve around Google's insistence on chaining the digital content to its Internet-leading search engine and the nine major libraries that have aligned themselves with the Mountain View-based company.

A group called the Open Content Alliance favors a less restrictive approach to prevent mankind's accumulated knowledge from being controlled by a commercial entity. "You are talking about the fruits of our civilization and culture. You want to keep it open and certainly don't want any company to enclose it," said Doron Weber, program director of public understanding of science and technology for the Alfred P. Sloan Foundation. The New York-based foundation on Wednesday will announce a $1 million grant to the Internet Archive, a leader in the Open Content Alliance, to help pay for digital copies of collections

UIUC is a member of the Open Content Alliance and soon will begin digitizing public domain materials that will be available through OCA. You can read more of the article quoted above at 12/19/06

Posted by P. Kaufman at 8:40 AM

December 19, 2006

Private Equity may buy the Book

Book publishing is a slow-growth business. But big media companies may be able to sell their book divisions to private equity firms.

There are new novels from popular authors like Stephen King, Michael Crichton and James Patterson, not to mention a Hannibal Lecter prequel from Thomas Harris. Jonathan Grisham has a non-fiction book out that has been near the top of the best-seller lists for the past few weeks. The big guns are all in stores for the holidays.

Yet, book publishing remains a tough business with little or no growth to be found. CBS, which owns publisher Simon & Schuster, reported that sales from its book division rose only 2 percent in the third quarter while operating profits were down 13 percent. For the first three quarters of 2006, sales were up only 5 percent and operating profits were flat.

More at 12/18/96

Posted by P. Kaufman at 1:45 PM

December 15, 2006

Are the Changes in the Publishing Rules for Scientists at the US Geological Survey Politically Motivated?

from Knowledgespeak, 12/15

Scientists at the US Geological Survey (USGS) are the latest to be subjected to controls on research, according to media reports. As per the new rules, screening is mandatory for all facts and interpretations by agency scientists who study a vast range of subjects – from caribou mating to global warming. The rules apply to all scientific papers and other public documents, including minor reports and prepared talks.

According to the new requirements, USGS' communications office must be alerted about articles containing high-visibility topics or topics of a policy-sensitive nature. Also, findings or data that may be especially newsworthy, have an impact on government policy, or contradict previous public understanding, should be communicated to the agency's director and its communications officer prior to submission for publication. Top officials at the Interior Department's scientific arm state that the rules only standardise what scientists must do to ensure the quality of their work, and give a heads-up to the agency's public relations staff.

The changes amount to an overhaul of commonly accepted procedures for all scientists, not just those in government, based on anonymous peer reviews. Effective immediately, USGS supervisors will demand to see comments of outside peer reviewers' as well any exchanges between the scientists seeking to publish their findings and the reviewers.

Some of USBS scientists have expressed fears that political interference may lead to censorship of their work . See , "USGS Scientists Object To Stricter Review Rules" in the Dec. 14th Washington Post

Posted by Katie Newman at 9:22 AM

December 13, 2006

Creative Commons Add-in for Microsoft Office

Microsoft has created a free add-in that enables you to embed a Creative Commons copyright license into a document that you create using the Microsoft application Word, PowerPoint, or Excel. With a Creative Commons license, authors can express their intentions regarding how their works may be used by others.

To learn more about Creative Commons, please visit its web site, To learn more about the choices among the Creative Commons licenses, see

Download the Creative Commons Microsoft Office add-in from the Microsoft website. For a short URL to this resource, use this tinyURL:

Installation of the Creative Commons Microsoft Office add-in will add an option to your File menu whereby you can easily add the CC logo and usage statement to your document.

Posted by Katie Newman at 9:25 AM

December 12, 2006

Open Access Could Lead to Cancelled Subscriptions

From Research Information, Dec 2006 / Jan 2007:

A study of 400 librarians has found that the length of the embargo period before material becomes open access, and whether peer-reviewed versions of articiles are available, are key determininants in a librarian's deision to maintain or cancel journal subscriptions,

The study was conducted by the Publishing Research Consortium (PRC). The founding partners of PRC are The Publishers Association (PA) of the UK, the Association of Learned and Professional Society Publishers (ALPSP), and the International Association of Scientific, Technical and Medical Publishers (STM). Corresponding partners include The Association of American University Presses and the Professional / Scholarly Publishing Division of the Association of American Publishers.
In sounding a potential alarm, the PRC site goes on to say:
This study raises questions about previous claims that librarians will continue to subscribe to journals, even when some or all of the content is freely available on institutional archives.

Read the full study.

Posted by Katie Newman at 1:27 PM

December 8, 2006

From Nature: a Call for Data Sharing

In today's Nature, there's an editorial calling on psychology researchers to make their primary data freely available so it is testable and usable by others. Some granting agencies are requiring this, and the Am. Psychological Assoc. has mandated it for those who publish in it's journals. Yet, as the editorial relates, there has been very poor adherence to these mandates.

Excerpt from "A fair share", Nature, December 7, 2006. An unsigned editorial. [Subscription required.]

In psychology there is little tradition of making the data on which researchers base their statistical analyses freely available to others after publication. This makes it difficult for anyone to independently reanalyse research results, and prevents small data sets from being combined for meta-analysis, or large ones mined for fresh insights or perspectives.

Psychologists need to rethink their reluctance to share data....

The need for more data sharing has just been amply demonstrated by Jelte Wicherts, a psychologist specializing in research methods at the University of Amsterdam, who tried to check out the robustness of statistical analyses in papers published in top psychology journals.

He selected the November and December 2004 issues of four journals published by the American Psychological Association (APA), which requires its authors to agree to share their data with other researchers after publication. In June 2005, Wicherts wrote to each corresponding author requesting data, in full confidence, for simple reanalysis. Six months and several hundred e-mails later, he abandoned the mission, having received only a quarter of the data sets. He reported his failure in an APA journal in October (J. M. Wicherts et al. Am. Psychol. 61, 726–728; 2006).

Researchers often have valid reasons for constraining access to their raw data, such as the privacy of research subjects. But data from most studies based on confidential information can be coded in a way that will guarantee their subjects’ anonymity. The few cases where this is not possible can be exempted from the move towards data sharing.

A second factor deterring openness is a natural desire to retain exclusive access to data that took years of care and attention to collect....

The APA’s editors and publishers are now planning their response to Wicherts’ report. One result should be the acceleration of moves, already under discussion, to require the deposition of data as supplementary electronic material in APA databases. Where the APA leads, other psychology journals are likely to follow.

Granting bodies must also play a part. In 2003, the US National Institutes of Health introduced rules requiring the public sharing of data in psychology studies for grants exceeding $500,000, allowing exemptions where confidentiality issues cannot be circumvented. Other agencies should follow suit. And university departments need to do more to teach the basics of note-keeping and data presentation, to prepare their students for an era in which data sharing will increasingly become the norm.

Thanks to Peter Suber for pointing out this editorial.

Posted by Katie Newman at 10:49 AM

December 6, 2006

Information Access Alliance Takes Action on Proposed Wiley Acquisition of Blackwell

John Wiley and Sons recently announced its plans to acquire Blackwell Publishing, a publisher of scientific, technical, and medical (STM) journals, for a price of $1.08 billion. This increase in concentration in an already concentrated market is cause for substantial concern on the part of the library community. The combined company will control more than 1,200 titles, many of them scholarly society journals.

The Information Access Alliance (IAA), representing the Association of Research Libraries (ARL), the American Library Association, the Association for College and Research Libraries, the American Association of Law Libraries, the Medical Library Association, SPARC, and the Special Library Association, wrote to the US Department of Justice on November 29 asking that they act to issue a second request for information from the two companies and review the market and the merger. The IAA letter to the Department of Justice is available on the Web

The IAA is deeply concerned that this transaction will exacerbate market dysfunctions and result in further reduction in access to critical research information that fuels the entire higher education and research enterprise. Both John Wiley and Sons and Blackwell Publishing currently use bundled pricing models; a recent study by ARL gathered data from its member libraries documenting that bundling practices reduce customer choice, hurt small publishers, and create barriers to entry (see

Information on publisher mergers and related antitrust issues is available on the Information Access Alliance Web site

Thanks to the Association of Research Libraries for distributing this information.

Posted by P. Kaufman at 7:47 AM

December 4, 2006

Are Books In Danger?

The December 1 issue of features an interesting collection of essays about books and book publishing. From the introduction:

Are books in danger?

The conventional wisdom would say yes. After all, more and more media--the Internet, cable television, satellite radio, videogames--compete for our time. And the Web in particular, with its emphasis on textual snippets, skimming and collaborative creation, seems ill-suited to nurture the sustained, authoritative transmission of complex ideas that has been the historical purview of the printed page.

But surprise--the conventional wisdom is wrong. Our special report on books and the future of publishing is brim-full of reasons to be optimistic. People are reading more, not less. The Internet is fueling literacy. Giving books away online increases off-line readership. New forms of expression--wikis, networked books--are blossoming in a digital hothouse.

People still burn books. But that only means that books are still dangerous enough to destroy. And if people want to destroy them, they are valuable enough that they will endure.

Posted by P. Kaufman at 2:55 PM