Hardin Scholarly Communication News

By SUSAN BROWN, Chronicle of Higher Education, Volume 53, Issue 8, Page A20

A new database that matches drugs to illnesses based on how human genes respond to the medications may speed the discovery of new therapies. The Web-based tool, developed in a collaboration between two universities, has already revealed promising leads for treating cancers.

The system, called the Connectivity Map, was developed by researchers at the Broad Institute, a joint project of the Massachusetts Institute of Technology and Harvard University. It works like an Internet search engine, said Justin Lamb, the project’s leader at the institute. Users can, for example, submit a list of genetic changes associated with a particular illness. The program will return a list of drugs ranked by how well they would restore a normal pattern of genetic activity.

An initial version of the program, based on more than 160 approved and potential drugs, is now freely available to scientists at other institutions, Mr. Lamb’s team reports in the September 29 issue of Science. The researchers built this initial reference collection by measuring genetic responses in human cells treated with each compound.

Continue article at: http://chronicle.com/weekly/v53/i08/08a02002.htm

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

Google is offering to digitize and provide OA to the back runs of scholarly journals. Excerpt from Google’s Overview and FAQ:

While many publishers and organizations are working on bringing journal collections online, a substantial fraction of scholarly journals are currently offline and may remain offline for the foreseeable future. Google is offering publishers an archival journal digitization program to bring these archival collections online and to make them more accessible.

Highlights:

* Publishers maintain copyright and ownership of their content. Publishers select the journal volumes to be digitized.
* This service is free and will make articles from the selected issues fully [and freely] accessible to all users.
* Hosted pages that display journal articles will include publisher co-branding/logo and a link back to the publisher’s website.
* This program is non-exclusive. There is no restriction on redigitization of this material or on working with other partners.

Additional Details:

* The digitized journal articles will be included in Google search indices including Google Web Search and Google Scholar.
* Publishers can create a table of contents on their website and link to their digitized articles in Google, allowing users to browse their archives from their website….
* Publishers have the option to include Google’s ads on the hosted pages that display the journal articles. This is setup as a revenue share between the publisher and Google.

Frequently Asked Questions

Q. Does this mean all my journals have to be offered openly accessible?
A. No, you can choose the journal volumes to be included. The goal of this program is to bring archival journal collections online.

Q. Can you provide us with the digital files?
A: We are unable to provide the digital files unless we terminate the service or the agreement. We would like to point out that this is a non-exclusive program….

Q: Will Google provide us with reporting tools so I know how many users are reading my digitized content?
A: Yes, we will provide tools for publishers to view the usage of their content.

Q: What will users see when they find my digitized articles?
A: Users will see the full digitized article and will have an option to download PDFs for reading or printing. The pages that display the article will also include the publisher’s
logo and url….

Open Access News, 12/17/06 - http://www.earlham.edu/~peters/fos/fosblog.html

UK PubMed Central (UKPMC) is now live and freely available at http://ukpmc.ac.uk

Based on PubMed Central (PMC), the U.S. National Institutes of Health free digital archive of biomedical and life sciences journal literature, UKPMC provides a stable, permanent, and free-to-access online digital archive of full-text, peer-reviewed research publications.

UKPMC is part of a network of PMC International (PMCI) repositories. PMCI is a collaborative effort between the US National Library of Medicine (NLM), the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NLM’s interest in archiving life sciences literature.

The set-up, maintenance and ongoing development of UKPMC is being funded by Arthritis Research Campaign, The Biotechnology and Biological Sciences Research Council, The British Heart Foundation, Cancer Research UK, The Chief Scientist Office of the Scottish Executive Health Department, the Department of Health, The Joint Information Systems Committee, the Medical Research Council and the Wellcome Trust.

UKPMC is a service of the UKPMC Funders Group working in partnership with the British Library, University of Manchester & the European Bioinformatics Institute.

As of today the UKPMC database holds over 620,000 full-text articles - mirrored from PMC in the US, whilst the UK Manuscript Submission System [UKMSS] - which grantees can use when they need to self-archive their research papers - contains details of 15000 grants awarded to over 8000 grantees.

For further information see:

Press release: http://www.bl.uk/news/2007/pressrelease20070105.html
UKPMC Home page: http://ukpmc.ac.uk
UK Manuscript Submission System: http://ukpmc.ac.uk/ukmss

Discussion with Chris Surridge, Managing Editor of PLoS ONE and Mark Funk, Head of Collection Development at Weill Cornell Medical Library, President-Elect of the Medical Library Association, and new PLoS ONE Advisory Board Member

MARK: Can you briefly explain what PLoS ONE is?

CHRIS: PLoS ONE is a journal which will take full advantage of the functionalities that the Web offers to make the publishing of primary research as efficient, effective and just plain useful as possible. ‘Journal’ may in fact be the wrong word to use. When we were designing PLoS ONE we tried to forget what we traditionally understood to be features of a ‘journal’. We wanted to create a way of publishing research to satisfy the needs of today’s scientists.

It turns out that a lot of things that are associated with journals are at best redundant and, at worst, actually unhelpful. For example, PLoS ONE isn’t going to cater to any particular subject area. Scientists already find the papers they need to read from a large number of journals using search engines. They don’t worry about the individual scopes of individual journals, and yet the editors of those journals spend a lot of time deciding which submissions fall within the scope of their journal. Having a large and broad corpus of material in a single venue makes the job of searching for the papers you want to read, and discovering papers that you didn’t realize that you needed to read, that much easier.

For PLoS ONE we are looking at creating the broadest possible journal. PLoS ONE will be happy to consider submissions from any scientific discipline. Given that PLoS’ other journals and its reputation are focused around biological and medical research, it is little surprise the bulk of submissions are from those areas, but we are open to all. In fact we have just received our first submission in geophysics.

That is just one example of how PLoS ONE, by not being a slavish recapitulation of a standard journal in electronic form, can meet the needs of readers far more effectively. In a sentence, PLoS ONE is a high volume, inclusive and highly efficient medium for publishing research from any scientific discipline

Other questions answered in the interview:
What makes PLoS ONE unique compared to other journals?
Is PLoS ONE peer-reviewed?
Will it be indexed?
Will there be a volume or issue number assigned to them?
Is it Open URL compliant?
Open access is an important new development in scientific publishing. Above and beyond increased access, what else do you hope PLoS ONE can contribute to science?

Read the whole interview: http://mailings.plos.org/strat/html/20061111.html#one

PLoS E-Newsletter for Institutional Members, November 14, 2006

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

September 2006 | Issue 4.06

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. Subscribers will also receive our newsletter News@Hardin.

Table of Contents:

U of Iowa Provost Supports Federal Research Public Access Act
New England Provosts Call for Broader Access to Publicly Funded Research
Rallying Behind Open Access
Three big publishers offer Open Access Options
Report on Oxford Open Experiment
Open access: Implications for Scholarly Publishing and Medical Libraries
Congress Pushes Plan to Make Papers Free
Support for the NIH Public Access Policy
BMC Collects Funder Policies on Open Access
Open Access for the Medical Librarian
Encouraging Society Publishers to Experiment with OA
‘Nature’ Opts for Open Peer-review Systems
The Canadian Breast Cancer Research Alliance (CBCRA) Provides OA to the Research it Funds
Journal of the Royal Society of Medicine – Three Essays on Open Access Issues

University Support for Public Access Act Expands

Washington, DC – August 3, 2006 –

Just one week after more than two dozen leading universities (including the University of Iowa) declared their strong support for the Federal Research Public Access Act of 2006 (S.2695), provosts from an additional 23 universities added their backing in a letter issued by the Greater Western Library Alliance (GWLA) and in individual correspondence. This brings the total to at least 48 universities that have gone on record as favoring the measure [ed note: as of 9/21/2006, the number is now at 125 higher education institutions].

The Federal Research Public Access Act was introduced on May 2, 2006 by Senators John Cornyn (R-TX) and Joseph Lieberman (D-CT). It requires federal agencies that fund over $100 million in annual external research to make electronic manuscripts of peer-reviewed journal articles that stem from their research publicly available on the Internet. The U.S. government funds an estimated 50% of university research, making this a particularly important cause for the higher education community.

The GWLA letter reads, in part: “Access to publicly funded research facilitates the open discussion needed to accelerate research, share knowledge, improve treatment of diseases, and increase human understanding. [The Public Access Act] is a crucial step in realizing this goal…”

“With the passage of this bill, researchers across the United States will have access to the results of work supported by federal government funding, which will help advance scientific understanding at a faster rate,” said David Pershing, Senior Vice-President, Academic Affairs, University of Utah. “No longer will knowledge created using public funds be limited to the wealthiest institutions and corporations. With everyone having access to up-to-date information, I am confident we will see a higher level of scientific research and innovation. This is a remarkable opportunity for educators and students across the nation.”

Signatories of the GWLA letter include provosts and vice presidents for state and non land-grant institutions, such as the University of Washington and Rice University. Their names are added to those of another twenty-five institutions, including Harvard University and Arkansas State University, who on Friday jointly issued “An Open Letter to the Higher Education Community.”

“The time is ripe for this legislation,” added Rodney Erickson, Executive Vice President and Provost of The Pennsylvania State University, who signed the Open Letter. “Many of us in the academic community believe the process of making the findings of publicly supported research more widely available will stimulate further research and education, and that is our primary mission as universities.”

The GWLA letter, available online, is at http://www.gwla.org/provostletter.html.

The Open Letter to the Higher Education Community signed by twenty-five provosts and issued on July 28, 2006 is online at
http://www.taxpayeraccess.org/frpaa/Provosts_openletter_06-JUL.pdf.

The American Association of Law Libraries, American Library Association, Association of Academic Health Sciences Libraries, Association of College & Research Libraries, Association of Research Libraries, Greater Western Library Alliance, Medical Library Association, SPARC, and The Special Libraries Association encourage taxpayers and other stakeholders in the scientific process to add their support for this important legislation. Details are online at http://www.taxpayeraccess.org/frpaa/.

SPARC News Release, Aug. 3, 2006

Washington, DC – September 19, 2006 – Six public land-grant universities in New England, representing six states and $700 million in annual research investments, have issued a letter of support for the Federal Research Public Access Act of 2006 (S.2695). The letter is signed by the Chief Academic Officers from University of Connecticut, University of Maine, University of Massachusetts Amherst, University of New Hampshire, University of Rhode Island, and University of Vermont. This brings the total number of leaders from the higher education community who have spoken out in support of the Act to 125.

The legislation, originally introduced by Senator John Cornyn (R-TX) and Senator Joseph Lieberman (D-CT), would require federal agencies that fund over $100 million in annual external research to make manuscripts of peer-reviewed journal articles stemming from that research publicly available via the Internet. The bill is currently under consideration by the Senate Committee on Homeland Security and Governmental Affairs, chaired by Senator Susan Collins (R-Maine).

Issued on September 6, 2006 by the Council of Presidents - New England Land-Grant Universities, the letter reads:

Dear Senator Cornyn,

As the chief academic officers of the six public land-grant universities, in New England, we are writing to you in support of the Federal Research Public Access Act of 2006. Our universities enroll over 100,000 students. They confer about 17% of the bachelor’s degrees and 20% of the doctoral degrees in New England. Collectively they invest more than $700 million per year on research, largely with the support of federal grants.

Dissemination of results is an essential component of the land-grant tradition of research and of our investment in science. We share your concern that far too often the results of research funded by the U.S. government are not broadly available to researchers, scientists, and members of the public. In addition to ensuring that this research is made available quickly, it is also critical that the published information remain broadly available for future use. We are pleased to see that your bill is designed to support both early, as well as long-term, access to scientific research results.

Open access to publicly funded research facilitates the candid discussion needed to accelerate research, share knowledge, improve treatment of diseases, and increase human understanding. Your bill is a crucial step in realizing this goal, and we look forward to working with you to secure the bill’s passage. .”

The provosts whose names appear below have endorsed the FRPAA. The deans and directors of the universities’ libraries also strongly endorse the FRPAA.

Sincerely,

Peter J. Nicholls, Provost and Executive Vice President for Academic Affairs,
University of Connecticut

Edna Szymanski, Senior Vice President for Academic Affairs and Provost,
University of Maine

Charlena Seymour, Provost and Senior Vice Chancellor for Academic Affairs,
University of Massachusetts Amherst

Bruce L. Mallory, Provost and Executive Vice President, University of New Hampshire

M. Beverly Swan, Provost and Vice President for Academic Affairs, University of Rhode Island

John M. Hughes, Provost and Senior Vice President, University of Vermont

Alliance for Taxpayer Access, Media Release,
http://www.taxpayeraccess.org/media/Advisory06-0919.html

By Scott Jaschik, Inside HigherEd, July 28, 2006

Excerpt:
If universities pay the salaries of researchers and provide them with labs, and the federal government provides those researchers with grants for their studies, why should those same universities feel they can’t afford to have access to research findings?

That’s part of the argument behind a push by some in Congress to make such findings widely available at no charge. The Federal Public Research Access Act would require federal agencies to publish their findings, online and free, within six months of their publication elsewhere. Proponents of the legislation, including many librarians and professors frustrated by skyrocketing journal prices, see such “open access” as entirely fair. But publishers — including many scholarly associations — have attacked the bill, warning that it could endanger research and kill off many journals.

In an attempt to refocus the debate, the provosts of 25 top universities are jointly releasing an open letter that strongly backs the bill and encourages higher education to prepare for a new way of disseminating research findings. “Widespread public dissemination levels the economic playing field for researchers outside of well-funded universities and research centers and creates more opportunities for innovation. Ease of access and discovery also encourages use by scholars outside traditional disciplinary communities, thus encouraging imaginative and productive scholarly convergence,” the provosts write.
While the letter acknowledges that the bill would force publishers and scholarly societies to consider potentially significant changes in their operations, the provosts conclude that the legislation “is good for education and good for research.”

The letter originated with the provosts of the Committee on Institutional Cooperation, which includes the universities of the Big Ten Conference plus the University of Chicago. Others joining the effort include the provosts of such institutions as Dartmouth College, Harvard University, Texas A&M University, the University of California, the University of Rochester, Vanderbilt University, and Washington University in St. Louis.

“I think the provosts are concerned that our scientists are doing important research, and their fields demand that they publish the research in highly respected journals, and then those journals become more and more expensive and control information in a way that is worrisome,” said R. Michael Tanner, provost and vice chancellor for academic affairs of the University of Illinois at Chicago and one of those who worked on the letter. When universities can’t afford to keep all of their subscriptions, universities face the prospect that their own faculty members can’t read the findings of fellow faculty members — even when taxpayers paid for the research.

To read the full article:
http://insidehighered.com/news/2006/07/28/provosts

BMJ Journals Announces the Launch of Unlocked - a New Open Access Initiative
BMJ Journals, a division of the BMJ Group, today announced the launch of a new open access service, which, if supported by authors, will make some of the important medical research being published today freely available to anyone in the world with an internet connection.

Unlocked is a new service that gives authors the option to make their articles freely available online for a fee. Unlocked is available to any author publishing an article in a BMJ Journals specialty journal. This includes some of the world’s pre-eminent medical titles including: Gut, Heart, Annals of the Rheumatic Diseases, Archives of Disease in Childhood, Thorax and Journal of Neurology, Neurosurgery and Psychiatry.
Read more….
https://mx2.arl.org/Lists/SPARC-OAForum/Message/3244.html

Cambridge Open Option
From August 14th 2006 authors submitting articles to selected Cambridge Journals will be able to make their articles freely available to everyone, immediately on publication. Building on the success of Breast Cancer Online, the first Cambridge Open Access project, and Neuron Glia Biology, which provides Open Access after 6-12 months, Cambridge Open Option introduces a new Open Access model to a further 15 journals from the Cambridge list.

Gavin Swanson, STM Editor-in-Chief at Cambridge Journals said: “I’ve been involved in the Open Access world for some time and the launch of Cambridge Open Option is the result of a great deal of painstaking research into best practice. I’m confident that we have a robust model that will benefit both authors and researchers equally. We’re hoping that this will become a major part of our journals publishing in the future and that it will help us give greater access to the results of scientific research reported in our journals.”
Read more…
https://mx2.arl.org/Lists/SPARC-OAForum/Message/3253.html

Wiley Announces New Funded Access Service
Hoboken, N.J., August 7, 2006 - Global publisher John Wiley & Sons, Inc., today announced a new funded access service forauthors of journal articles. Through this new program, authors will have the option of paying a fee to ensure that their article is available to non-subscribers upon publication via Wiley InterScience , Wiley’s online publishing platform, as well as the author’s funding agency’s preferred archive if applicable.

“Wiley developed the funded access program as a response to journal authors whose funding might have certain requirements,” said Mike Davis, Vice President, Global Life and Medical Sciences. “For those authors who want to publish in a Wiley journal, and whose funding agency requires deposit in an archive, this new program supports these requirements.”

As an initial offering, funded access will be available for 45 biomedical journals. Only authors of primary research articles qualify for this new service, and only those authors whose articles have been accepted for publication will be offered the funded access option at the point when the article is accepted, to ensure that the funded access option has no influence on the peer review and acceptance process. Wiley will deposit the final PDF of the article into the funder’s archive; this is the final, authoritative version of the article, after peer review, editing, any final corrections, online and print formatting, and publication. The fee for ensuring articles are made available through the funded access program is $3,000 per article.
Read more….
https://mx2.arl.org/Lists/SPARC-OAForum/Message/3247.html