Hardin Scholarly Communication News

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

March 14, 2006
Issue 2.06

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

NIH Proposes New Project and Database to Study Genetic Causes of Disease

The “Impact Factor” Revisited

OA Research Resources from the Wellcome Trust

Survey Points to Increase Author Understanding of NIH Policy

Call for OA to Flu Virus Genome Data

Balancing Openness and Security in Biomedicine

SPARC Partners with Science Commons

A Year in Review – PLoS 2005

Funder Requires Grantees to Share Data Every Two Months

Huge, Growing OA Medical Textbook

Royal Society Open Access Warning

Keeping Online Articles Available

Budget Cuts Threaten Canadian Medical Researchers

Open Access Medical Images

NLM Board of Regents Recommends Strengthening the NIH Policy

BioOne Progress Report

More on strengthening the NIH policy

Open Access Programs web site

In Debate, British MP’s Chastise the Government over its Response to 2004 STM Inquiry

DOAJ Marks 2000th Journal

Excerpt:

The National Institutes of Health announced on Wednesday a new research effort and free, public database about the genetic causes of common illnesses. The project, to be financed jointly by the NIH and biotechnology companies, will be designed to protect the publishing priority of researchers who put data in the repository.

The database, to be managed by the agency’s National Library of Medicine, would contain genetic data from thousands of patients with particular diseases, with details that could identify the patients removed. The NIH will require users of the database to wait nine months before publishing papers based on data that they did not deposit themselves, Elias A. Zerhouni, the agency’s director, said at a news conference. That policy is meant to prevent scientists who donate data from being scooped by competitors.

The database will allow researchers to comb through the DNA of ill and healthy people to explore whether the sick individuals have genes in common. The NIH will also pay to study how genes and environmental causes, like pollutants, combine to cause disease.

Chronicle of Higher Education, Feb 9, 2006 http://chronicle.com/daily/2006/02/2006020903n.htm (available to UI affiliates and subscribers only)

In an article in Biomedical Digital Libraries (December 2005), authors Peng Dong, Marie Loh, and Adrian Mondry demonstrate that online availability of articles greatly influences the impact factor. They studied document sets that included some online articles and some not available online. They learned that impact factors were increased for journals whose text was freely available online. They expect that this effect will increase as more powerful search engines penetrate deeper into the scholarly world and allow researchers to find relevant articles in an instant.

Biomedical Digital Libraries, Dec 5, 2005, http://www.bio-diglib.com/content/2/1/7

The Wellcome Trust has made a web page of the Wellcome-funded research resources (http://www.wellcome.ac.uk/fundedactivities/researchresources/) that support biomedical research. Some of the resources are physical (e.g. tissue specimens) and some digital. Apparently the digital resources are all free.

Open Access News 2/03/06
http://www.earlham.edu/~peters/fos/2006_01_29_fosblogarchive.html

Scientific, technical and medical publishers have called for an increase in communications to science and medical authors in light of a new survey that finds low understanding of the NIH’s Public Access Policy for posting peer-reviewed articles to PubMedCentral (PMC), NIH’s online database. The survey, conducted online in January 2006 by the Publishing Research Consortium (PRC), shows that although most authors are aware of the NIH policy, many do not post on PMC because they neither understand the process nor identify clear benefits for posting their work. Of the NIH-funded authors who responded to the survey, 15% have never heard of the policy and a further 23% have heard of it but know nothing about it. The survey found awareness of NIH-funded authors is only marginally higher than of all life sciences and medicine authors. http://www.alpsp.org/news/NIH_authorpostings_report.pdf

ISSUES IN SCHOLARLY COMMUNICATION: SC News for the UIUC Community, March 3, 2006

Helen Branswell, “Labs shouldn’t hoard flu data: Researcher”, Toronto Star, March 12, 2006. Excerpt:

A leading scientist in the field of genetic sequencing is calling on publicly funded U.S. researchers and research organizations to throw open their collections of H5N1 avian flu viruses to allow others to work toward lessening the pandemic threat the virus poses. Steven Salzberg wants the U.S. Centers for Disease Control as well as researchers funded by the National Institutes of Health to place their virus sequence data in open-access databanks on an as-processed basis. He hopes such a move would entice scientists elsewhere, as well as governments in H5N1-afflicted countries, to end a pattern of virus hoarding many believe is undermining the world’s ability to battle H5N1. “I think what ought to happen is that the U.S., starting with people funded by NIH and the CDC itself ought to start releasing all of their data and all of their samples — and lead by example,” says Salzberg, director of the Center for Bioinformatics and Computational Biology at the University of Maryland. “Because one complaint I’ve heard from other scientists in other countries is: ‘Hey, the CDC in the U.S. doesn’t release all their data. So why should we?’ And that’s a very legitimate complaint.”…Salzberg was involved in the historic human genome sequencing effort as well as the teams which sequenced the first plant genome, Arabidopsis (mustard weed) and the parasite that causes malaria. Most recently, he has been working on an NIH-funded project that is sequencing vast numbers of human flu viruses.

He is adding his voice to a campaign started by Dr. Ilaria Capua. An Italian influenza researcher, Capua is challenging the current system which gives a small network of prominent flu labs preferential access to data by virtue of the fact they do testing and surveillance for the World Health Organization. These labs register their findings in a secure database so that they and the WHO can track changes in H5N1 viruses. But those virus sequences are slow to trickle out to the rest of the research world. (Typically, scientists only post data publicly when they publish findings in a journal, a process that can take months or more.) Capua was offered a chance to join the 15 labs with access to the WHO’s secure database after she sequenced H5N1 bird viruses from Nigeria and Italy, according to a recent article in the journal Science. She turned down the offer, choosing instead to place her sequence data in the open access database Genbank. Limiting who can work on the WHO data isn’t just hindering science’s ability to crack the mysteries of H5N1’s incredible virulence, critics say. It also hampers efforts by countries outside the WHO network to keep their H5N1 diagnostic tests up to date….The WHO is hearing the growing chorus of complaints. But to some degree its hands are tied. The viruses belong to the countries where they were collected. WHO cannot force them to share. And it doesn’t own — or pay — its collaborating labs, which are doing huge amounts of science for the global good.

Open Access News 03/12/06
http://www.earlham.edu/~peters/fos/2006_03_12_fosblogarchive.html

Institute of Medicine and National Research Council, “Globalization, Biosecurity, and the Future of the Life Sciences” (http://darwin.nap.edu/books/0309100321/html), National Academies Press, 2006.

An excerpt from the summary by Research Research:

A new report from the National Research Council favors the “free and open” exchange of information in the life sciences, but also recommends the development of explicit global codes of ethics as well as the creation of “authorities” around the world to monitor and respond to potential misuse of biomedical capabilities. The report emphasizes the importance of ensuring that the results of fundamental research remain unrestricted, unless issues of national security require that they be classified, and it also stresses that any biosecurity regulations should be scientifically sound and non-obstructive to the progress of biology.

Research Research Feb 1, 2006

http://www.researchresearch.co.uk/news.cfm?pagename=newsStory&type=default&elementID=58860

SPARC and Science Commons, a project of Creative Commons, have teamed up to enhance the functionality of the SPARC Author Addendum. The SPARC Author Addendum allows authors to retain critical rights, including the right of authors to post articles in online repositories. Science Commons is creating a machine-readable version of the SPARC Author Addendum that can be read by Internet search engines, as well as a text version that functions as a legal tool. The enhanced SPARC Author Addendum will be made available on the SPARC Web site (www.arl.org/sparc) once the project is completed in early spring.

The effort represents a continuation of Science Commons’ effort to promote access and voluntary sharing in scientific publications. This cooperation advances three goals shared by SPARC and Science Commons: to support authors right to distribute scholarship over the Internet, to promote access and reuse of the scientific literature, and to facilitate author self-archiving. For more information about the enhanced SPARC Author Addendum, please see www.arl.org/sparc.

SPARC e-news, December 2005 – January 2006
http://www.arl.org/sparc/pubs/enews/dec05.html

PLoS Biology received its first Impact Factor from the ISI of 13.9, placing it #1 among general Biology journals, above the Proceedings of the National Academy of Science and the EMBO Journal, both well established journals published by prestigious scientific organizations.

The number of unique users visiting PLoS journal web sites, every month, as identified by their IP addresses, has more than doubled in 2005, from approximately 74,000 in January to over 160,000 in December (aggregated for all journals).

PLoS Biology and PLoS Medicine papers were downloaded over 180,000 times (full paper downloads, not just hits) in December 2005. The Community Journals’ usage stats are also growing nicely, with PLoS Computational Biology receiving nearly 22,000 hits in December, just six months after its launch.

PLoS e-newsletter, http://mailings.plos.org/strat/html/20060127.html#articles

Excerpt:
From Alzheimer’s and diabetes to cancer, schizophrenia and even baldness, the list of ailments that elude cure marches on. The crisis in “translational science,” or turning basic discoveries into therapies, has been brewing for years, but it hit a depressing nadir in 2005, when just 20 new drugs won approval from the Food and Drug Administration….[T]he three-year-old Myelin Repair Foundation…requires that the five biologists it supports share results in real time. Because they don’t keep discoveries under wraps until publication, they can build on each other’s work sooner….The foundation’s insistence that its scientists exchange results every two months is a sea change from the standard every-two-to-five-years progress report. “This has been one of the most difficult transitions, getting scientists to understand accountability in the short term,” says Robert Miller of Case Western Reserve University.

Sharon Begley, “In Switch, Scientists Share Data to Develop Useful Drug Therapies” (http://online.wsj.com/public/article/SB113771683011951408-jgbMO73Pdxsj4iLHFzY1tidhBhQ_20070120.html?mod=blogs), Wall Street Journal, January 20, 2006.