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