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August 23, 2007

Get SciFinder Scholar 2007 for Access to Chemical Abstracts

Does your research involve an interest in “chemicals”?
Insect pheromones? Agrochemicals? Neurotransmitters? Biological membranes? Drugs? Antibiotics? DNA / RNA / Proteins? Genomics? Hormones? Enzymes?

If so, you probably will profit from using SciFinder Scholar (SFS) to search Chemical Abstracts (CA), which indexes "chemistry" in the broadest sense!

About SciFinder Scholar…

Important! Our license agreement limits use of SciFinder Scholar to academic use by U of Illinois students, staff and faculty, only; any use related to paid, commercial work or non-academic research is forbidden. Full license details are available at the download web site and also appear with every login.

How can you access SciFinder Scholar?
Unfortunately, this resource is not web-based; it is only available for those who have loaded the SciFinder Scholar program onto their computers. (Or, you can use it at any public computer in any U of Illinois Library by clicking on this URL).

For instructions for downloading SciFinder Scholar (for PC and Mac) to your office computer, please contact the Chemistry Librarian, Tina Chrzastowski (, 217-333-3737) or the Biotechnology Librarian, Katie Newman (, 217-265-5386). We'll send you the web address of a secure web page from which you can download the two program files. There you will also find instructions for what you must do to access SFS from off-campus.

If you have a previous version of SciFinder Scholar on your computer, you will need to upgrade to the new version, SFS2007, in order to maintain your access to SciFinder Scholar. With this release, previous versions are no longer supported.

Posted by Katie Newman at 2:21 PM

SciVee: A YouTube for the Sciences

Thanks to if:book for word about SciVee, which could be a major innovation in science publishing. The National Science Foundation, the Public Library of Science and the San Diego Supercomputing Center have joined forces to launch SciVee, an experimental media sharing platform that allows scientists to synch short video lectures with paper outlines:

"SciVee, created for scientists, by scientists, moves science beyond the printed word and lecture theater taking advantage of the internet as a communication medium where scientists young and old have a place and a voice."

The site is in alpha and has only a handful of community submissions, but it's enough to give a sense of how useful it could become. Video entries can be navigated internally by topic segments, and are accompanied by a link to the full paper, jpegs of figures, tags, a reader rating system and a comment area.

Peer networking functions are supposedly also in the works, although this seems geared solely as a dissemination and access tool for already vetted papers, not a peer-to-peer review forum. It has the potential to grow into a resource not just for research but for teaching and open access curriculum building.

Hop on over to take a look at the pubcast and paper on the structural evolution of the protein kinase.

Posted by Katie Newman at 10:57 AM

August 9, 2007

Yale Drops It's Pre-Pay Membership to BioMed Central

As widely reported in the media, Yale University has dropped it's institutional membership in BioMed Central.

This isn't a reflection on lack of support on Yale's part for the idea of open access. In fact, membership was dropped because Yale authors are apparently flocking to publish their articles in the openly accessible BMC journals, which then made the cost to the library - which was picking up the publication fees for the papers -- soar out of hand! There were 41 BMC papers published by Yale authors in 2006; already in 2007 there have been 43. (Note: The corresponding author, whose institution pays the publication fee, was not necessarily a Yale author in all these cases.) By taking an institutional "pre-pay" membership in BMC, the Yale Library had opted to try to pay the BMC author publication fees (via the Institutional Membership program) and these fees just got to be too much for them to bear as more and more Yale authors opted for publishing in BMC titles.

To be sure, the article charges for publishing in BMC journals have been rising, too. Yale authors can, of course, continue to publish in BMC journals, and it will be interesting to see how many still opt for this. They will have to pay the page charges out of their grant money, as over half of the BMC authors have been doing.

As David Stern, Yale's science librarian, reported in his posting:

The libraries’ BioMedCentral membership represented an opportunity to test the technical feasibility and the business model of this OA publisher. While the technology proved acceptable, the business model failed to provide a viable long-term revenue base built upon logical and scalable options. Instead, BioMedCentral has asked libraries for larger and larger contributions to subsidize their activities. Starting with 2005, BioMed Central article charges cost the libraries $4,658, comparable to a single biomedicine journal subscription. The cost of article charges for 2006 then jumped to $31,625. The article charges have continued to soar in 2007 with the libraries charged $29,635 through June 2007, with $34,965 in potential additional article charges in submission.

He goes on to conclude...

"We believe in the widest possible access to scholarly research supported by workable business models and should BioMed Central develop a viable economic model which allows them to more equitably share costs across all interested stakeholders, we would consider renewing our financial support. "

BMC Publisher, Matthew Cockerill, has of course replied to the Yale news, pointing out that the article processing charges that BMC charges are still less than most commercial publishers. He goes on to suggest that libraries consider the future where instead of purchasing some subscriptions to journals it may be a role of the library to support open access publishing for the greater good. From his posting:

That is why BioMed Central introduced its institutional membership scheme, which allows institutions to centrally support the dissemination of open access research in the same way that they centrally support subscription journals, thereby creating a 'level playing field'.

In order to ensure that funding of open access publication is sustainable, we have encouraged institutions to set aside a small fraction of the indirect funding contribution that they receive from funders to create a central open access fund.

It should be noted that BMC's Institutional Membership program, whereby universities (usually the library) pre-pay all or most of the author's article fees is not the only way in which the institution can show it's support for the BMC flavor of open access. BMC also offers a "Supporting Membership" which is not tied to the number of articles submitted from an institution; it offers a modest (usually 15%) reduction in the article publication charge.

At this point, the University of Illinois at Urbana-Champaign is neither an Institutional nor Supporting member of BMC.

Posted by Katie Newman at 2:34 PM

August 1, 2007

BioText: Search for Text within the Captions of Journal Articles

Below is a posting from the BioMed Central blog announcing that the BioText search engine is available! Many of you will recall that several months ago it's developer, Marti Hearst gave a presentation at UI, to the Bioinformatics Group, about Biotext.

BioText, in it's current rendition allows one to perform text searches within the captions of figures (as well as the abstracts) in ~150 journals housed in BioMed Central.

Here's a link to the search engine:

Here's a listing of the journals you'll be searching (includes BMC Bioinformatics!) (click on the "Collection" tab): "The current collection consists of more than 150 journals, 20,000 articles, and 80,000 figures."

Research report (Bioinformatics):

Some searching tips...
If you search for several words, it does an OR search. That is, it's not like Google, which does an AND search!
To force it to search on several words in a Google-like mode, put a "+" in front of the word, or enclose a phrase in quotations. To search for word stems, put an asterisk after the word stem.

Examples of legitimate searches would be....
(Searching over "captions (list view)", with number of "hits"...)
bee 30
"honey bee" 5
bee bees 44
"Apis mellifera" 35
microarray genom* 4973
+microarray +genom* 107
+microarra* +genom* 128


As seen on the Open Access blog, an excerpt from the BioMed Central Blog:
Matt Hodgkinson, BioText - a search engine for open access figures, BioMed Central blog, July 31, 2007. Excerpt:

At the ISMB conference we met Anna Divoli, a postdoc at the University of California, Berkeley, who showed us the BioText Search Engine, which she was presenting as a poster, and has recently published....

I came across it briefly earlier this month thanks to the blog of medical librarian David Rothman, who described it as "A supercool way to search PubMed Central", which is a pretty good description!

It is part of the text mining BioText project and goes beyond the abstract searching in MEDLINE seen previously to extend searching to the figure legends of Open Access journals in PubMed Central.

As the homepage of PubMed Central notes, "All the articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access". Because Open Access explicitly allows the reuse of the content of the articles in these journals (which include all 170+ BioMed Central journals) this has allowed the BioText people to create a search engine that allows keyword searching of abstracts, figure legends, titles and authors, returning results sorted by date and relevance, and in two formats: abstracts with figure thumbnails and legends, or figure legends with thumbnails....

Anna hinted at upcoming functions such as returning snippets that match the search terms from the full text of the article (much as Google Scholar does). We look forward to these further developments, and we'd like to thank Anna, Marti Hearst and the others on the BioText team for developing such a useful and user friendly tool. This is a great example of how Open Access allows others to make further use of published work, in ways that the authors or publishers had not anticipated.

Posted by Katie Newman at 1:49 PM