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 Biotechnology Information Center Homepage

May 9, 2008

Bulk Download PDFs from SCOPUS

If the way you like to work is to download the PDFs of journal articles to your hard drive, here's some news you will welcome!

Scopus, a multidisciplinary database for the sciences, has just added a DOWNLOAD button that allows you to download up to 50 pdfs at a time to your hard drive.

Steps:

  1. Perform a search in Scopus
  2. Select the article(s) that you are interested in by checking the box to the left of the citation.
  3. Click on the DOWNLOAD button. A new window will open.
  4. You'll be asked how you want to have the files named, e.g., by first author's last name + title of the article, or however you like.
  5. Identify the folder on your hard drive where you want the files placed.
  6. If desired, check off that you'd like to have Abstract downloaded, if the pdf is not available.
  7. That's it! Press Begin Download.

If you use EndNote, you'll still need to pull the citations into EndNote in a separate step. Then can "link" from EndNote to the downloaded articles on your harddrive, if you like.

If you'd like to learn more about Scopus, here's a piece I wrote about it, when it was just in Trial mode at the University (we have since decided to subscribe to it):

The technology that Scopus is using to perform this minor miracle of pulling in the pdfs comes from Quosa.

Posted by Katie Newman at 3:36 PM

April 25, 2008

Local Assistance for NIH Grantees

The University of Illinois Library stands ready to assist local NIH grantees meet the requirements of the recently inaugurated NIH Public Access Policy.

We've created the NIH Public Access Mandate website that offers step-by-step help through the process and will help you decide if you have the RIGHT to deposit your manuscripts into the PubMed Central system.

Here you will find:

  • General Information and answers to frequently asked questions about the Policy.
  • Resources to help you figure out if you have the RIGHT to deposit your work in PubMed Central
  • Basic, step by step instructions for depositing your work.
  • How you can have the Library do the submission for you.
  • Useful Links & Local Contacts who can help you

Please let us know if we can be of assistance!

Katie Newman
Biotechnology Librarian and Scholarly Communication Officer
florador@uiuc.edu
217-265-5386

Sarah Shreeves
IDEALS Coordinator
sshreeve@uiuc.edu
217-244-3877

Posted by Katie Newman at 1:31 PM

April 8, 2008

The University of Illinois is Now a Member of BioMed Central

News that many of you have been eagerly awaiting!

The University of Illinois Champaign-Urbana is now a Supporting Member of the open access publisher, BioMed Central.

What this means is that when you submit a journal article for publication in one of nearly 200 BMC titles, you will receive a 15% discount off the article processing charge!

Here's a list of the BMC titles:
http://www.biomedcentral.com/browse/journals/.
This discount also applies to articles submitted to Chemistry Central
http://www.chemistrycentral.com/ and to PhysMath Central http://www.physmathcentral.com/.

Here's a list of the article processing charges for the various BMC journals (before discount):
http://www.biomedcentral.com/info/authors/apcfaq
For most of the journals, the fee is $1690, but may be as high as $2685 or as low as $500. A few are even free.

Many of the BMC journals have already earned quite respectable Impact Factors. See:
http://www.biomedcentral.com/info/about/faq?name=impactfactor
e.g., Genome Biology (7.17); BMC Bioinformatics (3.62); BMC Biology (4.43); BMC Evolutionary Biology (4.46)

Why should you consider publishing in a BMC journal?
First of all, know that all research submitted will receive rigorous and rapid peer review. If the article is accepted:

  • It will be accessible to anyone with an Internet connection - open access means no subscriptions or 'pay-per-view' charges for original research articles.
  • It is more likely to be cited, as it will be freely available to the entire global biological and medical community
  • It will be listed in PubMed within days of publication
  • You retain the copyright of your work
  • You will be able to view your article's access statistics, which average over 200 downloads per month per article
  • Your articles will be securely and permanently archived in PubMed Central

Papers published by our colleagues:
The University of Illinois' "homepage" lists papers that were published in BMC jouranls by U of I authors in the last year -- at this point 30 research articles, software, protocols, etc:
http://www.biomedcentral.com/inst/11700
For your interest, here's the U of I-Chicago's home page:
http://www.biomedcentral.com/inst/48900

Submitting a paper:
If you are on campus within our recognized IP range when submitting a manuscript you will be identified as belonging to a member institution and automatically granted a 15% discount on article processing charges If you are at home or at an external terminal when submitting your paper, you can still claim this discount by stating that you are a affiliated with the U of I. Papers may be submitted either via a journal home page or via http://www.biomedcentral.com/manuscript/.

Posted by Katie Newman at 3:56 PM

February 26, 2008

NCBI Field Course Will NOT be Held

In January, it was announced that the University of Illinois would be hosting the Field Guide to NCBI Resources Course.

Unfortunately, that tremendous training opportunity will NOT occur. Yesterday NCBI Field Guide coordinator, Peter Cooper, sent the following email:

Because of budgetary constraints, NCBI has made reductions in some of its programs, and the education programs are affected. In fact, all outreach education programs (Field Guide, Mini-courses, Structures, PubChem) are terminated effective immediately. At this point we cannot reschedule this course or accept requests for future courses of any kind. This was as much a surprise to me as it is to you. Feel free to contact me if you have questions.

The Field Course, as well as the Mini-Courses and the Structure course, has been tremendously popular and useful (see list of sites where the Field Course has been offered recently), but the NCBI budget situation will not allow NCBI to continue to travel and offer these courses for the foreseeable future.

If we would have been able to host the Field Course, registratants would have been asked to print out the PowerPoint slides for the 3-hour lecture presentation, and the Workshop exercises ahead of time. Here they are...

Additionally, you may find the following materials of interest, from the Mini-courses and the Structure Course:

Posted by Katie Newman at 4:49 PM

February 6, 2008

Web of Knowledge -- a recommendation

For Maximum Retrievals in the Agricultural / Biological / Medical Sciences, Search Web of Knowledge.

Recently the Web of Knowledge search platform was revamped, so that now, when you search "all databases", the records are automatically de-duplicated. If the record of interest is in multiple databases (as they frequently are), the default will be to show the Web of Science record for it if it is in Web of Science. In the case of a record that is present in multiple databases, there will be links to other versions of the record from the Web of Science record, in case you prefer to see the record as presented in another database.

Searching Web of Knowledge in the "all databases" searches the following resources, simultaneously:

Take a look at the results of several searches run in each database individually, vs run in the Web of Knowledge All Databases mode. From the results, you can see that you will get more search retrievals from searching the whole Web of Knowledge database, than from searching any of the individual databases.

Recommendation: Search Web of Knowledge in the "All Databases" mode UNLESS you need to:

  • Set up a email search alert. These can not be set to run across "all" the databases, so you will need to set them up in each individual database. Since Web of Science is updated weekly, it's recommended that you start by setting up topical or table of contents alerts from it. Depending on your topic, you'll want to set up alerts in other databases, too.
  • Run a cited reference search. Use Web of Science -- it is the only database running under the Web of Knowledge platform that has this feature.
  • Use some of the search handles that are specific to particular databases, e.g., Medline's MESH (Medical subject headings), CAB's descriptors, Biological Abstracts' Concept Codes, etc.
  • Export keywords, subject headings, and other database-specific information into EndNote or RefWorks. When you export records from an All Databases Web of Knowledge search, only the bibliographic information (author, title, citation) and the abstract will be exported.

Note: Many ag / bio / medical resources are NOT included in the Web of Knowledge platform, and, for now, you will need to continue to search them individually. For example:

Posted by Katie Newman at 2:14 PM

December 10, 2007

NIH Looks to Revise Peer Review Process to Help Young Researchers

From the Chronicle of Higher Education (12.10.07) [U of I access link]

NIH Panel Unveils Big Ideas for Revamping Peer Review and Grant Making

A committee studying ways to improve peer review and grant making at the National Institutes of Health called for major changes on Friday. They include slashing the length of grant applications and placing more weight in grant reviews on the scientific effects of the proposed research.

The working group, created by the advisory committee to NIH director Elias A. Zerhouni, also suggested providing more grants for young scientists who have never before received one. The agency should review grant proposals from such applicants separately from those of established, older investigators. The younger scientists make up a diminishing proportion of the agency's grantees, raising concerns about the future vigor of the biomedical-research work force.

In addition the working group proposed ways to improve the quality and efficiency of the NIH's peer review. One way was to require senior, established researchers to serve on the agency's review panels, which are made up largely of outside academics, as a condition of receiving certain grants. Those veterans are increasingly unwilling to volunteer because of the time commitment involved, but they possess the expertise and experience needed for quality reviews, the panel found....

One of the big changes would transform the peer-review committees of outside scientists who now review and rate applications for NIH grants, making them operate more like the editorial boards of scholarly journals. The committees, called study sections, would "outsource" grant applications to specialists in the discipline to review technical aspects. The study sections would be made up of generalists who would discuss the applications' scientific significance, broadly construed.

Further Reading:

Updated:
Read comments left at the Scientist (magazine) website about the NIH proposal.


Posted by Katie Newman at 2:57 PM

Coming in April: NCBI Field Course

Save the dates! The NCBI trainers will be returning to campus April 17th-18th to present the Field Course to NCBI Resources. The last time this was presented on Campus in the Fall of 2005, over 200 people registered to attend.

The course will consist of a 3-hour lecture on Thursday morning, April 17th and an optional 2-hour, hands-on computer workshop that will be held Thursday afternoon, Friday morning, and Friday afternoon (typically the workshop is offered 5-6 times).

The course is open to grad students, post docs, faculty, and other researchers. There is no fee to attend, but pre-registration will be required. Non-U of I researchers are also welcome to attend.

Registration for the course will open in February. In the mean time, please keep the dates open. If you are the instructor of a graduate-level course, please feel free to announce the course to your students.

Topics covered in the Field Course:

* GenBank Database: description and scope
* The NCBI Derivative Databases: RefSeqs
* Database Searching using Entrez
o Neighboring and Links
o Entrez searching
* The NCBI Structures Database
o The Molecular Modeling Database (MMDB)
o Structural Alignments
o Viewing Structures and Structural Alignments with Cn3D
* Similarity Searching using NCBI BLAST
o Local Alignment Statistics
o Scoring Systems
o Using BLAST web services
o PSI-BLAST
o RPS-BLAST (CDD Search)
o Specialized BLAST pages
* Genomic Resources at NCBI
o Complete Microbial Genomes in Entrez
o Higher Genome Resources
+ RefSeq and Genes
+ UniGene
+ Variation Data (SNPs)
+ The Human, Mouse and Rat genomes
+ The Map Viewer
+ Other Genomes

Posted by Katie Newman at 2:13 PM

November 15, 2007

Firefox Plugin for PubMed Users at the U of Illinois

If you're a bio researcher who uses the Firefox browser and PubMed, you'll want to read this!

Leslie McNeil, the NCSA researcher who manages the National Microbial Pathogen Data Resource (NMPDR), has created a Firefox plugin for U of I researchers who frequently search PubMed!

About Firefox Plugins:
Are you used to searching Google by typing in queries in the top right-hand side of the Firefox toolbar? Did you know that you can add additional search options so you can choose to search Wikipedia, Google Scholar, the U of I domain, or many other search sites, instead? All you need to do is add additional FireFox plugins.

You'll find many additional Firefox plugins from the following sources:
https://addons.mozilla.org/en-US/firefox/browse/type:4
http://mycroft.mozdev.org/
http://www.searchplugins.net/pluginlist.aspx

To load them into Firefox, all you have to do is click on the plugin's name.
Among my favorite plugins (available from the Mycroft site) are:
Wikipedia / Univ. of Illinois / Google Scholar / Google Books / Google News / Google Images / Amazon / Ebay / Flickr / Yahoo / Epicurious / IMDB / YouTube / ...

About the Firefox PubMed plugin for U of I Researchers:
Leslie McNeil has created a customized a PubMed FireFox plugin for the U of Illinois researchers. Install it from this site:
http://mycroft.mozdev.org/download.html?name=PubMed+U+of+I+full+text&sherlock=yes&opensearch=yes&submitform=Search

To install the plugin, just click on the link for the name of the plugin.
To use it, just click on the Firefox drop down indicator next to the box where you normally would type in a Google search. Choose to search PubMed instead of Google and type in your PubMed search. You'll be brought to the PubMed site with all the usual University of Illinois subscriptions and options** intact -- that is, you'll see which articles we have direct e-access to, and you'll see the UI Discover button that lets you discover other options for obtaining the articles.

Give it a try! I think you'll agree it's handy!

**That is, you'll go to the same PubMed search as if you started with this URL:
http://www.library.uiuc.edu/orr/get.php?instid=406312

Posted by Katie Newman at 4:39 PM

October 29, 2007

Science Has a Serious Marketing Problem

The Scientist (Vol 21, Issue 10) ran an interesting article, "The Future of Public Engagement" about the need for scientists to "frame" their research for public consumption. They should not just "dumb down" their science, so "the public" can understand it. Rather

...scientists must learn to focus on presenting, or "framing," their messages in ways that connect with diverse audiences. This means remaining true to the underlying science, but drawing on research to tailor messages in ways that make them personally relevant and meaningful to different publics. For example, when scientists are speaking to a group of people who think about the world primarily in economic terms, they should emphasize the economic relevance of science - such as, in the case of embryonic stem cell research, pointing out that expanded government funding would make the United States, or a particular state, more economically competitive.

How framing works..

Frames simplify complex issues by lending greater importance to certain considerations and arguments over others. In the process, framing helps communicate why an issue might be a problem, who or what might be responsible, and what should be done. A typology of frames specific to science-related issues summarizes a common set of frames specific to science.

The article gives examples from research in successes in communicating stem cell research, plant biotechnology, and nanotechnology.

Some scientists already frame their communications. Consider, for example, E.O. Wilson's Creation: An Appeal to Save Life on Earth. In his book, by recasting environmental stewardship as not only a scientific matter, but also one of personal and moral duty, Wilson has generated discussion among a religious audience that might not otherwise pay attention to popular science books.

Perhaps because I just read a similar idea in Alan Alda's book "Things I Overheard While Listening to Myself", this Scientist article resonated for me. In his book, Alda suggests that, along with all the science classes students take, perhaps they should also be taking communication classes!

We can't leave the popularization of science just to the science news writers. Their articles certainly help. But citizens need to hear about research from the scientists themselves. Last night I watched a wonderful program on Nature about colony collapse in honeybees, "Silence of the Bees". Two of our scientists from the U of I entomology department, May Berenbaum and Gene Robinson (together with other scientists) spoke eloquently of the catastrophe that will occur if honeybees continue to decline. One couldn't help but be drawn into the story and into the CSI-like research effort that's going on to solve this problem.

Posted by Katie Newman at 1:29 PM

September 18, 2007

Illinois Biotechnology Organization Formed

The Illinois Biotechnology Organization (IBO) was recently formed by several graduate students and post-docs for the purpose of "gathering together students, post-doc, professors etc. that are involved in the biotechnology area at the University of Illinois in Champaign-Urbana."

At the IBO website one will find gathered together University links of significance to biotechnology as well as a page of links that point to information about biotechnology.

The IBO is planning its first event, a social hour, for Monday, October 29th from 7-9 PM. It will be held in Room 210 of the Illini Union. All are welcome to attend, but it is requested that you register by October 22nd by sending an email to:uiuc.ibo@gmail.com.

The IBO social hour is being held in conjunction with the 2007 Biotechnology Job Fair, which is being held on Tuesday, October 30th, from 9-12 and 1-3:30, in the Illini Union. Deadline for registration for the Job Fair is October 1st.

Posted by Katie Newman at 11:14 AM

September 14, 2007

Lehigh University Offers Free Online BioScience Course

Lehigh University (Bethlehem PA) is offering a totally free online biology course, Bioscience in the 21st Century. It is described as:

A multidisciplinary survey course in which several theme-based topics in bioscience and their social/ethical considerations will be explored. ...
A major goal of the course will be to communicate the importance of a systems-driven, multidisciplinary approach in bioscience. Several contemporary issues (e.g., obesity, infectious diseases, cancer, stem cell biology, advances in cell biology and medicine, genome-based medicine, neurophysiology-related topics, bioinformatics, interfaces between organic chemistry and biology, advances in engineered biomedical systems, advances in bioimaging, social/ethical considerations) will be discussed.
Lectures will be presented by faculty from different disciplines in order to highlight cross-disciplinary perspectives on fundamental problems and potential solutions in bioscience. This course is envisioned as the initial tool for shaping an intellectual approach to bioscience that routinely values interconnections among disciplines and reduces/eliminates the tendency to compartmentalize learning “by subject.”
A second goal of the course is to provide scientific literacy for non-majors and the public. Students who are not formally registered for the course are encouraged to attend lectures based on their interests. Course materials including the syllabus, course materials, and all lectures are available on the web with full access for the entire Lehigh community and interested members of the public.
Lecturers will include Lehigh University professors from a variety of departments, as well as special guests. Check for weekly postings of lectures, and class resources.
This virtual classroom opportunity is funded through a grant from the Howard Hughes Medical Institute. The grant recognizes Lehigh’s innovative approach to preparing students to address emerging issues in modern biology and biomedical research.

Check out the
  • Syllabus
  • Schedule
  • Lecture PowerPoints
  • Videos

    Posted by Katie Newman at 2:02 PM

    September 12, 2007

    Scientific Memoirs from the U.S. National Academy of Sciences

    The U.S. National Academy of Sciences is providing open access to 500 scientific memoirs representing 150 years of scientific history. (Thanks to ResourceShelf.) From the NAS announcement:

    The National Academy of Sciences (NAS) is making 150 years of American scientific history available by publishing its entire collection of Biographical Memoirs on the Internet. Biographical Memoirs are brief biographies of deceased NAS members written by those who knew them or their work.
    Since 1877, NAS has published over 1,400 memoirs. Although the memoirs published since 1995 have been freely available on the Academy's Web site, over 900 memoirs were available previously only in print through archives and libraries.
    Among the additional 500 memoirs published online are those of famed naturalist Louis Agassiz; Joseph Henry, the first secretary of the Smithsonian Institution; Thomas Edison; Alexander Graham Bell; noted anthropologist Margaret Mead; and psychologist and philosopher John Dewey. More memoirs will be published regularly until the entire collection is available online.

    Posted by Katie Newman at 2:57 PM

    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 (chrz@uiuc.edu, 217-333-3737) or the Biotechnology Librarian, Katie Newman (florador@uiuc.edu, 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:
    http://biosearch.berkeley.edu/

    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."
    http://biosearch.berkeley.edu/index.php?action=about

    Research report (Bioinformatics):
    http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm301v1
    http://bioinformatics.oxfordjournals.org/cgi/reprint/btm301v1.pdf


    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


    Enjoy!
    Katie

    =====================
    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.http://blogs.openaccesscentral.com/blogs/bmcblog/

    Posted by Katie Newman at 1:49 PM

    July 12, 2007

    Learn of New Literature Based on Its Taxa

    If you're interested in keeping track of the literature for a particular species, read on to learn about a new service, uBioRSS, that harvests info from hundreds of publisher table of contents alerts!

    If you set up searches using this service based on any level of taxa for any type of organism, you'll receive email alerts as new articles are published.

    --------------
    Matthew Cockerill, Track the latest open access research relating to your favorite taxon, BioMed Central blog, June 26, 2007. Excerpt:

    uBioRSS is a nifty service from the MBLWHOI Library at Woods Hole, which harvests bibliographic information about new articles from publishers' RSS feeds, and then passes them through the uBio taxonomic classification system which identifies any species that are mentioned in the article, and classifies the article appropriately.

    This makes it possible to browse the literature taxonomically, so that, for example you might view a list of all the latest articles on cetaceans far more easily than can be done using plain text search.

    What's more, it is possible to filter articles by source, so you an easily taxonomically browse just BioMed Central's open access articles. The site also offers an alerting service, so you can choose to be notified of new articles which relate to your particular taxon of interest.

    uBioRSS is a great example of the way in which semantic enrichment can add value to the literature, and shows how it is particularly effective when combined with open access, as this then allows the semantic enrichment to be applied not just to the text of the title and abstract, but to the entire full text. To see an example of this in action, check out the UBio taxonomically-enhanced PubMed Central full text search....


    Comment:
    I tested this out to see if it had built-in feeds for the Honeybee, Apis mellifera, and it did! Click Here.

    It pulled articles published during the last month in such journals as:
    Florida Entomologist
    Journal of Medical Entomology
    BMC Genomics
    Southeastern Naturalist
    Australian Journal of Entomology
    Science
    BMC Developmental Biology
    New South Wales Department of Primary Industries
    PLOS Biology
    The Southwestern Naturalist
    Journal of Mammalogy
    Insect Molecular Biology
    Physiological Entomology

    So, you might want to sign up for this service from uBioRSS as an adjunct to the alerting emails that you are already receiving (I Hope!) from  Web of Science, PubMed, Biological Abstracts, Scopus, Faculty of 1000, CAB Abstracts, and so on!

    Please let me know if you'd like some help setting up alerts in your field!

    Posted by Katie Newman at 11:32 AM

    July 10, 2007

    Provost's Letter in Support of Retaining Publishing Rights

    From Provost Linda Katehi, in an email sent to the U of Illinois Faculty, 7/10/07
    ==========
    Dear Colleague,

    New opportunities created by electronic publishing and archiving are changing the business of scholarly publication. Because traditional publication agreements transfer copyrights to publishers and restrict electronic distribution by the author and their institution, publishers appear to have captured much of the benefit of these changes.

    In November 2006, faculty governance leaders from CIC universities discussed these issues that affect scholarly communication and called for a concrete strategy that would help faculty retain more control over their published intellectual property. Subsequently, the CIC provosts issued a
    Statement on Publishing Agreements and an Addendum to Publication Agreements for CIC Authors. (http://www.cic.uiuc.edu/programs/CenterForLibraryInitiatives/Archive/Report/CICAuthRtsFINAL16May07.pdf) The Addendum is intended to be used by faculty entering into publication agreements with journal publishers or presses. It supports authors rights to use their own published work in teaching and research, to post a publication on a personal website, or to deposit it in a repository maintained by their institution or a professional association. IDEALS (www.ideals.uiuc.edu) is the University of Illinois institutional repository.

    Late this Spring, the U of I Senate endorsed the principles expressed in the CIC Provosts Statement and Addendum; encouraged faculty to consider using it as well as other publication agreement addenda that increase their rights in reproducing, distributing, and archiving their own work; and asked the CIC Provosts to provide leadership in negotiating with publishers to develop new publication agreements that provide CIC authors and institutions greater rights for use, distribution and archiving their published scholarly works.

    It is our responsibility as scholars to ensure that our work is available as widely as possible to maximize its scholarly impact, accessibility, and educational use. I encourage you to use the Addendum and to deposit your research and scholarship in IDEALS, which provides reliable and persistent access to its holdings.

    ===============
    You may read more about what the U of I is doing at the Scholarly Communication website. See:
    What the U of I is doing
    What YOU can do.

    Posted by Katie Newman at 9:46 AM

    July 9, 2007

    Do the Criteria for Tenure in the Sciences Need to Change?

    The Scientist is currently running an open-comment survey on whether folks think that the criteria on which tenure is awarded in scientific disciplines needs to change.

    Among the questions to consider:


    • Do you believe reviewers of a scientist's achievements currently focus too heavily on citations?
    • What metrics should we use to evaluate researchers in fields that tend to rack up fewer citations?
    • Do you believe reviewers focus too heavily on grant funding when evaluating scientists?
    • Is tenure a good idea to begin with? Does it support a lot of tenured scientists who don't contribute as much as those still working for tenure?
    • Are tenure decisions getting off track? Are we evaluating scientists fairly?
    • And once scientists become tenured, is there enough structure to ensure they continue to contribute significant science?

    Source: The Scientist : Does tenure need to change?
    Address : <http://www.the-scientist.com/news/home/53370/>

    Posted by Katie Newman at 12:44 PM

    PLoS Hires ScienceBlogs Blogger to Encourage Interactivity

    With thanks to Becky Smith for the heads up...

    Bora Zivkovic, chief blogger at ScienceBlog's "A Blog Around the Clock", has been hired by the Public Library of Science to encourage readers to comment on the papers that are published by the various PLOS journals.

    Each PLOS article provides a link whereby readers may "provide a response" to the article. Browsing through several issues of PLOS Biology indicates to me that so far this option has been underutilized so it appears Bora will have a big task ahead of himself.

    It seems to me that such comments on articles could certainly add extra value to the original piece -- they could elaborate on related experiments, refute the findings, or comment on the significance of the article much as Faculty of 1000 Biology recommendations do.

    Good luck, Bora!

    Posted by Katie Newman at 11:24 AM

    July 6, 2007

    Web of Science Dates of Coverage Extended

    Web of Science fans will be pleased to learn that we were recently able to extend our coverage back in time significantly.

    Although the database is called Web of Science, it is actually composed of three databases. Until recently, searching was limited to references from 1980 to the present.

    Coverage for the three databases now is:

    Science Citation Index Expanded: 1970-present
    Social Science Citation Index Expanded: 1970-present
    Arts & Humanities Citation Index: 1975-present **

    **1975 is as far back in time as this database is available from the producer.

    Posted by Katie Newman at 5:30 PM

    Google Scholar is Adding Content from Elsevier's ScienceDirect Journals

    Big News! Google has recently been given permission to add content from the Elsevier ScienceDirect web portal. This means that, when searching Google Scholar (and possibly Google) we'll be able to search the full text of the nearly 2000 sci-tech journals published by Elsevier.

    Until now, the only search engine that searched the full text of Elsevier journals was Elsevier's own search engine for ScienceDirect and it's subscription product, Scopus.

    Many researchers are using Google Scholar due to it's ease of use and because it is capable of searching the full text (not just the titles / abstracts) of articles.

    If the U of I has a subscription to the retrieved citations, you'll be able to read the articles online. If we don't have a subscription, use the "Discover" link attached to each Google Scholar record to request the article from Interlibrary Loan.

    Read more about this announcement.

    Posted by Katie Newman at 5:28 PM

    July 3, 2007

    Check the Impact Factor of Your Favorite Journal!

    The latest edition of Journal Citation Reports (2006) is now available at
    http://www.library.uiuc.edu/orr/get.php?instid=258273

    JCR provides the Journal Impact Factors, a frequently cited and touted measure of the supposed importance or worth of a journal. Both the Science and Social Science versions of the JCR are available at the University of Illinois; for comparison, we have JCRs back to 1998.

    The 2006 impact factors are calculated from the average number of times articles from the journal published in the past two years have been cited by in articles published in journals monitored by Thomson/ISI in their Web of Science product during 2006. The Impact Factors are available for most of the over 8000 journals currently indexed in ISI/Thomson's Web of Science product. It's important to note that the only journals that are said to be citing a particular article are those 8000+ journals that are monitored by Thomson/ISI.

    An example of how an impact factor is calculated:

    JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
    Cites in "all" 2006 articles to articles published in this journal in:
    2005 = 236
    2004 = 321
    Sum: 557

    Number of articles published in this journal in:
    2005 = 79
    2004 = 61
    Sum: 140

    Impact Factor Calculation:
    Cites in 2006 journals to recent (2004-2006) articles / Number of recent articles published
    = 557/140
    = 3.979

    Note: Thomson/ISI is now calculating impact factors for quite a few open access journals. Among the highest ranked are two PLoS journals: 14.1 for PLoS Biology (14.7 in 2006); 13.8 for PLoS Medicine (8.4 in 2006). At least eighteen BioMed Central (BMC) journals also have impact factors.

    Posted by Katie Newman at 10:31 AM

    June 13, 2007

    One Million University of Illinois Books to be Digitized by Google

    Read my posting on this over at the UI Scholarly Communication News site!

    Posted by Katie Newman at 9:47 AM

    June 12, 2007

    NPG launches Two New Websites: Nature Reports Climate Change and Nature Reports Stem Cells

    From Knowledgespeak (June 12)

    Scientific publisher Nature Publishing Group (NPG), UK, has announced the launch of two new websites - Nature Reports Climate Change and Nature Reports Stem Cells. The Nature Reports sites highlight topical science issues by providing thorough investigative reporting based on peer-reviewed, primary research.

    The new websites will report ‘the science behind the news, the news behind the science,’ and explore the social, political and economic implications of the highlighted topic. Users of all levels of expertise, from scientists, journalists and students, to members of the general public, can access the content, a vast majority of which is freely available. Over the coming months, both Nature Reports: Stem Cells and Nature Reports Climate Change hope to develop further with increased community interactions, resources and media.

    The topics for discussion in the Nature Reports series were chosen based on the most popular search terms run on Nature.com in 2006. The first in the series- Nature Reports Avian Flu- was launched in March 2007.

    Nature news release (pdf).

    Posted by Katie Newman at 1:18 PM

    June 6, 2007

    A Farmer's Perspective on Biotechnology

    Art Brandli, who farms in Warroad, Minn., recently wrote an opinion piece in Ag Weekly about his impressions while attending the annual BIO conference, which was held in Boston this year. Some snippets from his report...

    The BIO Conference was huge, over 20,000 people from 64 countries and the amount of information nearly overwhelming. One quickly learns how much biotechnology is already used in our everyday lives, and how food and production agriculture is just a small part of the biotech industry.

    Michael J Fox was a keynote speaker, stressing the need for the biotechnology industry to continue to innovate and accelerate the translation of basic science into improved therapies for patients.

    I had an opportunity to meet a number of people committed to working for greater acceptance of biotechnology in agriculture, including Dr. Clive James, an ag scientist from the UK and former deputy director general at the International Maize and Wheat Improvement Center, where he worked with Dr. Norman Borlaug, “Father of the Green Revolution.” James now heads a nonprofit charitable organization whose mission is to alleviate hunger and poverty in developing countries. James cited FAO projections that world food-production needs to double by 2050, using less water and little more land than today, despite climate change, the increasing focus of cropland for biofuels, and the fact that one-third of the world’s population lacks food security now. He stressed that a successful strategy must have multiple approaches that include population stabilization, improved food distribution systems - and a technology component, a crop improvement strategy that integrates conventional and biotech crop approaches to optimize productivity and that can contribute to food, feed, fiber, and fuel security.

    One approach in communicating with consumers, James suggests, is not to refer to “biotech” or “genetically-modified” crops, but simply “bio crops.”

    Posted by Katie Newman at 9:58 AM

    June 5, 2007

    H-Index in Scopus

    Scopus now incorporates the h-index as a means to evaluate research performance, including unique graphs that enable users to interpret the value of the h-index by displaying publication and citation trends over time. The H-index is touted as being a objective measure of scientific research productivity.

    How to get the H-Index in Scopus:
    After performing an author search in Scopus, click on the "citation tracker" button to view the Citation Overview analysis, and then click on the h-graph button to view the graphical representation of the data.

    Caveat:
    Scopus only includes data for articles published from 1995 to the present. Thus the h-index data from Scopus is not complete for older researchers.

    ---------
    Read more about the "H-Index, from the Help file in Scopus:

    The h-Graph displays the h index for a single author, multiple authors, or a group of selected documents. The h index is based on the highest number of papers included that have had at least the same number of citations. The h index was developed by J.E. Hirsch. Hirsch defines the h index as follows:

    "A scientist has index h if h of his/her Np papers have at least h citations each, and the other (Np − h) papers have no more than h citations each."

    For Example An h-graph for a group of selected documents or selected author(s) with an h index of 12 means that out of the total number of documents selected to produce the graph, 12 of the documents have been cited at least 12 times. Published documents with fewer citations than h, in this case less then 12, are considered, but would not count in the h index.

    For more information about the h index, see Hirsch, J.E. "An index to quantify an individual’s scientific research output." Department of Physics, University of California, San Diego.

    The H-graph includes two lines: h index and the h-Line. The h index line represents the number citations received for each of the articles in descending order. The h-Line represents the number of citations equal to the number of articles.


    Posted by Katie Newman at 10:37 AM

    Broad Impact: Refreshing Your Statistics Knowledge

    Have you discovered Faculty of 1000 Biology, yet? It's a great tool for discovering hidden gems and important papers in particular areas. I like to think of it as a really good student advisory committee that selects, recommends, and critiques the top "must read" articles in all areas of Biology!

    Here's a news blurb from BioMed Central, the publisher of F1000:

    Five Faculty of 1000 Biology members have recently singled out an Exceptional Broad Impact paper that is of high relevance to researchers in all fields of Biology, as it provides guidance to biologists for navigating the often tricky world of data representation -- in particular the use of error bars.

    "This paper should be read by anyone who is trying to present experimental data graphically." comments David Stephens (University of Bristol, UK), Faculty of 1000 Biology member for Cell Biology.

    Andy Groves (House Ear Institute, USA), a Faculty of 1000 Biology member for Developmental Biology goes on to say "This wonderful article clearly explains how experimental variation is measured and displayed, and describes how different kinds of error bars can mean very different things. This paper is a must read for every scientist who thinks that triplicate plates from a single experiment counts as n=3 !!!!!"

    "Personally, I have filed the pdf in a safe place, and I plan to consult it every time I send a graph for publication." concludes Etienne Joly (CNRS, France), a Faculty of 1000 Biology Member for Immunology.

    The Faculty of 1000 Biology structure makes it possible to identify papers of broad interest, irrespective of the journal in which they are published. Go to the Faculty of 1000 Biology website to see the full comments of all the evaluating Faculty Members on this Exceptional Broad Impact paper.

    Posted by Katie Newman at 10:21 AM

    May 21, 2007

    Link to Full-text Articles from EndNote

    Are you an EndNote user? If so, you'll be interested in learning how you can set up EndNote so it communicates with our OpenURL resolver to provide you with links to the full-text of journal articles!

    You may have seen the Discover link DiscoverLink in PubMed, Web of Science, and many other article databases. When you click on the Discover link in these databases a new browser window pops up that provides links to the full text of the article (if we have an e-subscription), and several other facets about the article [read more about Discover].

    You may enable this same technology in EndNote by following the instructions provided on the page, Linking to Full-text Journal Articles from EndNote Using Discover.

    Posted by Katie Newman at 4:27 PM

    May 15, 2007

    Senate Endorses the CIC Provosts' Statement on Publication Agreements

    On April 30th, 2007, the U of Illinois Faculty Senate endorsed the CIC Provosts' Statement on Publication Agreements. This statement urges faculty to retain some of their copyrights when submitting papers for publication in order to maximize the scholarly impact, accessibility, educational use, and readership of their papers. To facilitate this, U of Illinois authors are urged to consider amending the standard publisher's Copyright Transfer Agreement with the Addendum to Publication Agreement for CIC Authors (Word doc).

    The Addendum stipulates that the authors will be able to make their papers freely available on the Internet within 6 months of publication, thus granting publishers the right of first impact. U of Illinois authors are urged to submit a copy of their paper to IDEALS -- the U of Illinois digital archive -- with the stipulation that it be made freely available after 6 months. Of course, some publishers already allow authors to mount their articles on institutional web sites; check the Sherpa/Romeo database for publisher policies.

    For more background on the CIC Provost's Statement on Publication Agreements, and why the U of Illinois Senate endorsed it, please read the background information provided by the U of Illinois Senate Committee on the Library.

    Posted by Katie Newman at 4:14 PM

    May 10, 2007

    Faculty of 1000 Biology Reaches 45,000 Evaluations!

    If you've not yet signed up for an account on Faculty of 1000 Biology, you really owe it to yourself to do so! Senior faculty select significant / controversial articles for inclusion in F1000 Biology, and comment on the relevance of the article. You can browse / search F1000 for articles in your research area. And be sure to sign up for email alerts so you can see keep up with the "hot" papers in your area!

    Here's a recent news bulletin about F1000 Biology --- If you haven't already, check it out!

    Faculty of 1000 Biology is pleased to announce the publication of its 45,000th evaluation! More than 33,000 distinct papers have now been evaluated on the site (since its launch in 2002) and these have come from over 1100 different journals, thereby fulfilling the aim of Faculty of 1000 Biology to highlight papers on the basis of their scientific merit rather than the journal in which they appear.

    The 45,000th evaluation was submitted by Michael Ehlers (University of Chicago, USA), a Faculty of 1000 Biology Member for Neuroscience, who selected a paper from Nature Neuroscience by Kee et al. that "provides compelling evidence that new granule cells of the adult rodent hippocampus born 1-2 months earlier are preferentially active during spatial memory tasks." [see full evaluation]

    Identifying evaluations in your areas of interest on the Faculty of 1000 Biology site couldn't be easier -- use 'Advanced Search' to find your papers by author, title, keywords or by F1000 factor -- so there's no need to read all 45,000 evaluations... unless you want to of course!

    Posted by Katie Newman at 11:04 AM

    April 20, 2007

    Nature and Cold Spring Harbor Protocols

    We have taken out subscriptions for BOTH the Nature and Cold Spring Harbor Protocols!

    Cold Spring Harbor Protocols http://www.library.uiuc.edu/orr/get.php?instid=598310
    FAQ: http://www.cshprotocols.org/misc/faqlist.dtl

    Nature Protocols http://www.library.uiuc.edu/orr/get.php?instid=545072
    FAQ: http://www.natureprotocols.com/about.php

    Please also remember that we have subscriptions for all the Wiley "Current Protocols", too.
    http://tinyurl.com/278luk

    Posted by Katie Newman at 4:33 PM