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

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

*******************************************
Melody Allison
Assistant Biology Librarian and Associate Professor of Library Administration
Biology Library
University of Illinois at Urbana-Champaign
101 Burrill Hall, 407 South Goodwin
Urbana, IL 61801
mmalliso@illinois.edu
(217) 333-7461; 3654

Automatic Term Mapping. The old Automatic Term Mapping was designed to recognize author names, journal titles, and MeSH terms when searched without field tags. This worked fine when an author or journal name was not the same as a MeSH term, but when that happened the search term was mapped to a MeSH heading and “Text Word” fields, not the author or journal fields – so the citation was missed. The new ATM has been modified to include author and journal field searches. Another ATM update relates to MeSH and journals translations. The new ATM now broadens these searches by searching individual words and multiple words in the “All Fields” field; multiple words are ‘ANDed’ together. Although ATM’s new design expands searches, it may provide less relevant results. Using field tags in the regular PubMed search box or doing field searches in the new (Beta) Advanced Search mode can focus strategies – and results. more

Citation Sensor. Citation Sensor displays results for searches using untagged terms that are characteristic of citation searching, e.g., author names, journal titles, and publication dates (e.g., woese c 1972). Citation(s) results are highlighted in a yellow area above the search results. more

NCBI Beta Version of Advanced Search. The Advanced Search is designed to provide more ease and flexibility to create your search strategy. It can be accessed from the main PubMed search page by a link next to the search box. The PubMed Search History, Search boxes with field options (including links to indexes when available), all PubMed Limits, and the Index of Fields / Field Values for Preview / Index search are all accessible and usable on the same page – a big and welcome change! Send your comments at the bottom of the search page via “Write to the Help Desk.” more

Online Clinic. There is a thirty minute NLM and the National Training Center and Clearinghouse (NTCC) online clinic on Thursday, July 17, 2008 (2:00 pm ET) to go over PubMed changes. It is limited to the first 300 that sign in that day, but will be recorded for viewing from the same page. more

Please let me know if I can help you with any questions about these updates.

Melody Allison
Assistant Biology Librarian and Associate Professor of Library Administration
Biology Library
University of Illinois at Urbana-Champaign
101 Burrill Hall, 407 South Goodwin
Urbana, IL 61801
mmalliso@illinois.edu
(217) 333-7461; 3654

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/.

Unfortunately, that tremendous training opportunity will NOT occur. Yesterday the 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...

• Field Guide - Part one (ppt)


• Field Guide - Part two - Entrez (ppt)


• Field Guide - Part three - Blast (ppt)


• Field Guide - Exercises (pdf)

• Mini-courses - Powerpoint presentations and Workshop exercises


• Structure Course -- Lecture Slides, Course handout, Workshop Exercises

Office: 123A Burrill Hall, MC-112
Email: florador@uiuc.edu
Phone: (217) 265-5386
Fax: (217) 333-3662

On Tuesday, March 11th, a Web of Knowledge training instructor from Thomson Scientific will offer hands on training for Web of Knowledge special features, and the Science Citation Index and Zoological Record databases.

Web of Knowledge The Web of Knowledge has recently released a newly designed interface with powerful new search features. A Web of Knowledge training instructor will review specific aspects and services offered to searchers such as creating alerts and RSS feeds, and researcher ID’s. This session is geared for Librarians and GSLIS students and will start at 1:00 PM.

The Science Citation Index is a multidisciplinary index to the journal literature of the sciences, indexing over 6650 major journals. A cited reference searching enables you to find articles that cite a previously published work. This session will be at 2:00 PM.

Zoological Record is the world’s leading taxonomic reference database indexing over 5000 journals plus monographs and conference proceedings. It is the unofficial registry of animal names and it covers the years 1864 to the present. There will be a general review of the database with an emphasis on locating records of new species. This session will be at 3:00 PM.

If you are interested in attending please sign up soon. Each session can accommodate up to 40 participants and seats may fill up quickly.

To sign up click on the following link to access the University Library calendar.
http://130.126.32.16/evanced/lib0/eventcalendar.asp

Go to the month of March and click on the event(s) you would like to attend. The popup window will direct you to an online registration form.

Contact Beth Wohlgemuth, Head Librarian, Illinois Natural History Survey Library, 244-4907 with any questions.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Melody Allison

Assistant Biology Librarian and Assistant Professor of Library Administration
Biology Library
University of Illinois at Urbana-Champaign
101 Burrill Hall, 407 South Goodwin
Urbana, IL 61801
(217) 333-7461; 3654

"If men were angels, no government would be necessary."

-- James Madison

Research Integrity: Whose Rights? Whose Responsibilities?

A symposium for graduate faculty, students, and alumni

THIS Monday, February 25, 2008, 1:00-5:00 p.m.

Illini Union Rooms B & C

Review the program:

http://www.grad.uiuc.edu/events/symposium/2008/program.htm

Register: (requested)

http://www.grad.uiuc.edu/events/symposium/registration.asp


Please note: At 1:10 Dr. Drummond Rennie , Adjunct Professor of Medicine, University of California-San Francisco and Deputy Editor of JAMA will give a talk: 

Who Wrote My Paper? R&R in Academia [Research & Responsibility}

Office:  123A Burrill Hall, MC-112

Email: florador@uiuc.edu

Phone: (217) 265-5386

Fax: (217) 333-3662

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

< http://www.library.uiuc.edu/orr/get.php?instid=396840 >

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.

6.  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): 

http://www.library.uiuc.edu/blog/bicnews/archives/2007/03/scopus_trial_co.html

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

Katie

--<- @ --<- @ --<- @ --<- @ --<- @

Prof. Katie Newman

Biotechnology Librarian, Biotechnology Information Center (BIC), 

and UIUC Scholarly Communication Officer

Office:  123A Burrill Hall, MC-112

Email: florador@uiuc.edu

Phone: (217) 265-5386

Fax: (217) 333-3662

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:

• Web of Science, 1970-
• Biological Abstracts, 1926-
• CAB Abstracts, 1910-
• Food Science & Technology Abstracts, 1969-
• Medline (= PubMed), 1950- 
• Zoological Record, 1864-

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:

• Embase
• Chemical Abstracts (via SciFinder Scholar)
• Faculty of 1000
• Scopus
• Compendex via EiVillage
• Environmental Sciences and Pollution Management
• More

with thanks to Katie Newman's Biotechnology Information Center Blog

Highlights include:

* More intuitive, streamlined design
* New tabular approach to accessing databases and database resources
* Search all databases that we subscribe to at the same time or individually
* PR describes a new multi-database search capability that uses "one common vocabulary that recognizes the varying terms used by different databases and maps them to a unified subject classification. Which means that a search with ISI Web of Knowledge will find all relevant items that may have originally been categorized differently. Newer terms recognize older terms. And specialized terms from one database recognize specialized terms from another."
* General Search now has 3 search boxes with database field options to select from -- you can add additional ones (I have not found a maximum yet!)
* Database indexes, such as Author, Publication Names, etc., easily accessible via small icon directly to the right of the field index box (when that field is selected)
* Searches can easily be refined by various categories via check boxes from Results page
* Search terms are highlighted (yellow) in Full Record
* Marked List functionality for all WOK search results

Biology Library database guides for Biological Abstracts, Science Citation Index, and Zoological Records have been updated.
For more see information from Thomson Scientific at http://isiwebofknowledge.com/currentuser_wokhome/cu_new/newface/.

If you have any questions, please let us know.

Melody Allison

Assistant Biology Librarian and Assistant Professor of Library Administration
Biology Library
University of Illinois at Urbana-Champaign
101 Burrill Hall, 407 South Goodwin
Urbana, IL 61801
(217) 333-7461; 3654

"If men were angels, no government would be necessary."

-- James Madison

You may remember that a year or so ago I sent out a message saying that I
was working on a database listing field guides from around the world. I'm
pleased to report that the U of I News Bureau just sent out a news item on
the database. If you need or use field guides please take a look, and as
always send suggestions for guides to add!

Diane Schmidt
Biology Librarian

Today's News From the University of Illinois at Urbana-Champaign

Jan. 29, 2008

U. OF I. LIBRARIAN LAUNCHES COMPREHENSIVE WEB DATABASE OF FIELD GUIDES
Diane Schmidt, the biology librarian at the U. of I. has built and
launched the most complete database of field guides to date. The
International Field Guides Web Site merges Schmidt’s own book, “A
Guide to Field Guides: Identifying the Natural History of North
America” (Libraries Unlimited, 1999), and its companion Web site,
International Field Guides, plus 2,000 new titles.
http://www.news.uiuc.edu/news/08/0129fieldguides.html

Visit the News Bureau for more news.

Enjoy !

Melody Allison

Assistant Biology Librarian and Assistant Professor of Library Administration
Biology Library
University of Illinois at Urbana-Champaign
101 Burrill Hall, 407 South Goodwin
Urbana, IL 61801
(217) 333-7461; 3654

************************************

The Savvy Researcher Workshop Series
http://www.library.uiuc.edu/learn/instruction/workshops.html
(registration preferred- access through website)
All workshops held in the Undergraduate Library, Room 291

Improving Your Library Research Skills

Are you struggling with your research? Need help locating articles and other materials? This workshop will go over how to locate items in the library system, including how to find online resources through library databases and when to use Interlibrary Loan. Bring your research paper with you -- time will be set aside to answer individual questions.
Tuesday 1/29, 3:30-4:30pm
Tuesday 2/26, 3:30-4:30pm

Drowning in Data? RefWorks can Help

Learn how to use RefWorks, a citation management software program subscribed to by the University of Illinois Library and CITES that is free to faculty, staff, and students of the University of Illinois. This workshop will cover the basics: how to access RefWorks, search catalogs, import references from library databases, retrieve and manage citations, create bibliographies according to various citation styles (e.g., MLA or APA), and use Write N Cite to add parenthetical references to your work. For more information about RefWorks see: http://www.library.uiuc.edu/refworks/
Friday 2/1, 1:00-2:00pm
Thursday 2/28, 3:30-4:30pm

Tools to Stay Current in Your Research

Save valuable research time! Online research resources are pervasive today, making it much harder to stay current in your field. This workshop will introduce several current awareness features including how to set up an RSS feed reader account, creating search alerts from library databases as well as Table of Contents alerts.
Tuesday 2/5, 3:30-4:30pm
Tuesday 3/4, 3:30-4:30pm

How To Be A Better RA/TA

Geared towards Research and Teaching Assistants, this library workshop will introduce several time-saving tips. Topics include the basics of working for others (e.g., proxy authorizations and departmental charge accounts), current awareness services, PapersInvited, how to locate dissertations, and how to use RefWorks, a personal citation database.
Friday 2/8, 1:00-2:00pm
Thursday 3/6, 3:30-4:30pm

Info Hacks **New**

Is your academic pile of information overwhelming? Are you looking for new ways to get organized? Learn from the best! Librarians will give you the low-down on how they organize their own research materials using several different strategies including the GTD method (Getting Things Done), citation management, current awareness tools, social bookmarking and quick tips.
Friday 2/15, 1:00-2:00pm
Friday 3/7, 1:00-2:00pm

What Google Scholar Can Do for You **New**

Even librarians use Google Scholar! Improve your searching by learning tricks of the trade using advanced features of Google Scholar. Learn the benefits and limitations of what Google Scholar can do for you. Also, learn about the new Google Book project and how to find online books.
Friday 2/22, 1:00-2:00-pm
Tuesday 3/11, 3:30-4:30pm

*************************************************************
Merinda Kaye Hensley
Instructional Services Librarian, Reference Library
University of Illinois at Urbana-Champaign
300 Main Library
1408 West Gregory Drive, Urbana, Illinois 61801
mhensle1@uiuc.edu, 217.244.1880 (v), 217.333.1116 (f)

--

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Melody Allison
Assistant Biology Librarian and Assistant Professor of Library Administration
Biology Library
University of Illinois at Urbana-Champaign
101 Burrill Hall, 407 South Goodwin
Urbana, IL 61801
(217) 333-7461; 3654

The NIH has now filled in many implementation details concerning the mandate and they may be found on the NIH Public Access site, FAQ, and Guide Notice for Public Access.

Details that will be of interest to the University of Illinois community:

TIMING
The policy applies to all peer-reviewed articles that are accepted for publication on or after April 7, 2008.

PUBLISHER AGREEMENTS & COPYRIGHT
From the FAQ:
“Authors should work with the publisher before any rights are transferred to ensure that all conditions of the NIH Public Access Policy can be met. Authors should avoid signing any agreements with publishers that do not allow the author to comply with the NIH Public Access Policy.”

A publisher’s compliance with the NIH policy can be checked by reviewing the SHERPA site. For example, from Sherpa one learns that both Nature and Science allow authors to comply with the NIH mandate, subject to restrictions, with just a 6 month embargo. In neither publication can the author archive the publisher's PDF (though it should be referenced); rather the author's final peer-reviewed version should be posted to PubMed Central. (The most convenient time to do this would be at the same that you send in the final version to the publisher.)

... more (see link below signature below) ...

Katie
--<- @ --<-@ --<-@ --<-@ --<-@
Prof. Katie Newman
Biotechnology Librarian, Biotechnology Information Center (BIC),
and UIUC Scholarly Communication Officer

Office: 123A Burrill Hall, MC-112
Email: florador@uiuc.edu
Phone: (217) 265-5386
Fax: (217) 333-3662

NIH Looks to Revise Peer Review Process to Help Young Researchers
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. ...

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 course was presented on Campus (Fall of 2005) over 200 people registered to attend. ...

Have a restful winter break, everybody.

Katie
--<- @ --<-@ --<-@ --<-@ --<-@
Prof. Katie Newman
Biotechnology Librarian, Biotechnology Information Center (BIC),
and UIUC Scholarly Communication Officer

Office: 123A Burrill Hall, MC-112
Email: florador@uiuc.edu
Phone: (217) 265-5386
Fax: (217) 333-3662

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 link .

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 by clicking on the "I":
http://www.searchplugins.net/pluginlist.aspx?q=PubMed+for+University+of+Illinois&mode=exactAfter installing the plugin, click on the Firefox drop down 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. Leslie has also embedded the proxy URL into the plugin, so you can load it on your home computers and still be able to access the full text journals from PubMed citations.

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

----
Note: this message has been archived on the Biotech Info Center blog:
http://www.library.uiuc.edu/blog/bicnews/

Katie
--<- @ --<-@ --<-@ --<-@ --<-@
Prof. Katie Newman
Biotechnology Librarian, Biotechnology Information Center (BIC),
and UIUC Scholarly Communication Officer

Office: 123A Burrill Hall, MC-112
Email: florador@uiuc.edu
Phone: (217) 265-5386
Fax: (217) 333-3662