Levy Library

New: Human Gene Mutation Database

Wouldn't it be nice if someone, somewhere out there decided to compile a nice big, searchable list of all the thousands of human disease-causing mutations that so many labs have been finding for so many years? So that instead of getting a googled list of websites, or a PubMed list of articles, you could just see a nice neat list of all the known mutations linked to Hodgkin Lymphoma or all the mutations in PTEN or NOD2 that cause inherited disease?

Here it is! Human Genome Mutation Database (HGMD) curators comb the literature for reports of inherited, disease-causing mutations and disease-associated polymorphisms in human nuclear DNA. Each gene record contains a list of published mutations organized by type (missense, splicing, regulatory, etc.), a list of diseases it is associated with, Gene Ontology terms and links to OMIM and other information sources. There's also a link to the PubMed record for the publication originally reporting each mutation. You can search the database several different ways: by gene, by disease or phenotype, by chromosomal location and more.

A few things to remember about HGMD: it contains published mutations in nuclear genes that cause inherited disease. No mitochondrial mutations (though there are links to Mitomap), no somatic mutations. And you may want to read about their criteria for inclusion if you are curious about what exactly "cause" means in "disease-causing", or just how "associated" a "disease-associated polymorphism" needs to be.

As always, please let us know if you have any questions or comments about this new resource!

Hooray for Chemistry!

It's National Chemistry Week and the theme Chemistry -- It's Elemental reminds us that if any group is geekier than librarians, it's chemists! And we mean that in a good way, of course. The American Chemical Society's National Chemistry Week 2009 website provides access to an interactive Periodic Table, which tells me that the melting point of Cobalt is 1769 Kelvins, that Zinc has 7 isotopes, and that Mercury is called "Rtęć" in Polish! There's also Podcasts, "Chemdoku" games and a store with scratch and sniff stickers and "Proud to be a Chemist" hoodies.

More interested in chemistry research? The Levy Library provides access to the premier chemistry database, SciFinder Scholar. You can search articles, patents, and more information sources using words, chemical structures, and chemical reactions. Or try searching for chemistry articles in Web of Science, which includes much greater coverage of the chemistry literature than PubMed.

The Classes are Back!

After a renovation-induced hiatus, we are happy to announce that we are teaching drop-in classes again in the Levy Library - and in a new, renovated space, no less! The schedule and registration form are up now at http://fusion.mssm.edu/levy/classes/.

Notice especially that there are two new classes: for the first time we will be teaching a Photoshop class that will help you improve your images for publications and presentations (without distorting or falsifying your data), and we also have several sessions to orient you to the new PubMed interface - it's in Beta-testing now and will soon be the only way to search PubMed.

EndNote X3: Advanced Features
11/19/2009 (Thursday) 4:00 - 5:00
12/17/2009 (Thursday) 4:00 - 5:00 
 
EndNote X3: An Introduction
10/29/2009 (Thursday) 4:00 - 5:00 
11/12/2009 (Thursday) 4:00 - 5:00
 12/10/2009 (Thursday) 4:00 - 5:00
 
Genome Browsers - UCSC, Ensembl and NCBI Map Viewer
12/02/2009 (Wednesday) 4:00 - 5:30
 
NCBI's Entrez and Blast: An Introduction
11/03/2009 (Tuesday) 4:00 - 5:30
12/14/2009 (Monday) 4:00 - 5:30 
 
Photoshop: Preparing Images for Publication
12/03/2009 (Thursday) 4:00 - 5:00
 
PowerPoint 2007: An Introduction
10/27/2009 (Tuesday) 4:00 - 5:30 
 
PowerPoint: Finding Images and Using Them in Presentations
12/08/2009 (Tuesday) 4:00 - 5:30
 
PubMed: Navigating the New Interface
11/10/2009 (Tuesday) 4:00 - 5:00
11/12/2009 (Thursday) 12:00 - 1:00
12/09/2009 (Wednesday) 4:00 - 5:00 
 
RefWorks: An Introduction
11/17/2009 (Tuesday) 4:00 - 5:00
12/16/2009 (Wednesday) 4:00 - 5:00

Register at http://fusion.mssm.edu/levy/classes/!

NEW - JAMAevidence and AccessAnesthesiology

We're happy to announce a couple of new resources that we think people will find very useful!

JAMAevidence is from, of course, JAMA, and provides evidence, guides, calculators and more to help find the best evidence available and translate that into clinical decisions. It's based on the popular textbooks Users' Guides to the Medical Literature: A Manual for Evidence-Based Clinical Practice and The Rational Clinical Examination: Evidence-Based Clinical Diagnosis, and also includes a lot of extra features.

AccessAnesthesiology is a companion to Library favorites AccessMedicine, AccessEmergencyMedicine and AccessSurgery. Quickly search important anesthesia guidelines and textbooks (including Longnecker's Anesthesiology, Morgan's Clinical Anesthesiology and more), view videos and diagrams of procedures (retrograde intubation, anyone? Bronchoscopy?), use the calculator for essential measurements and create a self-assessment quiz to study for the boards.

We hope these are useful for you! Please let us know what you think, and if there is anything else you need!

Biology info - from genomes to jobs

Much as we like seeing everyone's smiling faces in the library, we know that it's usually easier and quicker to find your information online - which is of course why we provide so many online journals, databases, books, etc., etc. But, sorting through them to find a good protocol to inoculate ferrets with influenza or the most recent impact factor of the Journal of Arachnology may not be as easy as googling Sarah Palin, so we make an effort to provide some suggestions and search tips for you.

The Library's How Do I? page has links to information ranging from how to renew a book to how to stay in compliance with the NIH Open Access policy to how to do IRB-required literature searches for animal testing alternatives. Some of the newest guides are the Biology Resources guide, which includes links to find protocols, articles, gene sequences, protein interactions, and lots more; and the Biology Career Resources guide, which includes links to sites with job listings and career advice as well as a list of the Career books that we have in the library (both print and online). Take a look, save some bookmarks, and of course let us know if you have any questions, comments or ideas for more ways we can help with your research!

Clinical Skills Week Resources

Last week was clinical skills week, when we got to meet all of the medical students entering their third year and learning some of the skills they'll need for their clerkships. One of those skills is being able to find the information necessary for patient care, so reference librarians Polly and Laura shared some of their favorite resources. Here they are, with a word about each:

PubMed: What library workshop would be complete with mention of PubMed? (OK, so there are a few). Specifically, remember MeSH searching, Boolean operators and the Limits tab, and try the Clinical Queries tool (found in the blue bar on the left side of the PubMed homepage) when you are looking for research studies for specific question types - e.g., therapy, diagnosis, prognosis, etc.

AccessMedicine, MDConsult, and the E-books database are good sources for textbook-style background information and sometimes images, videos, guidelines and more.

UpToDate (on campus only), eMedicine and PIER are full of clinical topic reviews that combine the latest evidence with expert recommendations.

ACP Journal Club and the Cochrane Library are evidence-based medicine resources: ACP Journal Club provides structured reviews and commentary on selected high-quality articles from 100+ journals, while the Cochrane Library publishes systematic reviews and meta-analyses of highly relevant topics. Search them separately using the above links, or together using EBM Reviews.

And, as always, you can Ask a Librarian. Happy third year!

Impact Factors and more

The Impact Factor, a metric that the Institute for Scientific Information (now Thomson-Reuters) calculates for select journals based on numbers of recent citations to articles, is as important in modern academia as it is controversial. The Impact Factors of journals a researcher publishes in may be used, with varying degrees of weight, in decisions about promotions, tenure, green card applications and more. Critics argue that the metric can oversimplify the complexity of scholarly research and publishing and present a skewed view of what topics and journals are influential. ISI has recently provided some additions to Journal Citation Reports, the database used to find Impact Factors, to provide more information and context for the metric. New features allow the user to find a 5-year journal Impact Factor as well as the standard 2-year Impact Factor. The effects of self-citations can be seen by removing them from the calculation, and a box plot can be displayed indicating how a particular journal's Impact Factor stacks up against others in the same field. Also provided are Eigenfactor scores, a more complicated metric produced by researchers at the University of Washington. Go to Journal Citation Reports to see the new features, and take a look at some of the sources below if you're interested in learning more about the Impact Factor, the controversy, and other measures of scholarly influence.

________

Pendlebury, DA. The use and misuse of journal metrics and other citation indicators. Arch. Immunol. Ther. Exp. 2009;75:1-11. (PMID 19219526)

Garfield, E. The history and meaning of the journal impact factor. JAMA. 2006;295:90-93.

Eigenfactor.org

And more...

  

NetAnatomy Now Available

The Library has added the popular online anatomy resource, NetAnatomy to our database collection. This interactive human anatomy resource uses images, labels, descriptions and quizzes to teach radiographic, cross-sectional and gross anatomy.  It's designed to teach human anatomy to medical students, nurses and others in the health sciences. 

Access NetAnatomy by clicking Databases on the library's home page. NetAnatomy is listed under the category Clinical Sciences.

Darwin and Lincoln

It was a busy week last week and I didn't have time to write much, but last Thursday was a notable day: the 200th birthday of both Charles Darwin and Abraham Lincoln. There was a lot written about both Darwin and Lincoln in newspapers, journals, blogs, etc. that day, so I just want to point out a few relevant resources from the Levy Library. Of course, we provide access to On the Origin of Species (published 150 years ago this year!) - search ebrary to find that title. We also have subscriptions to journals like Science and Nature, which have been including a lot of Darwin-themed material already this year. And PubMed can direct you to articles about Lincoln in medical journals. One of my favorite resources though, is the Historical New York Times from ProQuest. You can use nytimes.com or LexisNexis to find recent Times articles, but ProQuest lets me sit at the Reference Desk today and read an article from 1860 about "Mr. Darwin's remarkable work" which has a "delightful tone" and "fine atmosphere", "whatever may be one's intellectual attitude towards his biologic doctrine" and an article from April 15, 1865 entitled "President Lincoln Shot by Assassin". Articles from 1851-2004 are scanned into PDF and fully searchable - a great resource for research (or semi-productive time wasting!).

New: Wiley Encyclopedia of Clinical Trials

The Levy Library now provides online access to the Wiley Encyclopedia of Clinical Trials, a frequently requested resource that contains a wide range of information about designing, implementing and analyzing clinical trials. Take a look at it for topics including statistics, ethics, regulatory issues, data management methodologies and more.

You may have used the print version before - if so, please note that the online version looks more like a database and less like a book; i.e., there is no traditional Table of Contents or page numbers. Instead, you can use the links on the upper right of the page to Browse by topic or title, or to search for something specific.