A recently published article in the journal, Database: the Journal of Biological Databases and Curation, investigates the needs and behavior of PubMed users  through the analysis of log data.  The authors analyzed 23 million user sessions with more than 58 million user queries. 

It’s difficult to find large analyses such as these specific to health informatio seeking behavior, so it’s worth having a look.  The fulltext of the article is available here:

http://database.oxfordjournals.org/cgi/content/full/2009/0/bap018

Good times.

Yahoo!  The PMCID Converter will now list NIHMSIDs along with PMCIDs, so we’re all in luck.  Here’s the link:

http://www.ncbi.nlm.nih.gov/sites/pmctopmid

In the past, you couldn’t get the NIHMSID unless you were the one to submit the manuscript, so this should make everyone’s life a little bit easier.

Here are some brief tips:

• Enter PMIDs into the box – on separate lines OR with spaces OR with commas in between
• Only 2000 PMIDs can be entered in one box
• Check the “Write result to file” box to output the results into a CSV file (I’d highly recommend this)

Thanks, NCBI!

Hey All!  It’s been awhile (again) since I’ve posted.  Sorry about that.  Who knew how complicated it would be to manage work, life, AND Introduction to Biostatistics?  Yes, I have decided to try to increase my statistical knowledge….  At any rate, we are lucky enough that Dr. Peter Cooper, research scientist at the National Center for Biotechnology Information, is going to do another webinar for us!  Here are the details…

What: NCBI Webinar on Molecular Biology Resources

When: Friday, December 11

Time: 3:00pm – 5:00pm

Where: Taubman Library Classroom (2802 Med Sci II)

What’s Covered: New PubMed, New NCBI website, Discovery Initiative, Overview of databases (OMIM, SNP, BLAST), and more…

A full description and registration information is available here.

This should be good folks and space is limited so register early.  The webinar is being held in the classroom so that you can do hands-on work on the computer.  We look forward to seeing you there!

So, there is ton of information out there on the newly designed PubMed.  It looks different but all of the same information is in there – somewhere.  These are the things I love:

• No need to change views to see MeSH for each citation; simply click on the + sign next to Publication Types, MeSH, etc. at the bottom of the abstract to expand that section
• Database ads – click directly to Homologene, GEO, etc right from the citation view.  Awesome.
• Customizeability – is that a word?  It’s great that you can customize your search results without logging in.  I love having the login option (My NCBI is great folks!), but let’s face it – most of you don’t.

Just my two cents.  There’s a lot of info running around out there on the redesign.  Here’s a link to the NLM Technical Bulletin article on it.

Ah, I understand that people think that books are blase but…    Here’s a new one at the Health Sciences Libraries:

Statistics and informatics in molecular cancer research.  Edited by Carsten Wiuf, Claus L. Andersen

The call number is: RC267 .S83 2009

Our own Dr. Rhodes is the author of Chapter 7: Two methods for comparing genomic data across independent studies in cancer research: Meta-analysis and oncomine concepts map.

Have fun!

Hey, it’s been awhile.  I’m sorry.  The rush of the school year always seems to catch me a little off guard.  The Health Sciences Libraries is co-sponsoring some workshops you may be interested in.

• Bioinformatics Basics: Databases and Tools from the National Center for Biotechnology Information (NCBI)
• BLAST Overview
• Michigan Molecular Interactions (MiMI)
• Cytoscape

In addition, the National Center for Integrative Biomedical Informatics is also holding an overview of its resources.

• Overview of NCIBI Tools and Resources

(I know; it’s bad form to have a single bullet, but hey…)  Registration is available from the Health Sciences Libraries workshops registration page.  Have fun and thanks for being patient about my blogs!

NCBI will be hosting a webinar at the University of Michigan to give an overview on their latest tools and updates to existing ones.  The webinar will take place at 2pm on Tuesday, September 29th.  Those people on campus who are interested in attending should register using the Teaching and Technology Collaborative website (https://www-a1.lsa.umich.edu/es_conf/app/DisplaySession.asp?sessionid=3367).  Login is required.  Contact the Health Sciences Libraries if you have any questions.

NIH is accepting requests for human embryonic stem cell (hESC) lines to be approved for use in NIH-funded research. Information may be submitted at http://stemcells.nih.gov/.

Read the full NIH News release at:
http://www.nih.gov/news/health/sep2009/od-21.htm

The National Center for Biotechnology Information has announced that they have three mailing lists for announcing changes to specific resources:

• Molecular Modeling Database (MMDB)
  http://www.ncbi.nlm.nih.gov/mailman/listinfo/structure-announce
• Conserved Domain Database (CDD)

  http://www.ncbi.nlm.nih.gov/mailman/listinfo/cdd-announce

• BioSystems
  http://www.ncbi.nlm.nih.gov/mailman/listinfo/biosystems-announce

NIH will fund 22 grants on genome-wide studies on epigenomics for a total of $69 million over the next five years. Since many of you are studying epigenomics as part of your bioinformatics work, it may be worth checking out the projects that are getting funded.  The full NIH news release is available here.  Congratulations to the awardees!