30 August 2008

My Old Thesis Presentation

I found the my thesis presentation (in french, 2000) in the old iBook I left in my cellar.

It is really outdated now :-) ....

I wonder how I would write this presentation now... this makes me think about this presentation pointed out by Berci Mesko on twitter: I would make this presentation obligatory for all the speakers of the world.
Death by PowerPoint
View SlideShare presentation or Upload your own. (tags: powerpoint ppt)


Mesh Fequencies & Pubmed Articles

In a recent post on his blog, David Rothman was asked for a 3rd Party PubMed/MEDLINE Tool: What I’d like to do is to be able to enter the PMIDs of several citations and have the tool search MEDLINE via PubMed for the assigned MeSH terms, and return a single list of the terms used by any of the entered citations with a measurement of frequency. For example, if I input PMIDs 16234728, 15674923, and 17443536, the tool would return results telling me that 100% or 3 of 3 use the term “Catheters, Indwelling”, 2 of 3 use “Time Factors,” 1 of the 3 uses “Urination Disorders,” and so on. Although this example uses 3 PMIDs, I’d like to be able to input at least 10, just based on personal experience.

It took less than half an hour to write this tool using java. The source code is available here and an executable jar file is available here.

The input is a standard pubmed query :

java -jar pubmedfrequencies.jar -term "Lindenbaum P[Author]" -n 20 > ~/page.html
or a list of pmid
java -jar pubmedfrequencies.jar -pmid 8985320,16027742,15047801,18053270,9682060 > ~/page.html

The output is a simple html table:

Autistic DisorderXX
RNA-Binding ProteinsXX
Two-Hybrid System TechniquesX
Zinc FingersX

well... that was not Big Science....

Note: Rajarshi Guha also suggested another solution: http://www.chembiogrid.org/cheminfo/rest/mesh/16234728,15674923,17443536


Addendum:After the first comments, I've added a gui support and a count of the mesh terms in the result.