30 August 2008

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:











Mesh89853201602774215047801180532709682060
HumansXXX
AnimalsXX
Autistic DisorderXX
(...)
RNA-Binding ProteinsXX
RotavirusXX
SoftwareX
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

Pierre


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

5 comments:

David said...

Pierre, I'm not able to make the .jar executable work. Any thoughts about what I might be doing wrong?

Pierre Lindenbaum said...

What's your version of java ? You need java 1.6

David said...

Yep. That's what I've got (as a part of Java SE 6). I open the .jar, window opens for a split-second, then closes.

Rebs said...

The 1.6 through me a curve ball as well. My version was 1.5. Got 1.6 running and all is well.

The links back to the records is a nice touch ;)

This indicates which terms apply to a given pmid, but doesn't tell you how many times it was used, which I think was part of what was asked for, wasn't it? Or, perhaps I'm missing something...

Rebs said...

I know, I'm a lazy bum...I want it to count them up for me...I know I could just count them myself :)