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:

Mesh	8985320	16027742	15047801	18053270	9682060
Humans		X	X	X
Animals	X		X
Autistic Disorder		X		X
(...)
RNA-Binding Proteins	X		X
Rotavirus	X		X
Software					X
Two-Hybrid System Techniques			X
Zinc Fingers			X

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

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

Pierre

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