Using R to graph a subject trend in PubMed

May 15, 2012

(This article was first published on R Chronicle, and kindly contributed to R-bloggers)

The traditional way to show that your topic is worth studying in front of an audience is to show the state of the field based on a literature review. This is especially true if your subject is obscure except to a handful of scientists in the world.
I was confronted with this problem more than once and the last time I decided to plot the state-of-the-field using a few scripts.
I wrote three scripts for that: pubmed_trend.r that take your PubMed query and send it to the NCBI using the Eutils tools (Perl script). Then I plot the results. The details of the scripts are below but here is how you create your trend.
In this example, we plot the trend for the number of publications per year for papers annotated with MeSH terms for "sex characteristics" and "pain" and compare this search to the number of publication/year for "sex characteristics" and "Analgesics". We will run this search between 1970 and 2011. And here is the plot.

What we see here is that the number of publications per year talking about sex difference and pain or analgesics is growing but the number of publication per year is still small and more research is needed.
…and you are good to go, your talk is launched

Here are the details of the scripts and functions. The pubmed_trend.r takes a PubMed query string as you would type it in the search box through the web interface (space have to be replaced by '+').
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