More PubMed data mining: looking at top 20 CBT journals


Continuing from what I wrote in my article An R Script to Automatically download PubMed Citation Counts By Year of Publication, I’ve now looked at article counts for journals. I did this by extending my script to download the complete article records in XML from inside R. Then I simply extracted journal names from each article and counted how many times different journal occurred. What’s cool about my new script is that it’s possible to extract any PubMed field; so more data will surely follow in subsequent articles.

Specifically, I looked at journals related to Cognitive Behavior Therapy. I did tree searches, one for 2010, one for 2011 and lastly one for the total year range. By doing this I could visualize which journals had the most publications in total and compare that to recent years.

The query

I didn’t care to use a really comprehensive query, as I was more interested in testing my script. Nonetheless, the base query looked like this:


The total number of hits for all years was 14342 hits, from which I extracted 1667 different journals. After extracting the top 20 journals with the most publications over time I made these two graphs.

Top 20 Cognitive Behavior Therapy journals by PubMed citation
count. By Kristoffer Magnusson

As you can see the Journal of Consulting and Clinical Psychology has had the most publications over time, but Behavior Research and Therapy has had more publications in recent years. This is not really that surprising, since the Journal of Consulting and Clinical Psychology has existed since 1937 whilst Behavior Research and Therapy started out in 1963.

Where’s the R code?

Update: Here’s the R script: How to download complete XML records from PubMed and extract data

Written by Kristoffer Magnusson, a researcher in clinical psychology. You should follow him on Twitter and come hang out on the open science discord Git Gud Science.


Published April 26, 2012 (View on GitHub)

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Keep the visualizations coming!

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