PubMed Miner

For a few reasons you may want to get an overview of publications by you or your (broader) team. You could query PubMed manually, or be lazy and write a script to query the PubMed database semi-automatically.

Enter PubMed Miner: your go-to tool to retrieve PubMed publications for a list of authors (and their aliases) and departments from a given organization. It then analyzes the publication data and saves the results to a Word document (docx) and an Excel file (xlsx), and also produces a few graphs on the fly (also added to the Word document).

Yeah, it could be misused for practices not acceptable anymore. However, I found it useful to quickly create an overview of who published what and where, and how many publications there were. Quality over quantity anytime, yet: ‘the writer lives on’.

Working in the field of atherosclerosis, I ran an exemplar query for Russell Ross when he was working at the University of Washington, Seatle:

python pubmedminer.py --email some-email@email.domain --verbose --names "Ross R" --departments "Department of Pathology" --organization "University of Washington" --output-file russel_ross

You can find the results in the GitHub repository: https://github.com/swvanderlaan/PubMed_Miner.

Have fun!