Releasing PyMed

The PubMed library for Python

Gijs Wobben
Jul 2, 2018 · 1 min read

Today I’m happy to announce the public release of the PyMed library. This library provides access to the PubMed database through a simple Python interface.

PubMed is the most important and influential database of medical publications, and a goldmine of research. However, querying the database through code was difficult and not very efficient. The new library provides a Pythonic (typical Python) interface to query the database, it batches queries and pre-formats and cleans the results. PyMed provides access to titles, authors, keywords, abstracts and other meta-data associated with an article. Full-text is not (yet) supported.

Installation is simple! Just run:

pip install pymed

The GitHub repository contains examples on how to use the library to retrieve articles from the database, and how to perform analyses on the retrieved data. Check for example this author co-occurrence overview of the field of occupational health in the last 10 years (graph produced with Gephi)!

Author co-occurrence in the field of occupational health (with some filters applied and PageRank for the size of the nodes).

I’d love to hear what you can do with this goldmine! Leave a comment with your ideas and projects!

Gijs Wobben

Written by

Data scientist at ArboNed

Welcome to a place where words matter. On Medium, smart voices and original ideas take center stage - with no ads in sight. Watch
Follow all the topics you care about, and we’ll deliver the best stories for you to your homepage and inbox. Explore
Get unlimited access to the best stories on Medium — and support writers while you’re at it. Just $5/month. Upgrade