Pubmedy

A lightweight Biopython-based interface to NCBI's Entrez API, created to speed up systematic literature reviews.

Installation:

pip install git+https://github.com/lescientifik/pubmedy.git

If you want to install it in dev mode:

pip install -e git+https://github.com/lescientifik/pubmedy.git#egg=pubmedy

Or simpler, in the directory of your choice:

git clone https://github.com/lescientifik/pubmedy.git
cd pubmedy
pip install -e .

Usage:

usage: pubmedy [-h] --email EMAIL -s SEARCH -o OUTFILE

A CLI to query the Pubmed API and save the results. At the end, you get back 2
files:a logfile to keep track of your query and a csv file

optional arguments:
  -h, --help            show this help message and exit
  --email EMAIL         Your email address.
  -s SEARCH, --search SEARCH
                        Your search query. You should use the online Pubmed
                        website to build it more easily and copy-paste here
  -o OUTFILE, --outfile OUTFILE
                        The outfile. Don't include the file extension, this
                        will be generated for you

Note that your email adress is only used iff you do anything that bothers the Entrez managers, so they can contact you!