Query PubMed and download results to text files
pmquery.py searches Pubmed and saves article metadata in JSON-formatted text files. The purpose is to later mine the data. After saving the text files the script creates a zipped archive so things stay compact.
If you don't have the pip utility first install it with:
Install all the mandatory dependencies by typing:
pip install -r requirements.txt
Before running the script make sure you edit the config file. The
ident parameters indicate the search term and a unique identifier (no spaces allowed), respectively.
To execute the script pmquery uses a Makefile, although executing the python script will produce the same results.
Query the database:
make query python pmquery.py
Delete all data folders, this preserves zipped archives but removes the individual text files:
Copyright (c) 2013— Asif Rahman
License: MIT (see LICENSE for details)