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Query PubMed and download results to text files
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Query PubMed and download results to text files 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:

easy_install pip

Install all the mandatory dependencies by typing:

pip install -r requirements.txt


Before running the script make sure you edit the config file. The term and 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

Delete all data folders, this preserves zipped archives but removes the individual text files:

make clean

Copyright (c) 2013— Asif Rahman
License: MIT (see LICENSE for details)

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