Skip to content
Query PubMed and download results to text files
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
LICENSE
README.md
config
makefile
pmquery.py
requirements.txt

README.md

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.

Requirements

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

Usage

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 pmquery.py

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)

You can’t perform that action at this time.