Install

Environment

Assuming a linux environment, it shouldn't matter too much which, but we've only developed/tested on recent versions of Ubuntu.

Additional python modules

Over and above your base python install you will need to have the following

• pyzotero
• biopython
• pandas
• jsonpath_rw
• requests
• htmlentities
• unicodecsv
• nltk

All of which can be installed with pip, e.g.: sudo pip install pyzotero

The nltk package might need to be run separately to get the lookup file:

>> python2
>> import nltk
>> nltk.download('wordnet')

If you get compilation errors with pip then it might be because you need to install the python-dev package (e.g. sudo apt-get install python-dev).

Grab the source code

Clone of download from https://github.com/OllyButters/puma

API keys

Since we are using several APIs we need to register for a few of them and get some API keys.

• Scopus
• Biopython
• Google Maps (get key)

Configuration

Once you have the keys you need to place them in the configuration file and set the appropriate configuration settings. The guide for this can be found here.

Run it!

From the command line execute ./source/papers.py