Install

Environment

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

Grab the source code

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

Additional python modules

Over and above your base python3 install you will need to have the following

• pyzotero
• biopython
• pandas
• jsonpath_rw
• nltk
• sparqlwrapper

which you can install using the requirements.txt file in the source folder with a command like:

pip3 install -r requirements.txt

API keys

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

• Zotero
• Scopus

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.