SuLab / bioshovel

Biological text mining tool.

BioShovel

For text mining of biological research articles using DeepDive

Tong Shu Li and Sandip Chatterjee of the Su Lab

Getting Started

Requirements

• Python 3.4+
• Java 1.8 for various NER/NLP annotators
• PBS/Torque cluster for cluster workflows
• Python package dependencies in requirements.txt
  • lxml may require external libxml2 installation (using a tool like apt-get)

Installing DeepDive (v0.8)

• See DeepDive main page for the latest installation instructions
• Run bash <(curl -fsSL git.io/getdeepdive)
• Install DeepDive by selecting option from menu
• Install PostgreSQL by selecting option from menu

Ensuring pip3 and libxml2 are installed

• On Ubuntu (14.04), run sudo apt-get install -y python3-pip
• Install lxml dependencies using: sudo apt-get install -y libxml2 libxml2-dev libxslt1-dev lib32z1-dev

Installing Python dependencies

• Clone the repo and cd bioshovel
• Create a virtualenv: $ python3 -m venv venv
• Activate virtualenv: $ source venv/bin/activate
• Install dependencies: (venv) $ pip install -r requirements.txt

Run BioShovel modules

• Modules should be run from the src directory
• Use (venv) $ python3 -m [package_name].[module_name] [args]
• See preprocess and downloaders packages for more information

Running Unit Tests

• Tests should be run from the src directory
• Run test discovery using python3 -m unittest