Bio2BEL

Bio2BEL is a project aimed at integrating biological databases and other structured knowledge sources.

Because they come from a wide variety of schemata, this package provides tools for converting them into the unified framework of Biological Expression Language.

This package provides guidelines, tutorials, and tools for making standardized bio2bel packages as well as a unifying framework for integrating them.

Installation

Easiest

Download the latest stable code from PyPI with:

$ python3 -m pip install bio2bel

Get the Latest

Download the most recent code from GitHub with:

$ python3 -m pip install git+https://github.com/bio2bel/bio2bel.git

For Developers

Clone the repository from GitHub and install in editable mode with:

$ git clone https://github.com/bio2bel/bio2bel.git
$ cd bio2bel
$ python3 -m pip install -e .

Testing

Bio2BEL is tested with Python3 on Linux using Travis CI.

Table of Contents

• Introduction
  • Citations
• Repositories
• Sources
  • Protein Interactions Database (PID)
  • TFRegulons
• How to Make a Bio2BEL Package
  • Naming the Package
  • Organizing Constants
  • Making a Manager
  • Mixins
  • Organizing the Manager
  • Making a Command Line Interface
  • Setting up __main__.py
  • Entry Points in setup.py
  • Testing
• Reproducibility
• Input and Output
  • PyKEEN
  • Automation
• Using the CLI
  • bio2bel

Reference

• Downloading
• Utilities
• Testing

Indices and tables

• Index

• Module Index

• Search Page