aldisirana / pybel

A pure Python package for parsing, validating, compiling, and converting networks encoded in BEL

PyBEL

PyBEL is a pure Python package for parsing and handling biological networks encoded in the Biological Expression Language (BEL). It also facilitates data interchange between common formats and databases such as NetworkX, JSON, CSV, SIF, Cytoscape, CX, NDEx, SQL, and Neo4J.

Its companion package, PyBEL Tools, contains a suite of functions and pipelines for analyzing the resulting biological networks.

We realize there we have a name conflict with the python wrapper for the cheminformatics package, OpenBabel. If you're looking for their python wrapper, see here.

Citation

If you find PyBEL useful for your work, please consider citing:

[1]	Hoyt, C. T., et al. (2017). PyBEL: a Computational Framework for Biological Expression Language. Bioinformatics, 34(December), 1–2.

Getting Started

This example illustrates how the a BEL document from the Human Brain Pharmacome project can be loaded from GitHub.

>>> import pybel
>>> url = 'https://raw.githubusercontent.com/pharmacome/knowledge/master/hbp_knowledge/proteostasis/kim2013.bel'
>>> graph = pybel.from_url(url)

More examples can be found in the documentation and in the PyBEL Notebooks repository.

PyBEL also installs a command line interface with the command pybel for simple utilities such as data conversion. In this example, a BEL document is compiled then exported to GraphML for viewing in Cytoscape.

$ pybel compile ~/Desktop/example.bel
$ pybel serialize ~/Desktop/example.bel --graphml ~/Desktop/example.graphml

In Cytoscape, open with Import > Network > From File.

Installation

PyBEL can be installed easily from PyPI with the following code in your favorite terminal:

$ pip install pybel

or from the latest code on GitHub with:

$ pip install git+https://github.com/pybel/pybel.git

See the installation documentation for more advanced instructions. Also, check the change log at CHANGELOG.rst.

Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.rst for more information on getting involved. Please add your name to AUTHORS.rst!

Acknowledgements

• This package was originally developed as part of the master's work of Charles Tapley Hoyt at Fraunhofer SCAI.
• This software is proudly built with Paul McGuire's PyParsing package.
• Scott Colby designed our logo and provided sage advice
• Christian Ebeling for supervision and consultation

Links

• Specified by BEL 1.0 and BEL 2.0
• Documented on Read the Docs
• Versioned on GitHub
• Tested on Travis CI
• Distributed by PyPI
• Chat on Gitter