pybel 0.3.6

Parsing, validation, and analysis of BEL graphs

PyBEL is a Python software package that parses BEL scripts, validates their semantics, applies common graph algorithms, and facilitates data interchange between common formats and database systems like JSON, CSV, SQL, and Neo4J.

Stable
Development

Biological Expression Language (BEL) is a domain specific language that enables the expression of complex molecular relationships and their context in a machine-readable form. Its simple grammar and expressive power have led to its successful use in the IMI project, AETIONOMY, to describe complex disease networks with several thousands of relationships.

PyBEL provides a simple API so bioinformaticians and scientists with limited programming knowledge can easily use it to interface with BEL graphs, but is built on a rich framework that can be extended to develop new algorithms.

>>> import pybel, networkx
>>> g = pybel.from_url('http://resource.belframework.org/belframework/1.0/knowledge/small_corpus.bel')
>>> networkx.draw(g)  # NOTE: requires matplotlib as a dependency, which isn't automatically installed

Command Line Interface

PyBEL also installs a command line interface with the command pybel for simple utilities such as data conversion. Need help? All logs go to ~/.pybel or add -v for verbose output to the standard error stream

Export for Cytoscape

This example retrieves a BEL file from a path and exports to a GraphML file for use in Cytoscape.

$ pybel convert --path ~/Desktop/example.bel --graphml ~/Desktop/example.graphml

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

Export to Neo4j

This example retrieves a BEL file from a URL, and exports to Neo4j

$ URL="http://resource.belframework.org/belframework/1.0/knowledge/small_corpus.bel"
$ NEO="neo4j:neo4j@localhost:7474"
$
$ pybel convert --url $URL --neo $NEO

Multiple Export

This example gets a file from stdin and exports to multiple locations, with logging

$ URL="http://resource.belframework.org/belframework/1.0/knowledge/small_corpus.bel"
$ NEO="neo4j:neo4j@localhost:7474"
$
$ curl $URL | pybel convert --neo $NEO --json ~/Desktop/example.json --log-file ~/Desktop/log.txt

Installation

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

pip install pybel

See the 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.

Acknowledgements

• This software is proudly built with Paul McGuire’s PyParsing package.

• Scott Colby designed our logo and provided sage advice

• Core Team: Charles Tapley Hoyt, Andrej Konotopez, and Christian Ebeling

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