Parsing, validation, and analysis of BEL graphs
Project description
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.
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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 installedCommand 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.graphmlIn 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 $NEOMultiple 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.txtInstallation
PyBEL can be installed easily from PyPI with the following code in your favorite terminal:
pip install pybelSee 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
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