Parsing, validation, compilation, and data exchange of Biological Expression Language (BEL)
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.
If you find PyBEL useful for your work, please consider citing:
|||Hoyt, C. T., et al. (2017). PyBEL: a Computational Framework for Biological Expression Language. Bioinformatics, 34(December), 1–2.|
This example illustrates how the Selventa Small Corpus can be loaded.
>>> import pybel >>> graph = pybel.from_url('http://resources.openbel.org/belframework/20150611/knowledge/small_corpus.bel') >>> graph.number_of_nodes() # Will be smaller than expected because we have the most strict settings enabled 1207
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.
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
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