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. 2018 Feb 15;34(4):703-704.
doi: 10.1093/bioinformatics/btx660.

PyBEL: A Computational Framework for Biological Expression Language

Free PMC article

PyBEL: A Computational Framework for Biological Expression Language

Charles Tapley Hoyt et al. Bioinformatics. .
Free PMC article


Summary: Biological Expression Language (BEL) assembles knowledge networks from biological relations across multiple modes and scales. Here, we present PyBEL; a software package for parsing, validating, converting, storing, querying, and visualizing networks encoded in BEL.

Availability and implementation: PyBEL is implemented in platform-independent, universal Python code. Its source is distributed under the Apache 2.0 License at


Supplementary information: Supplementary data are available at Bioinformatics online.


Fig. 1
Fig. 1
Plotted is the distribution of the final heat on biological processes from the NeuroMMSig AD Knowledge Assembly (Domingo-Fernández et al., 2017) following heat diffusion analysis with a differential gene expression experiment from the brains of AD patients (E-GEOD-5281, Liang et al., 2007). The significant down-regulation of biological processes related to inflammatory response (heat = 69) and up-regulation of cellular death (heat = −13) and beta-amyloid formation (heat = −9) match common clinical observations and serve as a validation for this approach

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