pybel.github.io

This site serves as a central hub for the PyBEL universe.

PyBEL

We built PyBEL for parsing, validating, compiling, and converting networks encoded in BEL. PyBEL comprises five main components: (i) network data container, (ii) parser and validator, (iii) network database manager, (iv) data converter and (v) network visualizer.

Reference

Hoyt, C. T., Konotopez, A., Ebeling, C. (2018). PyBEL: a computational framework for Biological Expression Language. Bioinformatics, 34(4), 703–704.

Resources

• Code
• Documentation

Curation

Quality Assurance

We developed a workflow using git, GitHub, PyBEL, and a novel PyBEL extension in order to identify and address syntactical issues in BEL documents in a Continuous Integration setting.

Resources

• Source Code

Enrichment

Reference

Hoyt, C. T., et al (2019). Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language. Database, bay068.

BEL Repository

Content

Bio2BEL

BEL Cloud

BEL Commons

BEL Commons is an environment for curating, validating, and exploring knowledge assemblies encoded in BEL to support elucidating disease-specific, mechanistic insight. BEL Commons comprises five components: (i) the network uploader and validator, (ii) user rights and project management, (iii) the query builder, (iv) the biological network explorer and (iv) the analytical service.

Reference

Hoyt, C. T., Domingo-Fernández, D., & Hofmann-Apitius, M. (2018). BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. Database, 2018(3), 1–11.

Resources

• Web Application: https://bel-commons.scai.fraunhofer.de
• Code