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BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

By Charles Tapley Hoyt, Daniel Domingo-Fernández, Martin Hofmann-Apitius

Posted 30 Mar 2018
bioRxiv DOI: 10.1101/288274 (published DOI: 10.1093/database/bay126)

The rapid accumulation of knowledge in the field of systems and networks biology during recent years requires complex, but user-friendly and accessible web applications that allow from visualization to complex algorithmic analysis. While several web applications exist with various focuses on creation, revision, curation, storage, integration, collaboration, exploration, visualization, and analysis, many of these services remain disjoint and have yet to be packaged into a cohesive environment. Here, we present BEL Commons; an integrative knowledge discovery environment for networks encoded in the Biological Expression Language (BEL). Users can upload files in BEL to be parsed, validated, compiled, and stored with fine-granular permissions. After, users can summarize, explore, and optionally shared their networks with the scientific community. We have implemented a query builder wizard to help users find the relevant portions of increasingly large and complex networks and a visualization interface that allows them to explore their resulting networks. Finally, we have included a dedicated analytical service for performing data-driven analysis of knowledge networks to support hypothesis generation. This web application can be freely accessed at https://bel-commons.scai.fraunhofer.de.

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