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Introduction

Machines that build machines = Biology.  Networks are how biology communicates and computes.  BEL (Biological Expression Language) captures and communicates biological networks for both Biologists and Computational Scientists in an easy to use and powerful format.  

OpenBEL is an open source and open community project providing BEL (Biological Expression Language) and a set of tools to process/store biological knowledge.  The community was formed in earnest in May of 2012.

OpenBEL is collaborative project under the sponsorship of the Linux foundation.

See What is OpenBEL?.

Projects

Web

Web component for BEL input

Javascript parser for BEL

RDF

Semantic validation of BEL over RDF model

Supporting BEL annotation constraints in RDF model

Web visualizations into BEL RDF data

Data

Streamline and improve BEL data pipeline

 Convert BEL to BioPAX  

 Convert BEL to SBML

Past projects

Web visualization of BEL graphs (GSoC 2014 project)

GSoC 2014 project by Jonathan Boilesen.

openbel-webtools on GitHub

Description: Visualize one or more BEL files as a graph in the browser.  It would be awesome to collapse BEL terms to graph nodes based on namespace equivalency.

Results: A web application that displays a BEL graph provided one or more BEL files.

Prerequisites: Web tools, Javascript

Definitions

BEL - Biological Expression Language.  BEL is a language for representing scientific findings in the life sciences in a computable form. BEL is designed to represent scientific findings by capturing causal and correlative relationships in context, where context can include information about the biological and experimental system in which the relationships were observed, the supporting publications cited and the process of curation.

BEL terms - A BEL term represents either a biological abundance or biological process existing in the context of an experiment.  A biological abundance is the measure of some amount of an entity (e.g. increase in abundance of the AKT1 RNA).  A biological process is a class of complex phenomena taking place at the level of the cell or the organism, such as the process of cell cycle or the process of a disease such as cardiomyopathy.  BEL terms are encoded with a function type over one or more namespace parameters.  For example the RNA of AKT1 is encoded as rnaAbundance(HGNC:AKT1) and the cell cyle process is encoded as biologicalProcess(GO:"cell cycle").

BEL statements - BEL Statements are expressions that represent knowledge of the existence of biological entities and relationships between them that are known to be observed within a particular context, based on some source of prior knowledge such as a scientific publication or newly generated experimental data.

Annotations - Name value pairs that describe the biological context of the observed BEL statement. For instance a BEL statement observed in the Cell Nucleus of a Mouse could be annotated with Species = Mouse and CellStructure = "Cell Nucleus".

Namespace equivalences - Several identifiers and names are used to represent the same biological entity (e.g. the id 207 is the same as the symbol AKT1).  BEL supports namespace equivalencing in order to resolve these differences.

 

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