Biological Network Representation with BEL

Biological Network Representation with BEL

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BEL was adopted as the structured language to represent the network models in the sbv IMPROVER Network Verification Challenge (NVC). It enables the visualization of causal and correlative relationships between biological nodes and edges in computable and human-readable statements (see www.openbel.org). Please review this section to understand BEL Statement Syntax and the BEL Statement Editor that has been integrated into the NVC website.

 

BEL Statement Syntax

  • Semantic triple: BEL statements contain three components, a subject, predicate and object, representing discrete scientific findings and their relevant contextual information as qualitative causal relationships.
      • Subjects and objects: These are visualized as nodes in the biological networks.
      • Predicate: These are statements that connect two nodes (i.e. network edges), maintain the computability of the network, and are supported by evidence from the scientific literature.
  • Ontology: All semantic triples are in a defined ontology (e.g. HGNC, see www.genenames.org).

 

Overview of BEL Statement Syntax

 

BEL Statement Editor

BEL is relatively easy to learn and simple to use on its own.  However, the BEL Statement Editor that has been integrated into the NVC website is a tool that further facilitates the use of the language and syntax.

  • Terminology autocomplete: Provides support in entering terms based a known library of protein names, chemical compound names, Gene Ontology terms, and other biological entities.
  • Terminology recommendations: Displays statement functions and types of entities that are allowed at the cursor position when a BEL Statement is being created.

 

Additional Information

Saved by the BEL: ringing in a common language for the life sciences. Ted Slater and Diana H. Song. 2012. Drug Discovery World Fall 2012 75:80 (hosted with kind permission of DDW)

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