Network Verification Visual Glossary

BEL Language

BEL Language - openbel.org Wiki Language Overview

Powerpoint Tutorial - BEL Language Tutorial

Network definitions

  1. Node (e.g. p(HGNC:EGFR), bp(GO:"Oxidative Process"), a(CHEBI:Water)
  2. Network Edge - comprised of 1, 2 and 3 (node -> edge -> node)

Network Edge Examples:

  • p(HGNC:IL6) -> r(HGNC:ENO1)
  • p(HGNC:IL6) -> r(HGNC:XBP1)

Evidence - Supporting Statements

Network Edge: (1) -> (2)

3: Network Edge statement – each edge exists because there is at least one Evidence Statement that supports it, consisting of a node connected to another node by a relationship

4: Evidence statement - Each edge statement is supported by one or more Evidence (BEL) statements that provide the evidence for the edge, including the citation (usually PubMed ID) and experimental context

Evidence Statement

Evidence statement: protein abundance of CCND1 directly increases the kinase activity of the protein CDK4. Also shown is the Evidence statement context: Organism, Tissue, Cell and evidence for the Evidence (BEL) statement.

Causal Edge vs Non-causal Edge

Causal statements connect subject and object terms with a causal increase (symbol: -> ) or decrease (sympbol: -| ) relationship. Subject terms can be an abundance or process (including activities and transformations) and object terms can be either an abundance, a process, or a second BEL Statement.

A non-causal statement is any statement that does not have an increase or decrease relationship (e.g. positiveCorrelation or association).

Groupthink Bias

Allowing members to unduly influence others in their actions and comments

Reputation Actions

Actions on the NVC Site that lead to Reputation points. For example, adding Network Edges, Evidence and Evidence Annotations will provide reputation points to user. Up or down voting items that are created (Network Edges and Evidence) will also lead to reputation points.