Changes from BEL 1.0


  • Now represents sequence variants at DNA, RNA, and protein levels.

  • Now represents multiple substitutions within the same gene/RNA/protein

  • New BEL abundance modifier function variant(“”) / var(“”) is used for most variant types, replacing substitution() / sub() and truncation() / trunc(). Human Genome Variation Society (HGVS) nomenclature adopted to describe variants (Dunnen and Antonarakis, 2000) within the var(“”) modifier function, expanding supported types of variation to include insertions, deletions, duplications as well as non-specific variants.

  • Usage of fus() changed. Instead of a modifier function for a gene/RNA/protein abundance, fus() is used to compose new entities that can be used in place of a namespace value for abundance functions.

Protein Cleavage Fragments

  • New abundance modifier function fragment() / frag() to be used within protein abundances to specify protein fragments based on amino acid sequence range.

Post-Translational Protein Modifications

  • The proteinModification() / pmod() abundance modifier function can now use external vocabularies (e.g., PSI-MOD) for modification types, enabling users to add types without requiring a language change.

  • Now multiple pmod() expressions can be used within a protein abundance.

Translocations and Cellular Location

  • New abundance modifier function to specify location - location() / loc().

  • Change in translocation() / tloc() function format, to explicitly add BEL location functions to location arguments.

Activity Functions

  • The ten distinct BEL activity functions, e.g., kinaseActivity() / kin(), catalyticActivity() / cat(), transcriptionalActivity() / tscript(), are consolidated to a single activity function activity() / act().

  • New modifier function molecularActivity() / ma() can be used to specify specific activity types, using external vocabularies, e.g., GO Molecular Function, or a default BEL vocabulary.

Regulates Relationship

  • New causal relationship regulates to represent cases where A is reported to affect B, but it cannot be determined if A increases or decreases B.

Request an Edit