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List of needs/ideas for future development of the BEL language.

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Biological Process Functions

In BEL v1.0, there is no way to employ user-defined biological process functions.  For example, we need to be able to specify a target of the form biologicalProcess(object) where biologicalProcess is proliferation(), which is not one of the BEL v1.0 functions such as molecularActivity().  Right now, the target can only be the biological process itself, proliferation, without a way to specify the object of the biological process like proliferation(gene).

Other

  • means to distinguish/identify abundances which are drugs
  • activities on a cell, e.g. stimulation of osteoblasts

Addressed in BEL v2.0

Protein modifications - additional modification types  

In BEL v1.0, protein modifications are limited to phosphorylation, acetylation, farnesylation, glycosylation, hydroxylation, methylation, ribosylation, sumoylation, and ubiquitination (see Modifications).

  • e.g., palmitoylation, myristoylation, neddylation
  • perhaps use external namespace for modification types
  • increased specificity of modification types (e.g., N- vs. O-glycosylation, poly- vs. mono-ubiquitination, K63-poly-ubiquitination)
  • multiple modifications on same protein
  • modification of non-protein entities

Addressed in BEL v2.0 see Protein Modifications

Activity functions

BEL v1.0 is limited to 10 distinct activity functions; these activity functions are not easily extensible to accommodate activity functions needed by a specific user (see Activities).

  • additional activity types
  • support merging activity types within a network for some uses (e.g., merge catalyticActivity(p(HGNC:CASP3)) and peptidaseActivity(p(HGNC:CASP3)) to improve network consistency)

Addressed in BEL v2.0 - see Process Functions and Process Modifier Function

DNA/RNA/Protein variants/mutations

In BEL v1.0, mutations and variants can only be expressed at the protein level. The precise change (reference allele amino acid, position, and change) are required (see Modifications).

  • representing mutations/variants at level of DNA/RNA
    • SNPs, CNV, InDels
  • mutation with unspecified location (e.g. mutant EGFR)
  • multiple mutations in same sequence
  • zygosity

Largely addressed by BEL v2.0 changes - see Variants

Protein Cleavage products

In BEL v1.0, there is no means to represent a protein cleavage product based on the parent protein and position of cleavage. The modification truncation is intended to specify a variant protein which is truncated by substitution of a stop codon. The transformation degradation is intended to specify the complete proteolytic cleavage of a protein such that no functional cleavage products remain.

Addressed by BEL v2.0 - see Proteolytic fragments

 

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