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Goal

  • Provide a representation for protein fragments
    • Enable functional composition of fragments from a parent/root protein abundance and an amino acid range

BEL v1.0 representation

  • No specific means for protein fragment representation is available in BEL v1.0
  • Protein fragments can be represented as values (with or without a namespace, as applicable)
    • E.g., a(CHEBI:"angiotensin II")
    • E.g., p("Amyloid Precursor Protein Intracellular Domain")
  • Protein fragments could be connected to their parent via creating a specific BEL statement
    • Ideally represented as a reaction in which reactants include parent protein, and products include named fragment(s)

Proposed representation

  • Add a new modification function fragment(), frag()to be used as an argument within a protein abundance

 

p(ns:v, frag(<range>, <descriptor>))

 

  • <range> (required) amino acid sequence range
  • <descriptor> (optional) any additional distinguishing information like the fragment size or name

Examples

For these examples, HGNC:YFG is ‘your favorite gene’. For the first four examples, only the <range> argument is used. The last examples include use of the optional <descriptor>.

YFG (your favorite gene) cleavage fragment of amino acids 1-20
p(HGNC:YFG, frag(1_20))
YFG N-terminal cleavage fragment of unknown length
p(HGNC:YFG, frag(1_?))
 YFG C-terminal cleavage fragment of unknown length
p(HGNC:YFG, frag(?_*))
YFG cleavage fragment with unknown start/stop
p(HGNC:YFG, frag(?))
YFG 55kD cleavage fragment with unknown start/stop
p(HGNC:YFG, frag(?, 55kD))
YFG N-terminal cleavage fragment referred to in literature as “my fragment”
 p(HGNC:YFG, frag(1_?, "my fragment"))

Questions

  1. How should the compiler/parser best handle the <descriptor> argument?
    1. ignore it such that fragments with matching 1st arguments would equivalence to the same node in the network?
    2. or treat each unique argument combination as unique?

 

 

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