- 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)
- 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
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
YFG N-terminal cleavage fragment of unknown length
YFG C-terminal cleavage fragment of unknown length
YFG cleavage fragment with unknown start/stop
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"))
- How should the compiler/parser best handle the <descriptor> argument?
- ignore it such that fragments with matching 1st arguments would equivalence to the same node in the network?
- or treat each unique argument combination as unique?