represent protein cleavage

[tythomson]

Currently, protein cleavage does not appear to be represented in BEL upon import from reactome.

The messy example where I noticed this problem is R-HSA-1655842.1 (http://www.reactome.org/PathwayBrowser/#/R-HSA-1655829&SEL=R-HSA-1655842&PATH=R-HSA-1430728,R-HSA-556833). The output group is the cleaved members of the input group. Upon BEL import, the output group consists of the same full proteins as the input group. In this case, via the web interface the Uniprot IDs for the cleaved proteins appear to be appended with -1 (or -2, etc), so even if we couldn't properly represent cleavage, using these modified uniprot ids would enable us to differentiate between the full protein and the cleaved form. The modified uniprot IDs wouldn't be valid IDs, but would at least solve the immediate problem that these cleavage reactions don't diminish the amount of the protein.

A simpler example that is not in the export that I've looked at is R-HSA-202947.1 (http://reactome.org/PathwayBrowser/#/R-HSA-75153&SEL=R-HSA-202947&PATH=R-HSA-5357801,R-HSA-109581). I assume that this similarly won't capture the cleavage, but like I said, I dont' have the output from this one so I'm not sure. In this case the cleaved uniprot IDs aren't appended with anything, so we can't count on that always being the case in reactome.