Glycosylation mechanism term mapping

[vtoure]

Glycosylation is mapped to transferase activity, transferring glycosyl groups (GO:0016757).

This needs to be changed to protein glycosyltransferase activity - which have been requested by @thomaspd @thomaspd any update on the status of this new term? Doesn't look like it is there yet.

Thanks.

[dustine32]

@thomaspd @vtoure Sorry to throw this curveball out there at this point, but glycosylation doesn't appear to be a mechanism used in any of the pathway files:

$ python3 download_all_pathways.py -d downloaded_data_new
$ cut -f14 downloaded_data_new/SIGNOR-* | sort | uniq -c
 511
   4 acetylation
1006 binding
   1 catalytic activity
  11 chemical activation
   4 chemical inhibition
  52 cleavage
   2 deacetylation
 119 dephosphorylation
   4 deubiquitination
   5 gtpase-activating protein
  47 guanine nucleotide exchange factor
  50 mechanism
   4 methylation
2124 phosphorylation
 125 relocalization
  42 small molecule catalysis
  30 transcriptional activation
 220 transcriptional regulation
  20 transcriptional repression
  89 ubiquitination

It is of course in the full release file (6 statements):

$ cut -f10 signor_data/all_data_09_04_20.tsv | sort | uniq -c | grep glycosylation
   6 glycosylation

So, for this first pass of only converting the pathway files, we shouldn't need a glycosylation GO term mapping but it would be nice to get it ready for future use.

[thomaspd]

OK, great, then we don't need to request this GO term yet. We can revisit later, when we consider how to import the SIGNOR statements that are not currently in a pathway.

[vtoure]

Thanks for the info Dustin, I removed it from the mapping in the manuscript.