abbreviation of metabolite name for yeast map about yeast-gem

[edkerk]

I don't see any problem for displaying an abbreviated name when needed, especially for these species that are repeated (with different chain lengths) so many times. I assume they are still tagged with the metabolite ID from the yeast model?
Those specific ones seem to be abbreviated to PGP on LIPIDMAPS.

[feiranl]

Dear all, I compared the abbreviation name with the full name when I did the SLIMER project. Hongzhong may use the abbreviation name in the attached file with a tail to specify the species. Best regards, Feiran

[hongzhonglu]

@feiranl What do you mean about abbreviation name and full name ?

[feiranl]

For example, phosphatidylethanolamine (1-16:0, 2-16:1), the name for this metabolite in our model is its full name: phosphatidylethanolamine (1-16:0, 2-16:1), but I denoted the abbreviation for phosphatidylethanolamine is PE, so you can show that as PE with it tails: PE 16:0-16:1. Then PE 16:0-16:1 is its abbreviation name for phosphatidylethanolamine (1-16:0, 2-16:1),

[hongzhonglu]

@edkerk @feiranl Understand! So as Ed suggested, the short name of "phosphatidylethanolamine (1-16:0, 2-16:1)" may be like PE_s_xxx. As Feiran suggested, it can be like PE 16:0-16:1. In my view, the PE 16:0-16:1 may be clear for us to understand when we watch the map. How do you think of it?

[edkerk]

@feiranl It doesn't seem to work to send attachments when responding.

@hongzhonglu I agree with "PE 16:0-16:1" as abbreviation, and do not propose PE_s_xxx.

My point is that the name and id (in CellDesigner s1, s2, etc.) are two separate things. No problem to use "PE 16:0-16:1" as name, just make sure that the id in the final map is still refering to the correct metabolite in the model. I'm not sure you can directly change ids in CellDesigner, so might have to do this directly on the xml in the end. For this, it would be good to have a list of abbreviated metabolite names and their id in the yeast model (which is probably in Feiran's table that she tried to send).

[feiranl]

slimerlipidshortname.xlsx

[hongzhonglu]

@edkerk You are right that the id in cellDesigner could be changed if we corrected it in the xml file.
Great thanks for all your suggestions! @edkerk @feiranl