Lipid naming convention

[michaelwitting]

I'm working on the lipid metabolism (complex lipids) and have some issues with tracking all the different lipid IDs. Also BiGG is not very helpful here. Naming of the IDs makes (for me) not too much sense.

I'm suggesting the following nomenclature

Phosphatidylcholines: 1,2-diacylglycerophosphocholine --> 1ac2acg3pc (old pchol) 1-acylglycerophosphocholine --> 1acg3pc 2-acylglycerophosphocholine --> 2acg3pc

1-alkyl-2-acylglycerophosphocholine --> 1alk2acg3pc 1-alkylglycerophosphocholine --> 1alkg3pc

1-alkenyl-2-acylglycerophosphocholine --> 1alken2acg3pc 1-alkenylglycerophosphocholine --> 1alkeng3pc

All other lipid classes would be analog to this., e.g. 1ac2acg3pe or 1ac2acg3ps. These identifiers are not in BiGG (at the moment) and are therefore not compliant with BiGG, but would facilitate readability and helps in human curation.

Let me know your thoughts. If we do this, we should also add an column like "old_id" to the compound table to curate also the old IDs.

[michaelwitting]

@nel3 Maybe you have also some opinion on that?

[nel3]

@michaelwitting how many of these lipids are in BiGG (but with a different identifier)? I'm always a proponent of improved human readability of things in BiGG. I can also run this idea by the Palsson lab who is managing BiGG these days.

[michaelwitting]

@nel3 There are some lipids captured, e.g. ak2g_hs for 1-alkyl 2-acylglycerol, but no "systematic" way. Another example is pchol for phosphatidylcholines, which can be also missleading. According to lipidnomenclature can be any lipid that has a phosphocholine. lpchol denotes lysophosphatidylcholine, which is also not clear at which position the fatty acyl has been removed. May suggestion would be to use the new nomenclature I suggest in WormJam and describe it in a future upcoming paper and see if people will adopt.

[nel3]

@michaelwitting We can propose the ones that are not in BiGG. The ones that already have BiGG ids will be hard to change, given that so many models have those IDs

[michaelwitting]

Okay... I will compile a list in the next days and come back to you!

[michaelwitting]

@nel3 @zakandrewking

Please find below a few examples of systematic lipid IDs iI'm currently collecting for WormJam. They might be also of interest for BiGG. Ignore the column in the middle, I will add their the IDs from WormJam that will be replaced by the new ones.

Class	Metabolite	Old/ Wrong / Duplicated ID	Correct / New ID
MG	1-acyl-sn-glycerol		1acglyc
MG	2-acyl-sn-glycerol		2acglyc
MG-O	1-alkyl-sn-glycerol		1alkglyc
MG-P	1-(Z)-alk-1-enyl-sn-glycerol		1alkenglyc
DG	1,2-diacyl-sn-glycerol		1ac2acglyc
DG-O	1-alkyl-2-acyl-sn-glycerol		1alk2acglyc
DG-P	1-(Z)-alk-1-enyl-2-acyl-glycerol		1alken2acglyc
TG	Triacyl-glycerol		tag / 1ac2ac3acglyc
TG-O	1-alkyl-2,3-diacylglycerol		1alk2ac3acglyc
TG-P	1-(Z)-alk-1-enyl-2.3-diacylglycerol		1alken2ac3glyc
LPA	1-acyl-sn-glycero-3-phosphate	Alpa M_alpa_tag_c M_12dag3p_c M_1ag3p_SC_n	1acglyc3p
LPA	2-acyl-sn-glycero-3-phosphate		2acglyc3p
PA	1,2-diacyl-sn-glycero-3-phosphate	pa_pl	1ac2acglyc3p
PA-O	1-alkyl-2-acyl-sn-glycero-3-phosphate		1alk2acglyc3p
PA-P	1-(Z)-alk-1-enyl-2-acyl-sn-glycero-3-phosphate		1alken2acglyc3p
LPA-O	1-alkyl-sn-glycero-3-phosphate		1alkglyc3p
LPA-P	1-(Z)-alk-1-enyl-sn-glycero-3-phosphate		1alkenglyc3p
PC	1,2-diacyl-sn-glycero-3-phosphocholine(1+)	pchol	1ac2acg3pc
LPC	1-acyl-sn-glycero-3-phosphocholine(1+)	ag3pc	1acg3pc
LPC	2-acyl-sn-glycero-3-phosphocholine(1+)	2agpc	2acg3pc
PC-O	1-alkyl-2-acyl-sn-glycero-3-phosphocholine		1alk2acg3pc
LPC-O	1-alkyl-sn-glycero-3-phosphocholine		1alkg3pc
PC-P	1-(Z)-alk-1-enyl-2-acyl-sn-glycero-3-phosphocholine		1alken2acg3pc
LPC-P	1-(Z)-alk-1-enyl-sn-glycero-3-phosphocholine		1alkeng3pc
PE-O	1-alkyl-2-acyl-sn-glycero-3-phosphoethanolamine		1alk2acg3pe
LPE-O	1-alkyl-sn-glycero-3-phosphoethanolamine		1alkg3pe
PE-P	1-(Z)-alk-1-enyl-2-acyl-sn-glycero-3-phosphoethanolamine		1alken2acg3pe
LPE-P	1-(Z)-alk-1-enyl-sn-glycero-3-phosphoethanolamine		1alkeng3pe
PE	1,2-diacyl-sn-glycero-3-phosphoethanolamine	pe	1ac2acg3pe
LPE	1-acyl-sn-glycero-3-phosphoethanolamine	acg3pe	1acg3pe
LPE	2-acyl-sn-glycero-3-phosphoethanolamine	---	2acg3pe
PS	1,2-diacyl-sn-glycero-3-phospho-L-serine	ps	1ac2acg3ps
LPS	1-acyl-sn-glycero-3-phospho-L-serine		1acg3ps
LPS	2-acyl-sn-glycero-3-phospho-L-serine		2acg3ps
PI	1,2-diacyl-sn-glycero-3-phospho(1)-D-myo-inositol		1ac2acg3pi
LPI	1-acyl-sn-glycero-3-phospho(1)-D-myo-inositol		1acg3pi
LPI	2-acyl-sn-glycero-3-phospho(1)-D-myo-inositol		2acg3pi

[zakandrewking]

I crossposted this on the BiGG issue tracker to see if there are any opinions there:

https://github.com/SBRG/bigg_models/issues/354