Suspected duplicated metabolites from Bigg

[JHL-452b]

Current behavior:

Suspected duplicated metabolites from Bigg:

reference ID	met ID	Duplicate rxn pairs	Action for mets	Action for rxns	Comments
3hibutcoa	MAM00785m MAM03226m	(MAR00042 MAR03755)	remove MAM03226m	remove MAR00042
dmhptcoa	MAM00563m MAM03553m	No	replace MAM03553m to MAM00563m	No
xolest2_hs	MAM01451l MAM10004l MAM01451r MAM10004r	(MAR10037 MAR03537)(MAR10038 MAR03622)	remove MAM10004l and MAM10004r	remove MAR03537 and MAR03622
phyt	MAM02746c MAM03884c MAM02746e MAM03884e MAM02746x MAM03884x	(MAR00440 MAR01617)( MAR03480 MAR00740) (MAR09037 MAR00659 )(MAR03482 MAR05323)	remove MAM03884c and MAM03884e; replace MAM03884x to MAM02746x	remove MAR01617, MAR00740, MAR00659 and MAR05323
dmnoncoa	MAM00933c MAM03554c	(MAR03517 MAR01709)	remove MAM03554c	remove MAR01709
tag1p__D	MAM01746c MAM03960c		change BiGG ID annotation for MAM01746c to tag6p__D		Not duplicates
pristcoa	MAM03887x MAM00078x		change BiGG ID annotation for MAM00078x to CE5125		Not duplicates
galgluside_hs	MAM02328c MAM03586c MAM02328g MAM03586g MAM02328l MAM03586l MAM02328e MAM03586e MAM02328r		change BiGG ID annotation for MAM02328 to digalside_hs		Not duplicates
gm1_hs	MAM02008c MAM03635c MAM02008g MAM03635g MAM02008l MAM03635l MAM02008e MAM03635e MAM03635n		change BiGG ID annotation for MAM02008 to HC02161		Not duplicates

• remove mets MAM03226m, MAM03884c, MAM03884e, MAM03554c
• remove rxns MAR00042,MAR01617, MAR00740, MAR00659, MAR05323, MAR01709
• change BiGG ID annotations for MAM01746c, MAM00078x, MAM02328c, MAM02328g, MAM02328l, MAM02328e, MAM02328r, MAM02008c, MAM02008g, MAM02008l, MAM02008e
• replace mets

old ID	new ID
MAM03553m	MAM00563m
MAM03884x	MAM02746x

[feiranl]

As for dmhptcoa they are not 100% same, one is the general form, the other one is isomer, and they should have different BiGG IDs. The BiGG ID for MAM03553m should changed to CE4798. And I suggest we keep it for now, what do you think? @haowang-bioinfo

As for the xolest2_hs, I am not sure where these coefficients come from, and how should we deal with the coefficient difference @JonathanRob

[haowang-bioinfo]

@JHL-452b good to know this, nice work!

As for dmhptcoa they are not 100% same, one is the general form, the other one is isomer, and they should have different BiGG IDs. The BiGG ID for MAM03553m should changed to CE4798. And I suggest we keep it for now, what do you think? @haowang-bioinfo

they do appear to be the same compound, maybe in different chirality. agree to your proposal - only change BiGG id for now

[haowang-bioinfo]

a few questions:

• if to remove MAR01709, how about move its GPR to that of MAR03517?
• why should digalside_hs be assigned to MAM02328?
• why should HC02161 be assigned to MAM02008?

[JHL-452b]

a few questions:

• if to remove MAR01709, how about move its GPR to that of MAR03517?
• why should digalside_hs be assigned to MAM02328?
• why should HC02161 be assigned to MAM02008?

Thanks for your reply!

• the GPR of MAR01709 was annotated as ENSG00000116171 and it was already moved to MAR03517 in PR. As for other annotations have also been moved, such as EC, the direction of reaction, etc.
• The assignment of MAM02328 and MAM02008 were determined by mapping relationships with other databases. Such as
  MAM02328 links to MNXM269 in Human-GEM, and MNXM269 links to digalside_hs in MetaNetX;
  MAM02008 links to MNXM164818 in Human-GEM, and MNXM164818 links to HC02161 in MetaNetX.

[haowang-bioinfo]

fixed in #646