Regarding parsing error

[SANKAR MAHESH R]

I'm Sankar Mahesh, a PhD student from India working on genome scale modeling.

I've been trying to use Equilibrator to determine the dG0 values of metabolites that are not present in the BiGG database.

I'm doing this by using the MetaNetXID of the metabolite.

But Equilibrator returns the following error message:

INFO: Equilibrator reaction parsing error 1.0 MNXM735438 was not found in the compound cache       No dG0 can be given for this reaction!

Is there something that I can do to prevent this error and calculate dG0.

It'll be really very helpful if I can overcome this.

Thanks and Regards,

Sankar Mahesh

[Elad Noor]

Dear Sankar,

I guess you are trying to write a reaction that uses molecular oxygen (O2). Indeed, the current version of metanetx uses this ID (MNXM735438) for it. However, we trained our models on an older version of the database where the ID was still (MNXM4) which is now depracated.

One option for you is to use the old identifier.

Or, you can switch to annotations based on other databases such as BiGG or KEGG:

kegg.compound:C00007

bigg.metabolite:o2

Unfortunately, this bug is a bit difficult to solve and I can't give you a timeline for when the database will be updated next.

All the best,

Elad