different Metabolite annotation in the PKN

[jtorrejon81]

Dear Aurelien, Attila,

Excellent bioinfo tool, congratulations!

I have two questions concerning to the metabolite annotation in the PKN

1/ Looking the full PKN network, I have realized that metabolites IDs with different nomenclature than HMDB have been also included, for example see below:
-Metab__HMDB0000132_c (HMDB nomenclature)
-Metab__4782_c (PUBCHEM nomenclature)
-Metab__c226coa_c (KEGG nomenclature)
-Metab__pa_hs_c (Unknown nomenclature)

I am wondering if the different metabolites nomenclature are taking into account when the function "format_COSMOS_res" is applied to rename metabolites or only HMDB?

2/ it is possible to add manually new nodes/interactions in the PKN while keeping the same format, right?

Many thanks for your help
Best regards,

[adugourd]

Hi, sorry for delayed answer.

the metab IDs were alwys a bit tricky to set up consistently. We used by default and whenever we could a tranlsation to HMBD IDs. However, the metabolites comes from two ressources that themselves use PUBCHEM CIDs and BIGG IDs respectivelly. Therefore, whenever we couldn'T map a metab name in the network to HMDB (not all chemicals are referenced rthere), we left the ID of the original database in place.

You can add manually new interactions to the network of course :)

By default I would advise to use HMDB as well whenever possible.

Cheers,

Aurelien