readSBML issue with COBRA 3.0 (and SBML L2 V4)

[Uri David Akavia]

Hello.

I've updated to COBRA 3.0 and I'm having some issues with the RECON 2.2 xml file (as downloaded from biomodels).

I'm not sure if this is due to a problem in SBML standard, but I'm not sure

It seems that commit https://github.com/opencobra/cobratoolbox/commit/0e5d7dad5105150abcc758530ed9b836129f1ccc (updated SBMLIO) removed parseSBMLAnnotation functions, but did not replace the functionality (for SBML level 2). MODEL1603150001.xml has cvterms for species, but since it is SBML level 2 it is not called.

When trying to run readSBML in debug mode on this file, parseCVterms works, paraseSBMLAnnotation works, but neither is called. I can modify it back to include parseSBMLAnnotation, but parseCVterms would also work. As it currently stands, it means that InChi, Chebi and all the databases in RECON 2.2 XML file aren't loaded.

Yours,

Uri David

[Thomas Pfau]

Ok, this is due to a mistake that cvterms are not read in sbml Level 2.

I'll submit a fix for this today. However, please not that the only guaranteed SBML version supported by the toolbox is Level 3 version 1 with fbc-package version 2 (as mentioned here: https://github.com/opencobra/cobratoolbox/blob/master/docs/source/notes/notes.md ) . For all other SBML versions, things might be missing.

Best

Thomas

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