problems reading certain AGORA2 models about cobrapy HOT 3 OPEN

Hi, actually I have a lot of info on that since I had to prep them for the MICOM database release. Unfortunately it looks like something went wrong when the authors prepped the SBML models. A large fraction of them have some slight issues. In particular I found the following cases:

1. In some cases the models are actually Matlab models with just the file ending having been renamed to .xml.
2. A even larger fraction of models is declared as UTF in the XML but encodes in ISO Format which will raise an error in Most XML parsers.
3. In some cases the model names of the SBML have spelling mistakes so they can't be matched to the manifest.

Looks like you hit case 1. For now there is not much one can do. For MICOM we converted all the .mat models to SBML with cobrapy to get around that.

However, the Matlab models work just fine and you can read those with cobra.io.load_mat_model.

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Thanks a lot for your reply and explanations, and congratulations by the way for the great job you do around MICOM!

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Hi!
I can confirm the issue with several AGORA2 models (version 2.01).

In addition to the three points mentioned by @cdiener, some SBML parsers may fail to read specific models with brackets "("/ or ")" in the chemical formula of metabolites. E.g. in the model sbml Bacteroides_ovatus_CL03T12C18.xml.

Encountered '(' when expecting a capital letter. The chemicalFormula 'C10H14N5O7P(C5H8O5PR)n(C5H8O5PR)n' has incorrect syntax.

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