Issue with SBML model

[suetli19]

Hi,

I followed the instruction from this discussion (#62) to provide input SBML files to build a model. However, I encountered an error with reading the SBML model. May I know what is the best possible solution for this?

Thank you.

[cdiener]

Where did you get the model from? And did you try the validation link provided in the error message? It looks like it is not a valid SBML model.

[suetli19]

Where did you get the model from? And did you try the validation link provided in the error message? It looks like it is not a valid SBML model.

I got the AGORA2 models from here and found that certain models are not valid and also, this database version did not have all the strains I needed to build my model - https://vmh.life/files/reconstructions/AGORA2/version2.01/sbml_files_fixed/zipped/AGORA2_models/

I tried the validation link provided but it seemed that the website wasn't available anymore as this was what it shows me:

I found one recent paper that has database similar to AGORA2 but I'm not sure how to incorporate it to micom in building the models as their file formats are different (not strain names for each xml file):
Here's the paper - https://www.cell.com/cell-systems/fulltext/S2405-4712(25)00029-8#sec-8-1
Apollo database - https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/RL7E7G

I'm wondering if you could advise me if there is any other alternatives or solution for this?

Thank you so much!

[cdiener]

Ah okay, this looks like it is related to opencobra/cobrapy#1326 in that case. What will work with AGORA2 is to download the Matlab models (*.mat). Those can can be provided as the model files in the "file" column in the taxonomy table passed to build or can also be used as input when making your own model database.