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opencobra / cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.
http://opencobra.github.io/cobrapy/
GNU General Public License v2.0
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SBML file not getting uploaded #1337

Closed ksingh371 closed 12 months ago

ksingh371 commented 1 year ago

Checklist

Question

I had prepared my metabolic model on merlin and was trying to run the model for FBA on COBRApy. But on uploading the model the following error is coming up: 1912 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id

1912 is the NCBI taxonomic identifier of the organism used in merlin. Please suggest ways to overcome this problem

cdiener commented 1 year ago

Not sure what you mean by upload here. Can you give a minimal reproducible example and provide the model file? Looks like your model has incorrect annotations. If that file was generated by Merlin maybe also report it there?

Midnighter commented 12 months ago

NCBI txids are not recognized in https://registry.identifiers.org/registry. I would encourage you to remove that model annotation. You should be able to give it a RefSeq annotation for the genome used, if that is important to you.

Otherwise, please provide more information as @cdiener asked for.