feat: improve metabolite annotations

[sulheim]

Description of the issue:

All metabolites in the model should have chebi-identifiers. This was explicitly mentioned during the Cobra-conference 2018, and seems to be a consensus. The identifier is described here: https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000002

Expected feature/value/output:

Model where all metabolites have been annotated with a chebi-identifier.

Current feature/value/output:

511 of 2015 metabolites are missing the chebi-identifier

Reproducing these results:

import cobra
model = cobra.io.read_sbml_model("./ModelFiles/xml/scoGEM.xml")
j = 0
   ...: for i in model.metabolites:
   ...:     try:
   ...:         i.annotation["chebi"]
   ...:     except:
   ...:         j+=1
print("N metabolites: ", len(model.metabolites))
print("N metabolites without chebi-annotation: ", j)

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Done this analysis in the master branch of the repository
• Checked that a similar issue does not exist already

[sulheim]

I add a couple of more tasks to this issue, because I think all metabolites should have:

• formula (for the corresponding charge)
• charge
• mass (not really important)

[sulheim]

• make sure all chebi annotations follow the CHEBI:\d+$ pattern
• all metabolites chebi-annotated