feat: lost annotation field in .yml file

[BenjaSanchez]

Description of the issue:

I noticed that the annotation field in the .yml file, which is parsed from RAVEN's fields metMiriams & rxnMiriams, is skipped in writeHumanYaml.m, even though RAVEN's writeYaml.m has it. Any reasons for skipping it? Any plans of introducing it? I find it very useful when quickly querying annotation data. See below how it looks for yeast-GEM:

• Metabolites:
  

• Reactions:
  

I hereby confirm that I have:

• Done this analysis in the master branch of the repository
• Checked that a similar issue does not exist already

[haowang-bioinfo]

@BenjaSanchez thanks for the comments, which does make sense for adding back the annotations to the yml file. We'll make a plan and provide the follow-up progress here.

[haowang-bioinfo]

@BenjaSanchez the annotation information in Human-GEM is not lost, but preserved in JSON annotation files, as explained in #75.

This solution is a workaround to the pending spec of RAVEN/COBRA model fields, and the uncertainties of SBML libraries.

[mihai-sysbio]

A new TSV annotation format has been adopted through #212 .

As far as I can tell, there is no current plan of moving the annotation back into the yml file. That being said, the PMIDs are stored in the yml under - references: .

[haowang-bioinfo]

No plan for moving annotation from tsv to yml, so this issue is closed for now. Feel free to reopen.