add gene name to Human-GEM

[haowang-bioinfo]

It might be a good idea to include gene names (i.e. gene symbols) into Human-GEM, as a separate field model.geneNames.

[haowang-bioinfo]

this would introduce redundancy given the existing "geneSymbols" column in genes.tsv and they may co-exist a while. But this should help in many things due to the common use of gene symbols in numerous analysis and literature.

[JonathanRob]

I think it could be useful to add this field to the default model structure, as you suggest. There may be a potential issue when calling the annotateGEM function (part of the release process before generating the SBML file) which I believe might add either a geneSymbols or geneNames field, though I'm not certain.

[haowang-bioinfo]

a new field geneShortNames is added to Human-GEM in #549, it has now been enabled with compatibility to importYaml, annotateGEM, RAVEN, Cobra toolbox, and cobrapy

[haowang-bioinfo]

added in #549

[haowang-bioinfo]

reopen this, because the addition of geneShortNames field potentially lead to deprecation of translateGrRules function in multiple cases in the repo

[haowang-bioinfo]

translateGrRules seems fine