As noted in https://github.com/SysBioChalmers/yeast-GEM/pull/216, currently there's an inconsistency with how cobratoolbox and cobrapy store gene names in the xml file: cobratoolbox uses the fbc:label field, whereas cobrapy uses fbc:name. The latter is used by cobratoolbox to store protein information.
Ideally both packages should save the model in the same way, to allow opening an xml file with either and without loosing any info. I'm not sure if it makes more sense to change the cobratoolbox or cobrapy convention: name sounds more reasonable for a gene name, but as @Midnighter pointed out, label is a required field by SBML whereas name is not.
Dependency Information
System Information
==================
OS Windows
OS-release 10
Python 3.7.7
Package Versions
================
cobra 0.17.1
depinfo 1.5.3
future 0.18.2
numpy 1.18.3
optlang 1.4.4
pandas 1.0.3
pip 20.0.2
python-libsbml-experimental 5.18.0
ruamel.yaml 0.16.10
setuptools 46.1.3.post20200330
six 1.14.0
swiglpk 4.65.1
wheel 0.34.2
Problem description
As noted in https://github.com/SysBioChalmers/yeast-GEM/pull/216, currently there's an inconsistency with how cobratoolbox and cobrapy store gene names in the xml file: cobratoolbox uses the
fbc:label
field, whereas cobrapy usesfbc:name
. The latter is used by cobratoolbox to store protein information.Code Sample
cobrapy:
cobratoolbox:
Actual Output
cobrapy:
cobratoolbox:
Expected Output
Ideally both packages should save the model in the same way, to allow opening an xml file with either and without loosing any info. I'm not sure if it makes more sense to change the cobratoolbox or cobrapy convention:
name
sounds more reasonable for a gene name, but as @Midnighter pointed out,label
is a required field by SBML whereasname
is not.Dependency Information