Import/export of SBML <notes> #695
Description
Problem description
Hi all,
Do you intend to support import/export of <notes> from/to SBML files?
When a SBML model is parsed with some <notes> under, for instance, a <geneProduct>, those notes are not imported. I would have expected to retrieve the notes with mymodel.genes.mygene.notes, but the attribute is always empty.
I didn't saw in cobra.io.sbml3.parse_xml_into_model and cobra.io.sbml3.annotate_cobra_from_sbml where the <notes> are imported. I believe they are not; which would explain why they are not available in the python object.
Code Sample
Gist to mini_fbc2_notes.xml
import cobra
m = cobra.io.sbml3.read_sbml_model("mini_fbc2_notes.xml")
print([x.notes for x in m.genes])
# [{}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}]
print([x.notes for x in m.reactions])
# [{}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}]
print([x.notes for x in m.metabolites])
# [{}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}]Expected Output
print([x.notes for x in m.genes])
# [{"This is an important note for humans."}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}]
print([x.notes for x in m.reactions])
# [{"This is an important note for humans."}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}]
print([x.notes for x in m.metabolites])
# [{"This is an important note for humans."}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}]Output of cobra.show_versions()
System Information
OS Linux
OS-release 3.10.0-693.21.1.el7.x86_64
Python 3.6.4
Package Versions
pip 9.0.3
setuptools 39.0.1
cobra 0.11.3
future 0.16.0
swiglpk 1.4.4
optlang 1.4.0
ruamel.yaml 0.14.12
pandas 0.22.0
numpy 1.14.2
tabulate 0.8.2
scipy 1.0.0
matplotlib 2.2.2