Failure to extract Fruitfly-GEM.xml using COBRA

[gmhhope]

Description of the issue:

Trying to parse the Fruitfly-GEM.xml but face errors:
model = cobra.io.read_sbml_model(xmlFile)

---------------------------------------------------------------------------
CobraSBMLError                            Traceback (most recent call last)
File ~/.local/lib/python3.8/site-packages/cobra/io/sbml.py:249, in read_sbml_model(filename, number, f_replace, **kwargs)
    248     doc = _get_doc_from_filename(filename)
--> 249     return _sbml_to_model(doc, number=number, f_replace=f_replace, **kwargs)
    250 except IOError as e:

File ~/.local/lib/python3.8/site-packages/cobra/io/sbml.py:522, in _sbml_to_model(doc, number, f_replace, set_missing_bounds, **kwargs)
    519 for (
    520     gp
    521 ) in model_fbc.getListOfGeneProducts():  # noqa: E501 type: libsbml.GeneProduct
--> 522     gid = _check_required(gp, gp.getIdAttribute(), "id")
    523     if f_replace and F_GENE in f_replace:

File ~/.local/lib/python3.8/site-packages/cobra/io/sbml.py:1352, in _check_required(sbase, value, attribute)
   1351         msg += " with metaId '%s'" % sbase.getName()
-> 1352     raise CobraSBMLError(msg)
   1353 if attribute == "id":

CobraSBMLError: Required attribute 'id' cannot be found or parsed in '<GeneProduct>'.

The above exception was the direct cause of the following exception:

CobraSBMLError                            Traceback (most recent call last)
Input In [8], in <cell line: 1>()
----> 1 model = cobra.io.read_sbml_model(xmlFile)

File ~/.local/lib/python3.8/site-packages/cobra/io/sbml.py:263, in read_sbml_model(filename, number, f_replace, **kwargs)
    253 except Exception as original_error:
    254     cobra_error = CobraSBMLError(
    255         "Something went wrong reading the SBML model. Most likely the SBML"
    256         " model is not valid. Please check that your model is valid using "
   (...)
    261         "at https://github.com/opencobra/cobrapy/issues ."
    262     )
--> 263     raise cobra_error from original_error

CobraSBMLError: Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `cobra.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
	`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .

Then I follow the instruction and do validation

cobra.io.sbml.validate_sbml_model(xmlFile)
It renders the following:

(None,
 {'SBML_FATAL': [],
  'SBML_ERROR': ["E1 (Error): SBML component consistency (fbc, L299114); Allowed fbc attributes on <GeneProduct>; A <GeneProduct> object must have the required attributes 'fbc:id' and 'fbc:label' may have the optional attributes 'fbc:name' and 'fbc:associatedSpecies'. No other attributes from the SBML Level 3 Flux Balance Constraints namespace are permitted on a <GeneProduct> object. \nReference: L3V1 Fbc V3 Section 3.5\n Fbc attribute 'id' is missing from 'geneProduct' object.\n",
   "E3 (Error): SBML component consistency (fbc, L299114); Allowed fbc attributes on <GeneProduct>; A <GeneProduct> object must have the required attributes 'fbc:id' and 'fbc:label' may have the optional attributes 'fbc:name' and 'fbc:associatedSpecies'. No other attributes from the SBML Level 3 Flux Balance Constraints namespace are permitted on a <GeneProduct> object. \nReference: L3V1 Fbc V3 Section 3.5\n Fbc attribute 'id' is missing from 'geneProduct' object.\n"],
  'SBML_SCHEMA_ERROR': [],
  'SBML_WARNING': ['E0 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \nReference: L3V1 Section 6.3\n An invalid ModelHistory element has been stored.\n',
   'E2 (Warning): General SBML conformance (core, L3); RDF does not contain valid ModelHistory; LibSBML expected to read the annotation into a ModelHistory object. Unfortunately, some attributes were not present or correct and the resulting ModelHistory object will not correctly produce the annotation.  This functionality will be improved in later versions of libSBML. \nReference: L3V1 Section 6.3\n An invalid ModelHistory element has been stored.\n'],
  'COBRA_FATAL': [],
  'COBRA_ERROR': ["Required attribute 'id' cannot be found or parsed in '<GeneProduct>'."],
  'COBRA_WARNING': [],
  'COBRA_CHECK': []})

Expected feature/value/output:

I would expect to be able to parse the Fruitfly-GEM.xml which will have identifiers synchronized with metabolites.tsv and yml files.

Reproducing these results:

# https://cobrapy.readthedocs.io/en/latest/io.html#SBML
import cobra
import os
import requests

# Human-GEM e.g.,
model_name = 'Fruitfly-GEM'

outputfdr = f"../../output/ATLAS_collection/{model_name}"
try:
    os.makedirs(outputfdr)
except:
        None

BRANCH = 'main'
XML = os.path.join(outputfdr,f'{model_name}.xml')
with open(XML, 'w') as f:
    r = requests.get(f'https://github.com/SysBioChalmers/{model_name}/blob/' + BRANCH + f'/model/{model_name}.xml?raw=true')
    f.write(r.text)

with open(XML, 'r') as f:
    xmlFile = f.read()

model = cobra.io.read_sbml_model(xmlFile)

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Done this analysis in the main branch of the repository
• Checked that a similar issue does not exist already
• If needed, asked first in the Gitter chat room about the issue

[gmhhope]

Dear colleagues,

The issue still persists! Please see if you can help update it!

Many thanks,
Minghao Gong

[haowang-bioinfo]

The issue still persists! Please see if you can help update it!

@gmhhope thanks for reporting this, will fix it asap

[haowang-bioinfo]

The problems reported here are due to the invalid gene id (e.g. 5Ptasel) format that does not comply with libSBML standard. This was addressed by a fixing commit 1603557, which introduced a prefix G_ to gene ids, but might not be the optimal solution though.

[haowang-bioinfo]

This has been fixed in v1.2, free to reopen it if problem stays.