readCbModel error for SBML level 2 version 1 file. How to convert it to level 3?

[Chaitanya Bhave]

Hi!

I was trying to read Zymomonas mobilis - iEM439 model (Obtained from ----- http://pubs.rsc.org/en/Content/ArticleLanding/2016/MB/C5MB00588D#!divAbstract) but the Cobra Toolbox could not read it. Upon research on the internet I understood that the recent Cobra Toolbox is consistent only for SBML L3 while this file is L2V1. 

Is there a way to convert this file to L3 such that it is compatible with the recent Cobra Toolbox?

Other previous Z. mobilis models (iZM363 and iZmobMBEL601) are available here ------- https://github.com/opencobra/m_model_collection/tree/master/sbml3

in SBML L3 but the above model is not there.

I am using MATLAB2016b and my Cobra Toolbox is up to date. This is the error message which I receive

>> model=readCbModel('iEM439.xml')

The model contains 1 errors.

Error encountered during read.

Error using cellfun

Non-scalar in Uniform output, at index 1, output 1.

Set 'UniformOutput' to false.

Error in readSBML>extractGPRRule (line 453)

    ruleGenes = cellfun(@(x) regexp(x,'[^ \[\]\(\)\{\}]*','match'),geneFields);

Error in readSBML (line 214)

        [rule,cgenes] = extractGPRRule(grRule{i},model.genes,0);

Error in readCbModel (line 207)

        model = readSBML(fileName,defaultBound);

------------------------------------------------------------------------------------------------------------------------------------------

Chaitanya Bhave,

Senior Undergraduate,

Department of Biochemical Engineering and Biotechnology,

Indian Institute of Technology Delhi

[Thomas Pfau]

Hello Chaitanya,

As you can see from the output of readCbModel, the model file contains at least one error.

Checking it against the SBML Validator ( http://sbml.org/Facilities/Validator/index.jsp ) you can see, that this file is not valid SBML.

There is a reaction with a missing id field (which is a required atribute even for L2V1). If you add a id to that reaction (line 25863) the toolbox can read the model without issue.

Best,

Thomas

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[Chaitanya Bhave]

Thank you for this.

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