#11 Conversion to SBML L3 results in SBML L2

[Anonymous]

I selected input format SBML, then selected output format SBML Level 3 version 1, uploaded a Level 2 version 1 SBML file, hit convert. The resulting file has L3V1 suffix, however, the file header still says SBML Level 2 version 1.

I've attached the input file that I tried in case that helps.

[Nicolas Rodriguez]

It is an old "feature" of the converter. If the convrsion fail, it does return the original model to the user, we need to change that so that it does fail and return the errors to the user directly.

Here are the error detected for the model:

line 50572: (21111 [Error]) The value of a <speciesreference> 'species' attribute must be the identifier of an existing <species> in the model.
Reference: L2V1 Section 4.9.5
The <speciesreference> in the <reaction> with id 'biomass_bulk_c0' references species 'cpd11312_c0', which is undefined.</reaction></speciesreference></species></speciesreference>

line 50576: (21111 [Error]) The value of a <speciesreference> 'species' attribute must be the identifier of an existing <species> in the model.
Reference: L2V1 Section 4.9.5
The <speciesreference> in the <reaction> with id 'biomass_bulk_c0' references species 'cpdPolyPn1_c0', which is undefined.</reaction></speciesreference></species></speciesreference>

line 50598: (21111 [Error]) The value of a <speciesreference> 'species' attribute must be the identifier of an existing <species> in the model.
Reference: L2V1 Section 4.9.5
The <speciesreference> in the <reaction> with id 'biomass_bulk_c0' references species 'cpdPolyPn_c0', which is undefined.</reaction></speciesreference></species></speciesreference>

If you correct those errors, you should be able to convert the model. There is a way to force the conversion even if there are some errors which in your case should produce a usable result but it is not supported at the moment.

[Nicolas Rodriguez]

I have now updated the converter on the web app so that it return an error and I have updated libsbml to the latest version in the same time.
So next time you should have better result that will present the list of errors detected in your model.