Fatal error during SBML import

When trying to import an SBML file to use in SimBiology, I am getting the following error

>> x = sbmlimport('http://www.netpath.org/netslim/EGFR1/EGFR1_SBML.xml')

Error using SimBiology.SBMLReadWrite/sbmlread

A fatal error occurred reading in this file.

Error in sbmlimport (line 96)

ret = sbmlRW.sbmlread(modelString, {'stream'});

A similar error occurs if the linked file above is downloaded and added to the path instead. ( Throwing an error on line 89: ret = privatesbmlio('read',nargout,{tempFileName}); )

Why is this happening? How can I fix it?

Answer 1

[Rick Paxson]

Hello,

It appears that the SBML file you are trying to load is not valid because many of the species are missing the Compartment attribute. I.e. species must specify which compartment they are in.

There are a number of species that are missing this attribute (but not all of them).

E.g.

<species name="SRC" id="PB_1"/>

<species name="PTK2B" id="PB_2"/>

<species name="SRC_PTK2B" id="PB_3"/>

...

Here are some of the species that are properly specified:

<species name="F_PTPN11" compartment="compartment_1" id="PB_447"/>

<species name="T_PTPN11" compartment="compartment_9" id="PB_448"/>

<species name="F_PLCG1" compartment="compartment_1" id="PB_449"/>

...

The error message that you are getting from SimBiology is not helpful. We will fix that.

Rick Paxson