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An other problem with this file are the functionDefinition, most of the
ones I looked at are like that :

<functionDefinition id="kl_1" metaid="metaid_25" name="kl_1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci>Km_Value</ci>
</bvar>
<bvar>
<ci>pH_of_Experiment</ci>
</bvar>
<bvar>
<ci>Temperature_of_Experiment</ci>
</bvar>
<notanumber/> </lambda>
</math>
</functionDefinition>

So the body of the function is simply "notanumber" !!

I noticed that because I tried to print the math as an infix formula and
got back a strange character so it seems
that there is a problem in jsbml with notanumber, at least when printing
the math as an infix formula.
What do libSBML print in this case in the infix formula ? NaN or
something else ?

Nico


Lucian Smith wrote:
> The file does indeed have errors, but the errors you quoted are not the
> problems you seem to actually have. Using libsbml, one gets many error
> messages like:
>
> line 5221: (10301 [Error]) The value of the 'id' field on every instance
> of the following type of object in a model must be unique: <model>,
> <functionDefinition>, <compartmentType>, <compartment>, <speciesType>,
> <species>, <reaction>, <speciesReference>, <modifierSpeciesReference>,
> <event>, and model-wide <parameter>s. Note that <unitDefinition> and
> parameters defined inside a reaction are treated separately.
> Reference: L2V3 Section 3.3
> The Reaction id 'reaction_370769' conflicts with the previously defined
> Reaction id 'reaction_370769' at line 5167.
>
> All of the errors in the file are of this sort: you have multiple
> reactions with the same name. The reactions even seem to have slightly
> different 'kinetic laws' (which actually seem to be scrach pads to store
> certain bits of information), though the reactions themselves seem to have
> the same reactants and products.
>
> -Lucian
>
> * Dinasarapu, Ashok reddy <adinasarapu@ucsd.edu> [2011-03-30 23:32] writes:
>
>> Hi Andreas,
>>
>> I am sending you the file that I have to parse to get the required data.
>>
>> Thanks,
>> Ashok
>>
>> From: Dinasarapu, Ashok reddy
>> Sent: Wednesday, March 30, 2011 12:29 PM
>> To: 'jsbml-development@caltech.edu'
>> Subject: jsbml/parsing errors
>>
>> Hi,
>>
>> I am trying parse/read SBML data file from BRENDA.
>>
>> There are many errors like the following, while parsing.
>>
>> - The attribute constant on the element parameter is not recognize. Please, check the SBML specifications
>> - The attribute constant on the element parameter is not recognize. Please, check the SBML specifications
>> - The attribute constant on the element parameter is not recognize. Please, check the SBML specifications
>> - The attribute constant on the element parameter is not recognize. Please, check the SBML specifications
>> - The attribute constant on the element parameter is not recognize. Please, check the SBML specifications
>> ......
>>
>> Is there any wrong with the data file or library!.
>>
>> Regards,
>> Ashok
>>
>
>
>
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