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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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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

Attachment: Download_BRENDA_SBML.xml (Size: 628.50KB, Downloaded 223 time(s))

Dear Ashok,

By the way, there is an online validator for SBML files available:
http://sbml.org/Facilities/Validator
This helps to check whether an SBML file is correct or not. It seems
this one is not correct. We will now check why you get these strange
error messages from JSBML.

Best wishes
Andreas

--
Dipl.-Bioinform. Andreas Dräger
University of Tuebingen
Center for Bioinformatics Tuebingen (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-78982
Fax: +49-7071-29-5091
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Dinasarapu, Ashok reddy wrote:
> Hi Andreas,
>
> I am sending you the file that I have to parse to get the required data.
>
>
The problem is that we use the class LocalParameter, for all level and
version of SBML, for the local parameter of a reaction.
And this class as no constant attribute, like in SBML level 3. However,
the constant attribute was always set to true for local parameter.

One simple fix is to add a check for the constant attribute in the
readAttribute method of LocalParameter and return true there to tell
the main parser that the attribute is recognized. We can check there
that the value is always true by the way, and send a warning if it is not.

One question is, do we want to write back the constant attribute to keep
the file as it was ?? If yes, we probably need to add a class attribute
to tell us if the constantAttribute was set and then add it in the
writeAttribute method.

What do people thing about that ?

Nico


> 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
>
> ------------------------------------------------------------------------
>
> ____________________________________________________________
> To manage your jsbml-development list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/jsbml-development
>
> For a web interface to the jsbml-development mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the jsbml-development list,
> contact sbml-team@caltech.edu

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Am 31.03.2011 10:42, schrieb Nicolas Rodriguez:
> Dinasarapu, Ashok reddy wrote:
>> Hi Andreas,
>>
>> I am sending you the file that I have to parse to get the required data.
>>
>>
> The problem is that we use the class LocalParameter, for all level and
> version of SBML, for the local parameter of a reaction.
> And this class as no constant attribute, like in SBML level 3. However,
> the constant attribute was always set to true for local parameter.

Yes. But as far as I know, there was never the possibility to change the
constant attribute of a local parameter to something else than true.

> One simple fix is to add a check for the constant attribute in the
> readAttribute method of LocalParameter and return true there to tell
> the main parser that the attribute is recognized. We can check there
> that the value is always true by the way, and send a warning if it is not.

Hm, yes... but, we should only return true there if the value associated
to the constant attribute is also true. This means, if the readAttribute
method receives "constant" and "false" it should return false.
Furthermore, this may only be done for Level < 3. Otherwise, this
attribute is not recognized.

> One question is, do we want to write back the constant attribute to keep
> the file as it was ?? If yes, we probably need to add a class attribute
> to tell us if the constantAttribute was set and then add it in the
> writeAttribute method.

It does not really make sense to write "constant=true" in a local
parameter with Level < 3, because by default this is always the case. No
matter what was written in an original file, I would remove this in any
case.

Best wishes
Andreas

--
Dr. Andreas Dräger
University of Tuebingen
Center for Bioinformatics Tuebingen (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-78982
Fax: +49-7071-29-5091
____________________________________________________________
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https://utils.its.caltech.edu/mailman/listinfo/jsbml-development

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Andreas Draeger wrote:
> Am 31.03.2011 10:42, schrieb Nicolas Rodriguez:
>
>> Dinasarapu, Ashok reddy wrote:
>>
>>> Hi Andreas,
>>>
>>> I am sending you the file that I have to parse to get the required data.
>>>
>>>
>>>
>> The problem is that we use the class LocalParameter, for all level and
>> version of SBML, for the local parameter of a reaction.
>> And this class as no constant attribute, like in SBML level 3. However,
>> the constant attribute was always set to true for local parameter.
>>
>
> Yes. But as far as I know, there was never the possibility to change the
> constant attribute of a local parameter to something else than true.
>
>
>> One simple fix is to add a check for the constant attribute in the
>> readAttribute method of LocalParameter and return true there to tell
>> the main parser that the attribute is recognized. We can check there
>> that the value is always true by the way, and send a warning if it is not.
>>
>
> Hm, yes... but, we should only return true there if the value associated
> to the constant attribute is also true. This means, if the readAttribute
> method receives "constant" and "false" it should return false.
> Furthermore, this may only be done for Level < 3. Otherwise, this
> attribute is not recognized.
>
>

Of course, that was what I was suggesting without writing it :-)

>> One question is, do we want to write back the constant attribute to keep
>> the file as it was ?? If yes, we probably need to add a class attribute
>> to tell us if the constantAttribute was set and then add it in the
>> writeAttribute method.
>>
>
> It does not really make sense to write "constant=true" in a local
> parameter with Level < 3, because by default this is always the case. No
> matter what was written in an original file, I would remove this in any
> case.
>
>
There is nothing wrong to put the attribute to true, like this, you are
sure that other software that use your SBML file
will set the attribute to true even if they do not know the default
value that is written in the SBML specs.

But also, it is nice to give back the model as it was written by the
user or the tool that created it. This is why we are doing that for all
the other
attributes in all the other classes that have a default value in the
specs. If the user set it in the original file, we are writing it back
even if it is the default value.

Not sure why we should make an exception for the constant attribute in
the class parameter.

Nico





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Dear all,

There is currently a discussion going on in the JSBML mailing list that
requires the opinion of some people from the SBML community.

The question is:

Should we or should we not keep the information constant=true in local
parameters with SBML Level < 3 when writing an SBML file given that this
was written in an original file?

>>> One question is, do we want to write back the constant attribute to keep
>>> the file as it was ?? If yes, we probably need to add a class attribute
>>> to tell us if the constantAttribute was set and then add it in the
>>> writeAttribute method.
>>>
>>
>> It does not really make sense to write "constant=true" in a local
>> parameter with Level < 3, because by default this is always the case. No
>> matter what was written in an original file, I would remove this in any
>> case.
>>
>>
> There is nothing wrong to put the attribute to true, like this, you are
> sure that other software that use your SBML file
> will set the attribute to true even if they do not know the default
> value that is written in the SBML specs.
>
> But also, it is nice to give back the model as it was written by the
> user or the tool that created it. This is why we are doing that for all
> the other
> attributes in all the other classes that have a default value in the
> specs. If the user set it in the original file, we are writing it back
> even if it is the default value.
>
> Not sure why we should make an exception for the constant attribute in
> the class parameter.

Cheers
Andreas

--
Dr. Andreas Dräger
University of Tuebingen
Center for Bioinformatics Tuebingen (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-78982
Fax: +49-7071-29-5091
____________________________________________________________
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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
>>
>
>
>
>> ____________________________________________________________
>> To manage your jsbml-development list subscription, visit
>> https://utils.its.caltech.edu/mailman/listinfo/jsbml-development
>>
>> For a web interface to the jsbml-development mailing list, visit
>> http://sbml.org/Forums/
>>
>> For questions or feedback about the jsbml-development list,
>> contact sbml-team@caltech.edu
>>
>
> ____________________________________________________________
> To manage your jsbml-development list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/jsbml-development
>
> For a web interface to the jsbml-development mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the jsbml-development list,
> contact sbml-team@caltech.edu
>

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On Thu, 31 Mar 2011 11:05:38 +0200, Andreas Draeger wrote:
> Should we or should we not keep the information constant=true in local
> parameters with SBML Level < 3 when writing an SBML file given that this
> was written in an original file?

Hi Andreas,

I take it that the original model was also < 3, because otherwise there would be no question about the constant attribute on LocalParameter.

So I would suggest that, even though it is redundant for L2 models, you may as well write it out if the original model had it.

MH


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