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Hi Viji, Camille, all,

Thanks very much. Just so you know, I think I found a similar instance in
BioModels 195, in what I recall was species id "CycBt". I can run the test
again to be sure, if this doesn't seem to be a similar case.

thanks :) Allyson

On 28 June 2011 13:17, Vijayalakshmi Chelliah <viji@ebi.ac.uk> wrote:

> Dear Allyson,
>
> species: id="Y2_1" name="i_cyclinE_CDK2".
> There was indeed an error in the annotation of the above species. Both the
> bags should have "hasVersion" as qualifier.
> It has now been corrected.
> Thank you for pointing out the usage of incorrect qualifier in the
> annotation.
>
> I have also changed the annotation for "p27" with UNIPORT id. p27 was
> initially annotated with an Interpro term, which no longer exist.
>
> best regards,
> Viji
>
>
>
> Camille Laibe wrote:
>
>> Dear curators,
>>
>> Could you have a look at the annotations of BIOMD0000000169? Specially the
>> ones for the "i_cyclinE_CDK2" (there might be others).
>> Please refer to the message below from Allyson about a potential bug in
>> libSBML, but also a potential annotation error in BioModels Database.
>>
>> Thanks.
>>
>> -------- Original Message --------
>> Subject: [sbml-interoperability] accidental removal of MIRIAM annotation
>> from Biomodels 169
>> Date: Tue, 21 Jun 2011 16:05:07 +0100
>> From: Allyson Lister <allyson.lister@newcastle.ac.**uk<allyson.lister@newcastle.ac.uk>
>> >
>> Reply-To: SBML Software Interoperability Discussion List <
>> sbml-interoperability@**caltech.edu <sbml-interoperability@caltech.edu>>
>> To: SBML Software Interoperability Discussion List <
>> sbml-interoperability@**caltech.edu <sbml-interoperability@caltech.edu>>
>>
>>
>> Hi all,
>>
>> This is a question about libSBML 5.0.0 (java version), running on Natty.
>>
>> I have a test where, for each SBML element with such annotation, the
>> MIRIAM
>> annotation is extracted. This test is currently using Biomodels entry
>> number
>> 169.
>> It reorganizes all extracted annotation alphabetically, then adds the
>> annotation back into the sbml element (having deleted the original
>> annotation first). This is part of a bit of a comparison class, but that's
>> not really relevant to this discussion.
>>
>> In Biomodels 169, some weird behaviour is encountered during the parsing
>> of
>> the MIRIAM annotation for the species with ID Y2_1.
>>
>> Here is the relevant code:
>>
>> // here, all CV terms are copied via cloneObject() int a
>> variable called cvTerms
>> ArrayList<CVTerm> cvTerms = new ArrayList<CVTerm>();
>> for ( long iii = 0; iii < sbase.getNumCVTerms(); iii++ ) {
>> cvTerms.add( sbase.getCVTerm( iii ).cloneObject() );
>> }
>> // delete all terms
>> sbase.unsetCVTerms();
>>
>> // do some stuff here with cvTerms (unimportant for this
>> discussion I think)
>>
>> // print out the current state of cvTerms
>> if (sbase instanceof Species && sbase.getId().equals("Y2_1"))
>> {
>> System.err.println( "BEFORE number of cv terms = " +
>> cvTerms.size() );
>> for ( CVTerm cvTerm : cvTerms ) {
>> System.err.println( "BEFORE (start of cv term)" );
>> for ( long jjj = 0; jjj < cvTerm.getNumResources();
>> jjj++ ) {
>> System.err.println( "BEFORE resource URI: " +
>> cvTerm.getResourceURI( jjj ) );
>> }
>> }
>> }
>> // this is the only bit of code that's actually run in this
>> excerpt: add cvTerms back to sbase.
>> for ( CVTerm cvterm : cvTerms ) {
>> sbase.addCVTerm( cvterm );
>> }
>> // repeat the verbosity but with the sbase object this time
>> if (sbase instanceof Species && sbase.getId().equals("Y2_1"))
>> {
>> System.err.println( " AFTER number of cv terms = " +
>> sbase.getNumCVTerms() );
>> for ( long iii = 0; iii < sbase.getNumCVTerms(); iii++ ) {
>> System.err.println( "AFTER (start of cv term)" );
>> for ( long jjj = 0; jjj <
>> sbase.getCVTerm(iii).**getNumResources(); jjj++ ) {
>> System.err.println("AFTER resource URI: " +
>> sbase.getCVTerm( iii ).getResourceURI(jjj));
>> }
>> }
>> }
>>
>> So, all I'm doing here is adding a bunch of CVTerms to the sbase object.
>> But, take a look at the output:
>>
>> BEFORE number of cv terms = 2
>> BEFORE (start of cv term)
>> BEFORE resource URI: urn:miriam:uniprot:P24941
>> BEFORE resource URI: urn:miriam:uniprot:O96020
>> BEFORE (start of cv term)
>> BEFORE resource URI: urn:miriam:uniprot:P24941
>> BEFORE resource URI: urn:miriam:uniprot:P24864
>>
>> So far so good: the "BEFORE" lines match what you can see if you look at
>> biomodels entry 169. Then the addCVTerm method is run over each CVTerm,
>> and
>> then the output is:
>>
>> AFTER number of cv terms = 2
>> AFTER (start of cv term)
>> AFTER resource URI: urn:miriam:uniprot:P24941
>> AFTER resource URI: urn:miriam:uniprot:O96020
>> AFTER (start of cv term)
>> AFTER resource URI: urn:miriam:uniprot:P24864
>>
>> Yes, it is weird that 169 has both a isVersionOf and a hasVersion that's
>> pointing to P24941, but is libSBML doing some fancy checking at this stage
>> to remove what it thinks might be a duplicate? I would have thought it
>> would
>> preserve the way the annotation was to begin with. Is this expected
>> behaviour?
>>
>> Am I missing something obvious?
>>
>> Thanks,
>> Allyson
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>>
>>
>
>
> --
>
>
> Vijayalakshmi Chelliah PhD
>
> Computational Systems Neurobiology Group,
> European Bioinformatics Institute,
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge, CB10 1SD,
> United Kingdom
> Ph : +44-1223-494418
> Fax: +44-1223-494468
> http://twitter.com/emblebi
>
>


--
Allyson Lister

Please note this new email address, although the old email address of
a.l.lister@newcastle.ac.uk will still work.

Newcastle University, http://www.ncl.ac.uk
http://themindwobbles.wordpress.com
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