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On 09/02/12 12:35, Martijn van Iersel wrote:
> Dear Nico
>
> I have a question on jSBML: is there a code example, or documentation,
> describing how to parse RDF annotations in SBML?
>
> My particular problem is that I want to extract the Kegg compound
> identifiers from QualitativeSpecies from path2models files.
>

So the offical RDF annotation is already parsed into objects.
I am not quite sure how much javadoc we put in the jsbml class but you
can anyway look at the libsbml documentation :

http://sbml.org/Software/libSBML/docs/java-api/org/sbml/libsbml/CVTerm.html

Basicaly, any SBase object can have some CVTerms. One CVTerm correspond
to one qualifier with a list of uris (called resources). These
interfaces are not really
too nice to use but we tried to stay close to the libSBML api for those.

To look for some specific annotation, you can use the filterCVTerms
methods that are available on any SBase in JSBML.

see
http://sbml.org/Special/Software/JSBML/build/apidocs/org/sbml/jsbml/SBase.html


If you want to work on some other part of the annotation, the method
SBase.getAnnotationString() will
return the complete annotation as XML, including the SBML RDF part.
If you just want anything but the RDF, use
SBase.getAnnotation().getNonRDFannotation()

Hope this make things a bit clearer,
Cheers,
Nico



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