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On 12/09/2010 04:23 PM, Nicolas Rodriguez wrote:
> Hi,
>
> I tried to use the SBO class to display SBO term name and just notice
> that the OboParser from biojava
> seems to do some weird things.
>
> First which version of biojava did you add in the jsbml lib folder ? Is
> it a trimmed down jar, the official jar look a lot bigger ?
>
> Then the Term class strangely had no visible id/identifier getter or
> setter, the Term.name seem to contain a mix of the id + any is_a
> relationship and the
> Term.description seems to be random.
The strange things might come from the fact the SBO include some mathML
inside the definition ?

The first SBO terms look fine with the Term.name storing the id and the
Term.description storing the name, the definition being in the
Term.Annotation object.

> If the name is used to identify a Term, I thing all the methods using
> the biojava ontology will not work properly.
> I did not made any real test until now, Andreas did you tested the
> getTerm and isChildOf methods of the jsbml SBO class ?
the isObselete methods of the jsbml SBO class is probably not working as
well.

> Thanks,
> Nico
>

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