Hi Surajit,

A quick answer - the problem is  on line 56  OntResource dataset =
OT.OTClass.Dataset.getOntClass(jenaModel); 
Here in dataset variable you have the RDF node that is the declaration
of the type Dataset, not the dataset entry itself. Consequently, there
are no ot:dataEntry properties and it doesn't iterate over the model.

To get the dataset entry itself, you might again use SimpleSelector and
look for nodes of type ot:Dataset , i.e.  (null, rdf:type , ot:Dataset
)   - replace with Jena types.

Regards,
Nina
surajit ray wrote:
> Hi Nina,
>
> I was trying to read the dataset off your link in the RDF format .
>
> Attached is a java prog to do the same. However though in line 59 it does
> throw out the jena model ... it is not iterating over the model using the
> parsedataset function (all the code I have used is of the OpenTox website).
>
> Could you please tell me what I am doing wrong here ?
> (The Java code has a main function so you can run it standalone)
>
> Thanks
> Surajit
>
> On Fri, Feb 19, 2010 at 7:51 PM, Christoph Helma <helma at in-silico.de> wrote:
>
>   
>> Excerpts from Jörg Kurt Wegner's message of Mon Feb 15 23:52:22 +0100 2010:
>>     
>>> Nina, Surajit,
>>>
>>>       
>>>> http://ambit.uni-plovdiv.bg:8080/ambit2/dataset
>>>> The formats  (RDF, MOL, SMILES, CSV, arff, CML) can be retrieved via
>>>> specifying the corresponding mime type.
>>>>         
>>> Nice, I admit I am not reading all the posts on this list and you might
>>>       
>> have
>>     
>>> answered this already earlier.
>>> Anyway, I gotta ask:
>>>
>>> 1. Some of the data sets are simply empty, at least the first few in the
>>>       
>> list.
>>     
>>> Why?
>>>
>>> 2. Cross-indexing could be clearly enriched by enabling InChIKeys
>>> http://www.iupac.org/inchi/release102final.html
>>> and then using one of the services around for puling more indices and
>>>       
>> data, e.g.
>>     
>>> http://inchis.chemspider.com/
>>> http://cactus.nci.nih.gov/chemical/structure
>>>
>>> 3. In other words just in-case some structures might need curation I
>>>       
>> would
>>     
>>> rather prefer seeing the correct ones pulled from ChemSpider and you just
>>>       
>> host
>>     
>>> identifiers and tox endpoints ;-)
>>>
>>> 4. Finally, are there json data fetching options, too? I guess this is
>>>       
>> easier
>>     
>>> for (me) linking multiple sources in a browser, scripting, or wrapper.
>>> approach. Again, a universal chemistry ID like InChIKey or ChemSpiderID
>>>       
>> is much
>>     
>>> appreciated.
>>>       
>> +1 for JSON/YAML
>>
>> I have initially used InChiKeys as identifers for compounds but have
>> reverted to plain InChIs (despite URI encoding problems), because there
>> is no way to calculate structures from InChiKeys (except by storing them
>> in a database). I do not understand, why it is necessary to use encryption
>> instead of say URI safe base64 encoding.
>>
>> Regards,
>> Christoph
>> _______________________________________________
>> Development mailing list
>> Development at opentox.org
>> http://www.opentox.org/mailman/listinfo/development
>>
>>     
>
>
>
>   
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