Hi Nina,

Ok got it working with attached file (included the code from lines : 56-65)

Which brings me to two questions :

a) The SMILE seems to be the value of a feature. Therefore when posting
dataset URI to the Maxtox algo, should another parameter called feature name
be included ? (otherwise how would we know which feature contains smiles)

b) how do I retrieve the value contained in the Feature node in the
statement :

                RDFNode value = fv.getProperty(OT.value).getObject();
                out.write(String.format("%s=%s\n",
                        //Feature
                        fv.getProperty(OT.feature).getObject().toString(),
                        //Value
                        value));

Value is a string representation of the node like so
: Cc1ccc(N=Nc2c(O)ccc3ccccc23)c(c1)N(=O)O^^
http://www.w3.org/2001/XMLSchema#string

I would like to retrieve the just the value (the smile string ...)

Thanks
Surajit

On Fri, Feb 19, 2010 at 11:06 PM, Nina Jeliazkova <nina at acad.bg> wrote:

> 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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> >
>
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-- 
Surajit Ray
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