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
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>



-- 
Surajit Ray
Partner
www.rareindianart.com
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