Hi Nina,

I have know that - but I would like upload and use a single compound and not
a full dataset. Does every compound have to have a parent dataset ? If so is
there a "other" or "miscellaneous" dataset where I can upload single
compounds.

Also would appreciate an HTML interface (form) for upload (with a Restlet to
do the RDF call on the backend). Is one available (for ready use OR
package/class for integrating in our framework) ? Although personally I can
use curl commands to upload - I did not find any of the people I asked to
test, interested in doing it via this method.

Regards
Surajit

On 13 July 2010 15:34, Nina Jeliazkova <jeliazkova.nina at gmail.com> wrote:

> Hi Surajit,
>
> Yes, via dataset service POST / PUT operations , as defined in OpenTox API
> .  Any of SDF, MOL, CSV (with smiles) , SMI, RDF, CML and other formats
> defined as supported in the API.
> http://opentox.org/dev/apis/api-1.1/dataset
>
> TUM and NTUA are using these services on daily basis for uploading data,
> descriptors and prediction results.
>
> Examples can be found in any of the partners' code as well as
>
> https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/opentox-client
> (look at tests)
>
> Once a dataset is created, it is accessible in any other format via
> Accept:media-type  HTTP header.
>
> Hope this helps.
> Nina
>
> On Tue, Jul 13, 2010 at 12:54 PM, surajit ray <mr.surajit.ray at gmail.com
> >wrote:
>
> > Hi Nina,
> >
> > Is there a mechanism yet of entering a smiles/(other formats)  in a form
> > field (or through RDF call) and putting it into a location on a server
> > (ambit ?) - so that hence forward the compound service can be used to
> > deliver the compound to other components/algorithms/models ?
> >
> > Cheers
> > Surajit
> >
> > On 13 July 2010 15:00, Nina Jeliazkova <jeliazkova.nina at gmail.com>
> wrote:
> >
> > > Hi Surajit,
> > >
> > > One approach is to consider using representations with lower inherent
> > > ambiguity (InChI, MOL, CML, etc.) - needless to say all of these are
> > > available via OpenTox dataset services.
> > >
> > > Best regards,
> > > Nina
> > >
> > > On Tue, Jul 13, 2010 at 12:21 PM, surajit ray <
> mr.surajit.ray at gmail.com
> > > >wrote:
> > >
> > > > Hi Egon,
> > > >
> > > > Our workflow uses the CDK Smilesparser object to read in the smiles.
> In
> > > the
> > > > light of these bugs - should we be wary of certain smiles OR look at
> > some
> > > > other means of reading in the smiles ?
> > > >
> > > > If so what would you advise as the best alternative to the smiles
> > parser
> > > ?
> > > >
> > > > Cheers
> > > > Surajit
> > > >
> > > > On 13 July 2010 11:37, Egon Willighagen <egon.willighagen at gmail.com>
> > > > wrote:
> > > >
> > > > > Dear Dmitry,
> > > > >
> > > > > On Mon, Jul 12, 2010 at 9:42 AM, Druzhilovsky
> > > > > <dmitry.druzhilovsky at ibmc.msk.ru> wrote:
> > > > > > In my opinion, CDK is the most correct for sensing. On the other
> > > hand,
> > > > > CDK
> > > > > > has some bugs with SMILES periodically . So, I daresay CACTVS do
> > for
> > > > > SMILES
> > > > > > in complex apps.
> > > > >
> > > > > I'd very much look forward to an OpenSMILES (re-)implementation. A
> > lot
> > > > > of bugs have been resolved, and most reside in the aromaticity
> > concept
> > > > > of SMILES, which is needlessly complex, partly because the whole
> > > > > aromaticity concept is ill-defined...
> > > > >
> > > > > There are some unit tests indeed still failing for the SMILES
> parser,
> > > > > but we welcome more bug reports on the SMILES parser if you find
> > > > > them... this is a very easy way to contribute to the CDK project...
> > > > >
> > > > > Egon
> > > > >
> > > > >
> > > > > --
> > > > > Post-doc @ Uppsala University
> > > > > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
> > > > > Homepage: http://egonw.github.com/
> > > > > Blog: http://chem-bla-ics.blogspot.com/
> > > > > PubList: http://www.citeulike.org/user/egonw/tag/papers
> > > > > _______________________________________________
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> > > > > Development at opentox.org
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> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Surajit Ray
> > > > Partner
> > > > www.rareindianart.com
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> > > >
> > > _______________________________________________
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> > > http://www.opentox.org/mailman/listinfo/development
> > >
> >
> >
> >
> > --
> > Surajit Ray
> > Partner
> > www.rareindianart.com
> > _______________________________________________
> > Development mailing list
> > Development at opentox.org
> > http://www.opentox.org/mailman/listinfo/development
> >
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-- 
Surajit Ray
Partner
www.rareindianart.com