Hi Surajit,

There are several options.

1) (Highly preferred , to minimize duplicates) Find if there is a compound
with this SMILES already on the compound service. You may query for any
identifier, not SMILES only.

http://apps.ideaconsult.net:8080/ambit2/query/compound/CCCCCCCCCCC  (URI
only)
<http://apps.ideaconsult.net:8080/ambit2/query/compound/c1ccccc1/all>
http://apps.ideaconsult.net:8080/ambit2/query/compound/CCCCCCCCCCC/all  (URI
with names )

Use the URI as usual in subsequent request


2) Create a compound by POST -ing its content in any of the supported
chemical mime formats to the compound service.  Use the URI as usual

3) Create a (set of) compounds by POST -ing the content with any of
the supported chemical mime formats to the dataset service. Use the URIs as
usual.

All the options 1-3 are currently used by ToxPredict application.

Hope this helps,
Nina




On 1 May 2011 10:19, Nina Jeliazkova <nina at acad.bg> wrote:

>
> -------- Original Message --------
> Subject: [OTDev] Posting a new compound within an RDF dataset ...
> Date: Sat, 30 Apr 2011 12:25:55 +0530
> From: surajit ray <mr.surajit.ray at gmail.com>
> To: opentox development mailing list <development at opentox.org>
> Reply-To: opentox development mailing list <development at opentox.org>
>
> Hi Nina, All,
>
> I require to upload a new compound within a dataset (with features +
> feature values). Lets say only the SMILE is known (as in the case of a
> user input). In that case how do we represent the compound in the RDF
> for upload to the ambit dataset service ? Since I do not have the URI
> in advance I am creating a new compound like so :
>
> Individual newcompound =
>
> resultDataset.createIndividual(OT.OTClass.Compound.getOntClass(resultDataset));
>
> The Question is how do I supply the SMILE representation after this.
> Do I have to define a certain "feature" which denotes the SMILE
> representation of the compound. If so what is the URI of this
> "feature" ?
>
> P.S. The other option I guess would be to run a local instance of a
> compound service and supply the URI in the dataset ...
>
> Regards
> Surajit
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