Hi Nina,

I made a query with :
curl -X GET  http://apps.ideaconsult.net:8080/ambit2/query/compound/C

and got many hits.

http://apps.ideaconsult.net:8080/ambit2/compound/738/conformer/144568
http://apps.ideaconsult.net:8080/ambit2/compound/14190/conformer/154443
...

(see attached RDF).

The question is which to use ? Also if in future if the duplicates are
going to be cleaned out which should we assume as the "permanent one"
? Or am I getting this wrong and all those entries are different ? If
so how to differentiate between them ?

Regards
Surajit


On 1 May 2011 13:06, Nina Jeliazkova <jeliazkova.nina at gmail.com> wrote:
> 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
>> _______________________________________________
>> Development mailing list
>> Development at opentox.org
>> http://www.opentox.org/mailman/listinfo/development
>>
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>>
>>
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-- 
Surajit Ray
Partner
www.rareindianart.com
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