Suggest would be good to consider and discuss addition of quality 
labelling to all OpenTox resources including measure of reliability to 
API. (Would be nice to have done for Munich workshop.)
Barry

Am 02.05.2011 07:20, schrieb Nina Jeliazkova:
> On 1 May 2011 12:47, surajit ray<mr.surajit.ray at gmail.com>  wrote:
>
>> 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 ?
>>
> Duplicates might appear because :
>
> 1) these are different chemical entities , wrongly assigned the same
> structure  in the dataset(s) imported , as here. It is clearer if you look
> at the names, in this case they are all different entities :
> http://apps.ideaconsult.net:8080/ambit2/query/compound/C/all
>
> or
> 2) on import it was requested not to match the structures and import as a
> new entity.   (option as in the form on the top
> http://apps.ideaconsult.net:8080/ambit2/dataset?max=25 )
>
> We have quality labels assigned in case of duplicates, but as the concept of
> quality labels is not in the OpenTox API , this is not exposed via the web
> services.  Perhaps this should change shortly, following a similar idea as
> discussed recently for models / datasets status labels.
>
> Best regards,
> Nina
>
>
>> 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
>>>> _______________________________________________
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>>>> 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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