Hi Nina,

If the quality labels cannot be accessed, then how to decide which
compound URI to use ?

Also if quality labels are a future development, then it would be
beneficial if we could reach a consensus now.

Regards
Surajit

On 2 May 2011 12:46, Barry Hardy <barry.hardy at douglasconnect.com> wrote:
> 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
>>>>> _______________________________________________
>>>>> Development mailing list
>>>>> Development at opentox.org
>>>>> http://www.opentox.org/mailman/listinfo/development
>>>>>
>>>>> Scanned and tagged as non-SPAM with DSPAM 3.9.0 by Your ISP.com
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Development mailing list
>>>> Development at opentox.org
>>>> 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
>>>
>>>
>>> Scanned and tagged as non-SPAM with DSPAM 3.9.0 by Your ISP.com
>>>
>> _______________________________________________
>> Development mailing list
>> Development at opentox.org
>> http://www.opentox.org/mailman/listinfo/development
>>
>>
>
> _______________________________________________
> Development mailing list
> Development at opentox.org
> http://www.opentox.org/mailman/listinfo/development
>



-- 
Surajit Ray
Partner
www.rareindianart.com