Hi,

On 2 May 2011 20:50, surajit ray <mr.surajit.ray at gmail.com> wrote:

> Hi Nina,
>
> If the quality labels cannot be accessed, then how to decide which
> compound URI to use ?
>
>
If it is an interactive application (user enters smiles), let the user to
select one.


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

Sure, it's just a matter of consensus how to represent these in RDF,
implementation-wise I could setup the code to serialize labels from database
into RDF right away.

Regards,
Nina



>
> 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
> _______________________________________________
> Development mailing list
> Development at opentox.org
> http://www.opentox.org/mailman/listinfo/development
>