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
> >>
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> >>
> >>
> > _______________________________________________
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> >
>
>
>
> --
> Surajit Ray
> Partner
> www.rareindianart.com
>
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