[OTDev] Posting a new compound within an RDF dataset ...
Nina Jeliazkova jeliazkova.nina at gmail.comSun May 1 09:36:41 CEST 2011
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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 > >
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