[OTDev] Posting a new compound within an RDF dataset ...
surajit ray mr.surajit.ray at gmail.comSun May 1 11:47:53 CEST 2011
- Previous message: [OTDev] Posting a new compound within an RDF dataset ...
- Next message: [OTDev] Posting a new compound within an RDF dataset ...
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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 ? 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: compound.rdf Type: text/xml Size: 4640 bytes Desc: not available URL: <http://lists.opentox.org/pipermail/development/attachments/20110501/9cd0c933/attachment.xml>
- Previous message: [OTDev] Posting a new compound within an RDF dataset ...
- Next message: [OTDev] Posting a new compound within an RDF dataset ...
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
More information about the Development mailing list