[OTDev] Posting a new compound within an RDF dataset ...
Nina Jeliazkova jeliazkova.nina at gmail.comMon May 2 07:20:47 CEST 2011
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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 >
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