[OTDev] Posting a new compound within an RDF dataset ...
surajit ray mr.surajit.ray at gmail.comMon May 2 19:50:02 CEST 2011
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Hi Nina, If the quality labels cannot be accessed, then how to decide which compound URI to use ? Also if quality labels are a future development, then it would be beneficial if we could reach a consensus now. 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
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