[OTDev] Posting a new compound within an RDF dataset ...
Nina Jeliazkova jeliazkova.nina at gmail.comMon May 2 19:54:34 CEST 2011
- Previous message: [OTDev] Posting a new compound within an RDF dataset ...
- Next message: [OTDev] Validation server down
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Hi, On 2 May 2011 20:50, surajit ray <mr.surajit.ray at gmail.com> wrote: > Hi Nina, > > If the quality labels cannot be accessed, then how to decide which > compound URI to use ? > > If it is an interactive application (user enters smiles), let the user to select one. > Also if quality labels are a future development, then it would be > beneficial if we could reach a consensus now. > Sure, it's just a matter of consensus how to represent these in RDF, implementation-wise I could setup the code to serialize labels from database into RDF right away. Regards, Nina > > 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 > _______________________________________________ > Development mailing list > Development at opentox.org > http://www.opentox.org/mailman/listinfo/development >
- Previous message: [OTDev] Posting a new compound within an RDF dataset ...
- Next message: [OTDev] Validation server down
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
More information about the Development mailing list