[OTDev] Classified + Urgent
surajit ray mr.surajit.ray at gmail.comTue Jul 13 14:01:15 CEST 2010
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Hi, On 13 July 2010 17:15, Nina Jeliazkova <jeliazkova.nina at gmail.com> wrote: > On Tue, Jul 13, 2010 at 2:31 PM, surajit ray <mr.surajit.ray at gmail.com > >wrote: > > > On 13 July 2010 16:46, Nina Jeliazkova <jeliazkova.nina at gmail.com> > wrote: > > > > > Hi, > > > > > > On Tue, Jul 13, 2010 at 2:03 PM, surajit ray <mr.surajit.ray at gmail.com > > > >wrote: > > > > > > > Hi Nina, > > > > > > > > I have know that - but I would like upload and use a single compound > > and > > > > not > > > > > > > > > > A file with a single compound is still considered a dataset. > > > > > > > > > > > why should it be implemented like that ? seems like overkill to "fit > things > > in" > > > > > It might seems an overkill, but it has advantages for keeping track where > those compounds are coming from, espesially when allowing uploads of > arbitrary compounds and data. > > > > > > > > a full dataset. Does every compound have to have a parent dataset ? > > > > > > > > > Could have many - or none. Ambit services use datasets to keep track > > > where > > > compounds are coming from. > > > > > > > > Yeah I am interested in the "none' condition. How do I upload one > compound > > to a location and use it - without going into making a dataset ? > > > > > > > Creating a dataset is a completely transparent that needs not to bother > you. > > > > > On the other hand, you could always search if your compound is already > > > available and just reuse its URI. > > > > > > > > > > > Thats a possibility. Is there a search for lets say a smiles that I have > ? > > Meaning given my smiles can I search the datasets to reach my target URI > > for > > the compound ? > > > > Yes, Smiles, name, registration ID, InChI, etc. > > http://apps.ideaconsult.net:8080/ambit2/query/compound/{anything}/all<http://apps.ideaconsult.net:8080/ambit2/query/compound/%7Banything%7D/all> > > http://apps.ideaconsult.net:8080/ambit2/query/compound/phenol/all > > http://apps.ideaconsult.net:8080/ambit2/query/compound/c1ccccc1O/all > > > > > > > > > > If so is > > > > there a "other" or "miscellaneous" dataset where I can upload single > > > > compounds. > > > > > > > > > > > Any new file POSTed to the dataset service will create a new dataset , > > only > > > if you PUT the dataset to existing dataset URI a new one will be > created. > > > Partners have already created more than thousands datasets. > > > > > > > > That part was unclear - do you mean that "put"ing in an existing dataset > > will create a new compound URI ? > > > > > > > Examples as pointed in the previous email. > > > > > > > > > > > > > Also would appreciate an HTML interface (form) for upload (with a > > Restlet > > > > to > > > > do the RDF call on the backend). > > > > > > > > > There is an HTML form for file upload here > > > > > > http://ambit.uni-plovdiv.bg:8080/ambit2/dataset > > > > > > > > > > > Doesn't work at this point .... > > > > Could you tell what exactly doesn't work ? > It does, at least with Firefox and IE - there have been reported HTML > rendering issues with some browsers as Safari . > > Using Chrome - and the url goes into an indefinite "Waiting for server .... ". I tried on Firefox and it works. Is Chrome based out of Safari core ? Regards Surajit Please note HTML front end for services is completely _optional_, and not in > the API - services are supposed to be used by other programs, not by end > users. > > > > > > > > > > > Is one available (for ready use OR > > > > package/class for integrating in our framework) ? Although personally > I > > > can > > > > use curl commands to upload - I did not find any of the people I > asked > > to > > > > test, interested in doing it via this method. > > > > > > > > > > Recall we are building services and applications as separate entities, > > not > > > a > > > single web application ; this gives flexibility to build as many web > > > applications as one would like. > > > > > > curl and API in general are useful to use opentox services as building > > > blocks for applications and integrating services into other > applications; > > > ToxPredict and ToxCreate are examples of end-user applications with web > > > interface ; you might try to develop web front end for uploading > > compounds > > > or any other functionality you think is necessary. > > > > > > > > All things said it would really be useful to have "One HTML Form" > somewhere > > on the opentox site or ambit where a user can upload a compound via HTML > > form. The reason is there will be use cases other than the two you > mention > > and each of them will have to develop a separate mechanism to upload > > compounds to a common place. I think its better we have one place where > we > > can upload compounds independent of use case and in an easily usable > manner > > (like an HTML form). IHMO this makes more sense for the developers who > can > > direct the end-user to first upload the compound and then continue using > > the > > use-case wit the URI. > > > > Both demo applications currently allow file uploads, so this is in a way > redundant. > > But I agree with you that another application, simply for compound > registration is a nice use case to have. We might do something like this > shortly. > > Regards, > Nina > > > > > > > > > Regards, > > > Nina > > > > > > > > > > > > > > > > > Regards > > > > Surajit > > > > > > > > On 13 July 2010 15:34, Nina Jeliazkova <jeliazkova.nina at gmail.com> > > > wrote: > > > > > > > > > Hi Surajit, > > > > > > > > > > Yes, via dataset service POST / PUT operations , as defined in > > OpenTox > > > > API > > > > > . Any of SDF, MOL, CSV (with smiles) , SMI, RDF, CML and other > > formats > > > > > defined as supported in the API. > > > > > http://opentox.org/dev/apis/api-1.1/dataset > > > > > > > > > > TUM and NTUA are using these services on daily basis for uploading > > > data, > > > > > descriptors and prediction results. > > > > > > > > > > Examples can be found in any of the partners' code as well as > > > > > > > > > > > > > > > > > > > > https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/opentox-client > > > > > (look at tests) > > > > > > > > > > Once a dataset is created, it is accessible in any other format via > > > > > Accept:media-type HTTP header. > > > > > > > > > > Hope this helps. > > > > > Nina > > > > > > > > > > On Tue, Jul 13, 2010 at 12:54 PM, surajit ray < > > > mr.surajit.ray at gmail.com > > > > > >wrote: > > > > > > > > > > > Hi Nina, > > > > > > > > > > > > Is there a mechanism yet of entering a smiles/(other formats) in > a > > > > form > > > > > > field (or through RDF call) and putting it into a location on a > > > server > > > > > > (ambit ?) - so that hence forward the compound service can be > used > > to > > > > > > deliver the compound to other components/algorithms/models ? > > > > > > > > > > > > Cheers > > > > > > Surajit > > > > > > > > > > > > On 13 July 2010 15:00, Nina Jeliazkova < > jeliazkova.nina at gmail.com> > > > > > wrote: > > > > > > > > > > > > > Hi Surajit, > > > > > > > > > > > > > > One approach is to consider using representations with lower > > > inherent > > > > > > > ambiguity (InChI, MOL, CML, etc.) - needless to say all of > these > > > are > > > > > > > available via OpenTox dataset services. > > > > > > > > > > > > > > Best regards, > > > > > > > Nina > > > > > > > > > > > > > > On Tue, Jul 13, 2010 at 12:21 PM, surajit ray < > > > > > mr.surajit.ray at gmail.com > > > > > > > >wrote: > > > > > > > > > > > > > > > Hi Egon, > > > > > > > > > > > > > > > > Our workflow uses the CDK Smilesparser object to read in the > > > > smiles. > > > > > In > > > > > > > the > > > > > > > > light of these bugs - should we be wary of certain smiles OR > > look > > > > at > > > > > > some > > > > > > > > other means of reading in the smiles ? > > > > > > > > > > > > > > > > If so what would you advise as the best alternative to the > > smiles > > > > > > parser > > > > > > > ? > > > > > > > > > > > > > > > > Cheers > > > > > > > > Surajit > > > > > > > > > > > > > > > > On 13 July 2010 11:37, Egon Willighagen < > > > > egon.willighagen at gmail.com> > > > > > > > > wrote: > > > > > > > > > > > > > > > > > Dear Dmitry, > > > > > > > > > > > > > > > > > > On Mon, Jul 12, 2010 at 9:42 AM, Druzhilovsky > > > > > > > > > <dmitry.druzhilovsky at ibmc.msk.ru> wrote: > > > > > > > > > > In my opinion, CDK is the most correct for sensing. On > the > > > > other > > > > > > > hand, > > > > > > > > > CDK > > > > > > > > > > has some bugs with SMILES periodically . So, I daresay > > CACTVS > > > > do > > > > > > for > > > > > > > > > SMILES > > > > > > > > > > in complex apps. > > > > > > > > > > > > > > > > > > I'd very much look forward to an OpenSMILES > > > (re-)implementation. > > > > A > > > > > > lot > > > > > > > > > of bugs have been resolved, and most reside in the > > aromaticity > > > > > > concept > > > > > > > > > of SMILES, which is needlessly complex, partly because the > > > whole > > > > > > > > > aromaticity concept is ill-defined... > > > > > > > > > > > > > > > > > > There are some unit tests indeed still failing for the > SMILES > > > > > parser, > > > > > > > > > but we welcome more bug reports on the SMILES parser if you > > > find > > > > > > > > > them... this is a very easy way to contribute to the CDK > > > > project... > > > > > > > > > > > > > > > > > > Egon > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > Post-doc @ Uppsala University > > > > > > > > > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg > > > > > > > > > Homepage: http://egonw.github.com/ > > > > > > > > > Blog: http://chem-bla-ics.blogspot.com/ > > > > > > > > > PubList: http://www.citeulike.org/user/egonw/tag/papers > > > > > > > > > _______________________________________________ > > > > > > > > > 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 > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > 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 > > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > > > > _______________________________________________ > > > 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 > > > _______________________________________________ > Development mailing list > Development at opentox.org > http://www.opentox.org/mailman/listinfo/development >
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