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"


> > 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 ?


> 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 ?


> > 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 ....

>
> > 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.


> 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
> > > > > > > _______________________________________________
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> > > > > >
> > > > > >
> > > > > > --
> > > > > > Surajit Ray
> > > > > > Partner
> > > > > > www.rareindianart.com
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> > > >
> > > >
> > > > --
> > > > Surajit Ray
> > > > Partner
> > > > www.rareindianart.com
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> >
> >
> >
> > --
> > Surajit Ray
> > Partner
> > www.rareindianart.com
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-- 
Surajit Ray
Partner
www.rareindianart.com