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/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 .

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
> > > > > > > > _______________________________________________
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> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > Surajit Ray
> > > > > > > Partner
> > > > > > > www.rareindianart.com
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> > > > >
> > > > >
> > > > > --
> > > > > Surajit Ray
> > > > > Partner
> > > > > www.rareindianart.com
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> > > > > Development at opentox.org
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> > >
> > >
> > >
> > > --
> > > Surajit Ray
> > > Partner
> > > www.rareindianart.com
> > > _______________________________________________
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> > > Development at opentox.org
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>
>
> --
> Surajit Ray
> Partner
> www.rareindianart.com
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