Hi,

Well having them as features will not cut it - for the simple reason
that the "feature" in this case belongs to the the input dataset (or
whichever set is being worked upon). The compound itself may not have
a substructure but it may be a a part of a dataset which when examined
will have the substructure appearing while doing the pairwise
comparisons.

Using the features system in this manner is not (IHMO) the solution to
this problem. It will be really be cumbersome to maintain the feature
URIs which may number in many thousands and will be extremely
transient. In effect it will be lot of resources being hogged by a
system which could do with a much more simpler implementation.
Moreover a certain feature in such a system will be a part of a
compound if its a part of Dataset A and may not be a part of the same
compound when examined in Dataset B.

Summing up heres a few things I would like in the next API

a) Ability to upload bulk compounds from scratch, using a dataset
construct (and not posting single compounds)
b) Ability to assign features to datasets
c) Ability to have non-standard datasets/compounds which contain
substructures rather than molecules.

Regards
Surajit

On 27 September 2010 18:31, chung <chvng at mail.ntua.gr> wrote:
> Hi Surajit,
>   As far as I can understand you have a problem similar to the one I
> was discussing with Alexey from IBMC. You need  a way to define which
> substructures are present in a certain structure. For this purpose you
> have to use features and not compounds. So you need a collection of
> features each one of which corresponds to a certain substructure.
> However in Ambit you can create a new compound by POSTing it
> to /compound in a supported MIME (e.g. SMILES, SDF etc) for example
> 'curl -X POST --data-binary @/path/to/file.sdf -H Content-type:blah/blah
> +sdf http://someserver.com/compound'. What is needed in OpenTox though
> is a collection of substructures in a feature service and a way to
> lookup for a certain feature according to its structure (e.g. providing
> its SMILES representation).
>
> Best Regards,
> Pantelis
>
> On Mon, 2010-09-27 at 14:18 +0530, surajit ray wrote:
>
>> Hi Nina,
>>
>> Need to upload some fragments (have smile representations) into a
>> dataset. Is this possible in the current framework ?
>>
>> To be more elaborate -
>> Currently I am uploading a dataset with compounds as the links to the
>> respective compound URIs (which happens at the end of the online
>> MaxtoxTest service). How would I upload new compounds (with smile/mol
>> representations) ? And secondly if these (the upload set) happen to be
>> fragments (and not molecules) is there a way to store such information
>> using the ambit dataset service ?
>>
>> Thanx
>> Surajit
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>>
>
>
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