Hi Surajit, All,

Let's start a wiki page on this topic and compile a "wish list" as a first
step.


Best regards,
Nina

On 21 October 2010 17:06, surajit ray <mr.surajit.ray at gmail.com> wrote:

> Hi Nina, All,
>
> I was wondering if an ontological class called "substructure" can be made
> available in the next API. The basic functionality could just be a replica
> of the "compound" class and its corresponding functionality.  In addition
> we
> could include some other properties which would be things like
> "ot:isPartOf"
> etc. (we could have a discussion in the SWDT about needed properties)
>
> Also the atomic features can be considered to be features of a single atom
> substructure. This way we could make space for atom features as well.
>
> Substructures have become very important in the latest in-silico model
> making strategies. Some papers that Om discussed from the EURO Qsar
> outlined
> the importance of substructures in clustering groups of molecules. Our
> ability to have substructures as an available unit of operation  (through
> the API) - will greatly enhance the ease of integration with the recent
> trends in in-silico small molecule testing. Right now the only way is to
> internalize this information within models/algorithms.
>
> Another big usefulness  of this would be a ready audience with drug-dev
> companies. They usually are looking for substructures in their repos (of
> existing compounds). More often the whole upstream workflow for the drug
> development chemistry is based on concepts of substructure recombinations
> using tightly controlled reactions. However I must admit this benefit -
> does
>  have a weak correlation with our toxicity related goals.
>
> Overall I feel it will be a useful and very needed addition to the API.
>
> Thanks
> Surajit
>
>
>