[OTDev] Adding class for substructures in opentox ontology Was: Re: [OTP] Summary of API 1.2 discussions
surajit ray mr.surajit.ray at gmail.comThu Oct 21 16:43:40 CEST 2010
- Previous message: [OTDev] Adding class for substructures in opentox ontology Was: Re: [OTP] Summary of API 1.2 discussions
- Next message: [OTDev] [OTP] Adding class for substructures in opentox ontology Was: Re: Summary of API 1.2 discussions
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Hi, Started a discussion stub at http://opentox.org/dev/apis/api-1.2/substructure-api-wishlist Regards Surajit On 21 October 2010 19:45, Nina Jeliazkova <jeliazkova.nina at gmail.com> wrote: > 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 > > > > > > > _______________________________________________ > Development mailing list > Development at opentox.org > http://www.opentox.org/mailman/listinfo/development > -- Surajit Ray Partner www.rareindianart.com
- Previous message: [OTDev] Adding class for substructures in opentox ontology Was: Re: [OTP] Summary of API 1.2 discussions
- Next message: [OTDev] [OTP] Adding class for substructures in opentox ontology Was: Re: Summary of API 1.2 discussions
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
More information about the Development mailing list