Excerpts from Nina Jeliazkova's message of Fri Oct 22 10:30:21 +0200 2010:
> All,
> 
> Since this is important topic, I made the wiki page externally visible.
> 
> http://opentox.org/dev/apis/api-1.2/substructure-api-wishlist
> 
> 
> Would be good to have comments from everybody, working with:
> 
> 1) Fragment features of any kind
> Do we need specific extension of the API for fragmens , and how does it
> integrates with existing modeling algorithms?  There are at least two
> partners, which already use the current API for representation of fragments
> and fragment based algorithms.  What / is a new extension necessary?
> 
> 2) Interested in representing properties, calculated not to from a single
> compound, but to two (or more)
> How to extend the API , to be able to represent entities, related to two
> compounds - e.g. common substructure, alignment matrix ,etc. ?
> 
> Best regards,
> Nina

I cannot see the point of inventing a separate API for fragments. IMHO
everything can be done with the current feature API which we have been
using since the beginning to represent fragments. What could be useful
are ontology entries for ot:smarts (I don't think it exists in
blueobelisk) and ot:Fragment (or ot:Substructure).

For features originating from supervised feature mining we can use
ot:hasSource together with ot:parameters to specify its origin.

With that a fragment feature can be represented as

<http://webservices.in-silico.ch/dataset/2/feature/1>
  ot:smarts "cN" ;
  ot:isA ot:Substructure;
  ot:hasSource <http://webservices.in-silico.ch/algorithm/fminer/bbrc>;
  ot:parameters [
        dc:title "dataset_uri" ;
        ot:paramValue <http://webservices.in-silico.ch/dataset/1> ;
        a ot:Parameter
    ], [
        dc:title "feature_uri" ;
        ot:paramValue <http://webservices.in-silico.ch/dataset/1/feature/Hamster%20Carcinogenicity>
;
        a ot:Parameter
    ] ;
  a ot:Feature . 

Best regards,
Christoph