Hi Andreas, All,

Andreas Maunz wrote:
> Hi Christoph and all,
>
> Christoph Helma wrote:
>   
>> For the format I would prefer YAML (lightweight, human readable, easy
>> (de)serialisation of datastructures), but I think we will have to
>> provide XML too.
>>
>> As datastructure I would suggest a hash with compound_uris as keys and
>> arrays of feature_uris as values. In YAML this would look like:
>>
>> compound1_uri:
>> 	- feature1_uri
>> 	- feature2_uri
>> 	- ...
>> compound2_uri:
>> 	- feature1_uri
>> 	- feature3_uri
>> 	- ...
>> ...
>>     
>
> I wonder if the data interchange format could be based on existing work 
> in order to make it compatible to existing standards.
>
> For example, the blue obelisk descriptor ontology that is used by CDK 
> and OB could be a start, as pointed out by Egon Willighagen in an 
> earlier post to this list.
>
> The question IMHO is, what niveau we choose to start from: a completely 
> customized lightweight protocol entirely defined by ourselves, or a 
> (subset of an) existing  format/ontology.
>   
It depends on the final objective - do we strive to get something
working with minimal efforts quickly, having in mind it might be
necessary to redesign a lot in few months, or the aim is to develop
truly open system, acceptable by users and developers outside of the
OpenTox project as well. 

I would vote for the latest; thus making use of e.g. Blue Obelisk
ontology and CML and everything else that is relevant.  Otherwise, we
will  be just increasing the number existing uncompatible formats and
software.

Regarding the descriptors, we would definitely need to design something
similar to Blue Obelisk ontology, and IMHO the best way is to start with
it and suggest modifications, if necessary. 

Best regards,
Nina
> Andreas
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